Site- or sequence-specific process for cleaving analytes and library of analytes

• US 20060024738A1
• Filed: 09/27/2005
• Published: 02/02/2006
• Est. Priority Date: 03/12/2002
• Status: Active Grant

• Current Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Original Assignee: Enzo Life Sciences Incorporated (Enzo Biochem Incorporated)
• Inventors: Stavrianopoulos, Jannis G., Donegan, James J., Rabbani, Elazar, Coleman, Jack, Liu, Dakai
• Granted Patent: US 7,396,647 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer
• CPC Class Codes: C12Q 1/6834 Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2565/101 Interaction between at least two labels
• CPC Class Codes: G01N 21/64 Fluorescence; Phosphorescence
• CPC Class Codes: G01N 21/6486 Measuring fluorescence of biological material, e.g. DNA, RNA, cells G01N21/6428 takes precedence

Abstract

This invention provides for compositions for use in real time nucleic acid detection processes. Such real time nucleic acid detection processes are carried out with energy transfer elements attached to nucleic acid primers, nucleotides, nucleic acid probes or nucleic acid binding agents. Real time nucleic acid detection allows for the qualitative or quantitative detection or determination of single-stranded or double-stranded nucleic acids of interest in a sample. Other processes are provided by this invention including processes for removing a portion of a homopolymeric sequence, e.g., poly A sequence or tail, from an analyte or library of analytes. Compositions useful in carrying out such removal processes are also described and provided.

Claims

1-485. -485. (canceled)

12. A composition of matter comprising at least two parts:

a first part comprising at least two segments, wherein said first segment comprises a first nucleic acid primer or nucleic acid construct and at least one first energy transfer element, and said second segment comprises primer-extended complementary to at least a portion of a nucleic acid of interest; and

a second part comprising at least two segments, wherein said first segment of said second part comprises a second nucleic acid primer or nucleic acid construct and at least one second energy transfer element; and

wherein said second segment of said second part comprises a primer-extended nucleic acid sequence which is identical to at least a portion of said nucleic acid of interest;

wherein said first nucleic acid primer or nucleic acid construct does not comprise said second energy transfer element, and wherein said second nucleic acid primer or nucleic acid construct does not comprise said first nucleic acid energy element.

13. The composition of claim 12, wherein either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

14. The composition of claim 12, wherein said first nucleic acid primer or construct comprises more than one first energy transfer element.

15. The composition of claim 12, wherein said second nucleic acid primer or construct comprises more than one second energy transfer element.

16. The composition of claim 1, wherein said first part comprises more than one nucleic acid primer or nucleic acid construct, or said second part comprises more than one nucleic acid primer or nucleic acid construct, or both said first part and said second part comprise more than one nucleic acid primer or nucleic acid construct.

17. The composition of claim 16, wherein said more than one nucleic acid primer or nucleic acid construct comprise identical or different nucleic acid sequences.

18. The composition of claim 12, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

19. The composition of claim 18, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

20. The composition of claim 12, wherein at least one of said nucleic acid primers or constructs is fixed or immobilized to a solid support.

21. The composition of claim 20, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

22. The composition of claim 12, wherein said fixation or immobilization is direct or indirect.

23. The composition of claim 12, wherein said primer extended sequence was added or effected by a DNA polymerase.

24. The composition of claim 12, wherein said primer extended sequence was added or effected by a ligase.

25. A composition of matter comprising two nucleic acid strands, wherein the first of said two strands comprises at least one first energy transfer element, and the second of said two strands comprises at least one second energy transfer element and wherein said first strand or a portion thereof is hybridized to said second strand or a portion thereof, and wherein said first strand lacks said second energy transfer element and said second strand lacks said first energy transfer element.

26. The composition of claim 25, wherein either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

27. The composition of claim 25, wherein said first strand comprises more than one first energy transfer element.

28. The composition of claim 25, wherein said second strand comprises more than one second energy transfer element.

29. The composition of claim 25, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein. (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

30. The composition of claim 29, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

31. The composition of claim 25, wherein at least one of said strands is fixed or immobilized to a solid support.

32. The composition of claim 31, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

33. The composition of claim 25, wherein said fixation or immobilization is direct or indirect.

34. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) the composition of claim 1;

(ii) a sample suspected of containing said nucleic acid of interest; and

(iii) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii) and (iii) above;

(c) contacting under hybridization conditions said first nucleic acid primer in said composition (i) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer in said composition (i) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if said complementary strand is present;

(e) separating said first primer-extended nucleic acid sequence from said nucleic acid of interest and separating said second primer-extended nucleic acid sequence from said complementary strand of said nucleic acid of interest if present;

(f) contacting under hybridization conditions said first nucleic acid primer in said composition (i) with said nucleic acid of interest or said second primer-extended nucleic acid sequence from step (e), and contacting under hybridization conditions said second nucleic acid primer in said composition (i) with said first primer-extended nucleic acid sequence from step (e); and

(g) detecting by means of said first and second energy transfer elements in said composition (i) the presence or quantity of said nucleic acid of interest.

35. The process of claim 34, wherein said complementary strand of the nucleic acid of interest is present.

36. The process of claim 34, wherein after said contacting step (f), said process further comprises repeating said extending step (d).

37. The process of claim 36, said process further comprising the step (e′

) of separating said first primer-extended nucleic acid sequence from said second primer-extended nucleic acid sequence, and repeating step (f) thereafter.

38. The process of claim 37, wherein steps (d), (e′

) and (f) are repeated.

39. The process of claim 38, wherein said detecting step (g) is carried out at specific intervals during or after said extending step (d), said separating step (e′

), or said contacting step (f).

40. The process of claims 34, 36, 37 or 38, wherein in the providing step (a), said reagents (iii) comprise DNA polymerase, DNA ligase, or both.

41. The process of claim 40, wherein said DNA polymerase, DNA ligase, or both, are thermostable.

42. The process of claims 34, 36, 37 or 38, wherein said separating step is carried out by thermal denaturation or strand displacement.

43. The process of claims 34, wherein said nucleic acid of interest (ii) has been rendered single stranded before or during said reaction mixture forming step (b).

44. The process of claim 34, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

45. The process of claim 34, wherein in said providing step (a), said first nucleic acid primer or construct comprises more than one first energy transfer element.

46. The process of claim 34, wherein in said providing step (a), said second nucleic acid primer or construct comprises more than one second energy transfer element.

47. The process of claim 34, wherein in said providing step (a), more than one first nucleic acid primer or nucleic acid construct, or more than one second nucleic acid primer or nucleic acid construct, or both, are provided.

48. The process of claim 34, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

49. The process of claim 48, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

50. The process of claim 34, wherein at least one of said first or second nucleic acid primers or constructs is fixed or immobilized to a solid support.

51. The process of claim 50, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

52. The process of claim 50, wherein said fixation or immobilization is direct or indirect.

53. The process of claims 34, 36, 37 or 38, wherein any or all of said steps are carried out in a closed container system.

54. The process of claim 53, wherein said closed container system comprises an illumination source and a detection device or unit.

55. A composition of matter that comprises a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer or a nucleic acid construct;

and said second segment comprising a primer-extended sequence,

wherein said primer or nucleic acid construct comprises a first energy transfer element, and wherein said primer-extended sequence comprises a second energy transfer element, and wherein said primer-extended sequence comprises more than one nucleotide.

56. The composition of claim 55, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

57. The composition of claim 55, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

58. The composition of any of claims 55, 56 or 57, wherein said first nucleic acid primer or construct comprises more than one first energy transfer element.

59. The composition of any of claims 55, 56 or 57, wherein said primer-extended sequence comprises more than one second energy transfer element.

60. The composition of claim 55, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

61. The composition of claim 60, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

62. The composition of claim 55, further comprising a second nucleic acid strand, said second strand comprising two segments, the first segment comprising a primer or a nucleic acid construct;

and said second segment comprising a primer-extended sequence,

wherein said primer or nucleic acid construct comprises a first energy transfer element, and wherein said primer-extended sequence comprises a second energy transfer element.

63. The composition of claim 55 or 62, wherein at least one of said nucleic acid primers or constructs is fixed or immobilized to a solid support.

64. The composition of claim 63, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

65. The composition of claim 63 or 64, wherein said fixation or immobilization is direct or indirect.

66. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a nucleic acid primer or nucleic acid construct that comprises;

(A) a nucleic acid sequence complementary to at least a portion of said nucleic acid of interest and

(B) a first energy transfer element;

(iii) labeled nucleotide or nucleotides comprising a second energy transfer element; and

(iv) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii) and (iv) above;

(c) contacting under hybridization conditions said nucleic acid primer in said composition (ii) with said nucleic acid of interest;

(d) extending said nucleic acid primer by more than one nucleotide, thereby incorporating said labeled nucleotide or nucleotides; and

(e) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element in said nucleic acid primer and said second energy transfer element in an incorporated nucleotide.

67. The process of claim 66, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

68. The process of claim 66, wherein prior to the detecting step (e), said process further comprises the step of (b′

) separating said extended nucleic acid from the nucleic acid of interest and repeating the contacting step (c) and the extending step (d).

69. The process of claim 68, wherein said separating step (b′

), said contacting step (c) and said extending step (d) are repeated one or more times.

70. The process of claim 66, wherein in the providing step (a), said reagents (v) comprises a thermostable DNA polymerase.

71. The process of claim 68 or 69, wherein said separating step is carried out by thermal denaturation or strand displacement.

72. The process of claim 66, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

73. The process of claim 66, wherein in said providing step (a), said nucleic acid primer or construct comprises more than one first energy transfer element.

74. The process of claim 66, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

75. The process of claim 74, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

76. The process of claim 66, wherein said nucleic acid primer or construct is fixed or immobilized to a solid support.

77. The process of claim 76, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

78. The process of claim 76, wherein said fixation or immobilization is direct or indirect.

79. The process of claims 66, 68 or 69, wherein any or all of said steps are carried out in a closed container system.

80. The process of claim 79, wherein said closed container system comprises an illumination source and a detection device or unit.

81. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a first nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of one strand of said nucleic acid of interest;

(iii) a second nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence identical to at least a portion of said one strand;

(iv) labeled nucleotide or nucleotides comprising a first energy transfer element; and

(v) reagents for carrying out nucleic acid strand extension;

wherein (ii), (iii) or both (ii) and (iii) comprise a second energy transfer element;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if said complementary strand is present, thereby incorporating said labeled nucleotide or nucleotides;

(e) separating said first primer-extended nucleic acid sequence from said nucleic acid of interest and separating said second primer-extended nucleic acid sequence from said complementary strand of said nucleic acid of interest if present;

(f) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said nucleic acid of interest or said second primer-extended nucleic acid sequence from step (e), and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with said first primer-extended nucleic acid sequence from step (e); and

(g) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between a second energy transfer element in said first nucleic acid primer, said second nucleic acid primer, or both, and a first energy element in an incorporated nucleotide.

82. The process of claim 81, wherein said complementary strand of the nucleic acid of interest is present.

83. The process of claims 82, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

84. The process of claim 81, wherein after said contacting step (f), said process further comprises repeating said extending step (d).

85. The process of claim 84, said process further comprising the step (e′

) of separating said first primer-extended nucleic acid sequence from said second primer-extended nucleic acid sequence, and repeating step (f) thereafter.

86. The process of claim 85, wherein steps (d), (e′

) and (f) are repeated.

87. The process of claim 81, 84, 85 or 86, wherein said detecting step (g) is carried out at specific intervals during or after said extending step (d), said separating step (e′

), or said contacting step (f).

88. The process of claims 81, 84, 85 or 86, wherein in the providing step (a), said reagents (v) comprise a thermostable DNA polymerase.

89. The process of claims 81, 84, 85 or 86, wherein said separating step is carried out by thermal denaturation or strand displacement.

90. The process of claim 81, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

91. The process of claim 81, wherein in said providing step (a), said first nucleic acid primer or construct comprises more than one first energy transfer element.

92. The process of claim 81, wherein in said providing step (a), said second nucleic acid primer or construct comprises more than one second energy transfer element.

93. The process of claim 81, wherein in said providing step (a), more than one first nucleic acid primer or nucleic acid construct, or more than one second nucleic acid primer or nucleic acid construct, or both, are provided.

94. The process of claim 81, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

95. The process of claim 94, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

96. The process of claim 81, wherein at least one of said first or second nucleic acid primers or constructs is fixed or immobilized to a solid support.

97. The process of claim 96, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

98. The process of claim 96, wherein said fixation or immobilization is direct or indirect.

99. The process of claims 81, 84, 85 or 86, wherein any or all of said steps are carried out in a closed container system.

100. The process of claim 99, wherein said closed container system comprises an illumination source and a detection device or unit.

101. A composition of matter that comprises a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer or a nucleic acid construct;

and the second segment comprising a primer-extended sequence,

wherein said primer-extended sequence comprises one or more first energy transfer elements and one or more second energy transfer elements.

102. The composition of claim 101, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

103. The composition of claim 101, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

104. The composition of claim 101, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

105. The composition of claim 104, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

106. The composition of claim 101, further comprising a second nucleic acid strand, said second strand comprising two segments, wherein the first segment of said second strand comprises a primer or a nucleic acid construct, wherein the second segment of said second strand comprises a primer-extended sequence, and

wherein said primer-extended sequence of said second segment comprises one or more first energy transfer elements and one or more second energy transfer elements.

107. The composition of claim 101 or 106, wherein at least one of said nucleic acid primers or constructs is fixed or immobilized to a solid support.

108. The composition of claim 107, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

109. The composition of claim 107, wherein said fixation or immobilization is direct or indirect.

110. The composition of claim 101 or 106, wherein at least one of said nucleic acid primers or constructs further comprises a quencher.

111. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of said nucleic acid of interest and

(iii) one or more first nucleotides, said first nucleotides comprising a first energy transfer element, and one or more second nucleotides, said second nucleotides comprising a second energy transfer element;

(iv) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii) and (iv) above;

(c) contacting under hybridization conditions said nucleic acid primer in said composition (ii) with said nucleic acid of interest;

(d) extending said nucleic acid primer, thereby incorporating said first and second nucleotides; and

(e) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

112. The process of claim 111, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

113. The process of claim 111, wherein said first nucleotide and second nucleotide comprise identical bases.

114. The process of claim 111, wherein said first nucleotide and second nucleotide comprise different bases.

115. The process of claim 111, wherein prior to the detecting step (e), said process further comprises the step of (b′

) separating said extended nucleic acid from the nucleic acid of interest and repeating the contacting step (c) and the extending step (d).

116. The process of claim 115, wherein said separating step (b′

), said contacting step (c) and said extending step (d) are repeated one or more times.

117. The process of claim 111, wherein in the providing step (a), said reagents (v) comprises a thermostable DNA polymerase.

118. The process of claim 115 or 116, wherein said separating step is carried out by thermal denaturation or strand displacement.

119. The process of claim 111, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

120. The process of claim 111, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

121. The process of claim 120, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

122. The process of claim 111, wherein said nucleic acid primer or construct is fixed or immobilized to a solid support.

123. The process of claim 122, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

124. The process of claim 122, wherein said fixation or immobilization is direct or indirect.

125. The process of claims 111, 115 or 116, wherein any or all of said steps are carried out in a closed container system.

126. The process of claim 125, wherein said closed container system comprises an illumination source and a detection device or unit.

127. The process of claim 111, wherein said nucleic acid primer or construct further comprises a quencher.

128. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a first nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of one strand of said nucleic acid of interest;

(iii) a second nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence identical to at least a portion of said one strand;

(iv) one or more first nucleotides, said first nucleotides comprising a first energy transfer element, and one or more second nucleotides, said second nucleotides comprising a second energy transfer element; and

(v) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if said complementary strand is present, thereby incorporating said first and second nucleotides; and

(e) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

129. The process of claim 128, further comprising:

(b′

) separating said first primer-extended nucleic acid sequence from said nucleic acid of interest and separating said second primer-extended nucleic acid sequence from said complementary strand of said nucleic acid of interest if present;

(c′

) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (b′

), if said second strand is present, and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with said first primer-extended nucleic acid sequence from step (b′

); and

repeating said extending step (d) thereafter.

130. The process of claim 129, further comprising the step (b″

) of separating said first primer-extended nucleic acid sequence from said second primer-extended nucleic acid sequence, and the step (c″

) of contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (b″

), and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with said first primer-extended nucleic acid sequence from step (b″

); and

repeating said extending step (d) thereafter.

131. The process of claim 130, wherein said separating step (b″

), said contacting step (c″

) and said extending step (d) are repeated.

132. The process of claim 128, wherein said complementary strand of the nucleic acid of interest is present.

133. The process of claims 132, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

134. The process of any of claims 128, 129, 130 or 131, wherein said detecting step (e) is carried out at specific intervals during or after any contacting step, extending step, or separating step.

135. The process of claims 128, wherein in the providing step (a), said reagents (v) comprise a thermostable DNA polymerase.

136. The process of claims 129, 130 or 131, wherein said separating step is carried out by thermal denaturation or strand displacement.

137. The process of claim 128, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

138. The process of claim 128, wherein in said providing step (a), more than one first nucleic acid primer or nucleic acid construct, or more than one second nucleic acid primer or nucleic acid construct, or both, are provided.

139. The process of claim 128, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

140. The process of claim 139, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

141. The process of claim 128, wherein at least one of said first or second nucleic acid primers or constructs or any primer-extended nucleic acid sequence is fixed or immobilized to a solid support.

142. The process of claim 141, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

143. The process of claim 141, wherein said fixation or immobilization is direct or indirect.

144. The process of claims 128, 129, 130 or 131, wherein any or all of said steps are carried out in a closed container system.

145. The process of claim 144, wherein said closed container system comprises an illumination source and a detection device or unit.

146. The process of claim 128, wherein at least one of said nucleic acid primers or constructs further comprises a quencher.

147. A composition of matter that comprises a nucleic acid strand, said strand comprising two or more ribonucleotides, wherein at least one ribonucleotide comprises a first energy transfer element and wherein at least one other ribonucleotide comprises a second energy transfer element.

148. The composition of claim 147, wherein said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

149. The composition of claim 148, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

150. The composition of claim 149, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

151. The composition of claim 147, wherein said nucleic acid strand is fixed or immobilized indirectly to a solid support.

152. The composition of claim 151, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

153. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) at least one first nucleic acid primer or nucleic acid construct and optionally, a second nucleic acid primer or nucleic acid construct, wherein either the first nucleic acid primer or nucleic acid construct, or said optional second nucleic acid primer or nucleic acid construct comprises an RNA promoter sequence;

(iii) one or more first ribonucleotides, said first ribonucleotides comprising a first energy transfer element, and one or more second ribonucleotides, said second ribonucleotides comprising a second energy transfer element;

(iv) reagents for carrying out nucleic acid strand extension and RNA transcription;

(b) forming a reaction mixture comprising (i), (ii) and (iii) above;

(c) contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with one strand of said nucleic acid of interest;

(d) extending said nucleic acid primer to form a primer-extended nucleic acid sequence;

(e) synthesizing a second nucleic acid strand complementary to said primer-extended nucleic acid sequence or a portion thereof, thereby forming a double-stranded nucleic acid;

(f) transcribing said double-stranded nucleic acid formed in step (e) to incorporate said first and second ribonucleotides (iii) into transcripts;

(g) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element;

wherein said transcribing step (f) is carried out by said RNA promoter sequence in either the primer-extended nucleic acid sequence or the second nucleic acid strand synthesized in step (e).

154. The process of claim 153, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of RNA fragments produced by the action of RNase H.

155. The process of claim 153, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of said optional second nucleic acid primer or nucleic acid construct.

156. The process of claim 153, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by terminal addition or terminal ligation to said primer-extended nucleic acid sequence, which terminal addition or ligation is followed by contacting said terminally added or ligated sequences with one or more of said optional second nucleic acid primers or constructs complementary to said terminally added or ligated sequences, followed by extension of said optional second nucleic acid primers or constructs.

157. The process of claim 153, wherein said. RNA promoter comprises a T3 promoter, a T7 promoter or an SP6 promoter.

158. The process of claim 157, wherein said transcribing step (f) is carried out by a cognate RNA polymerase.

159. The process of claims 153, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

160. The process of claim 153, wherein said detecting step (e) is carried out one or more times or at specific intervals.

161. The process of claim 153, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

162. The process of claim 153, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

163. The process of claim 162, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

164. The process of claim 153, wherein said transcripts obtained in step (f) are fixed or immobilized to a solid support.

165. The process of claim 164, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

166. The process of claim 164, wherein said fixation or immobilization is direct or indirect.

167. The process of claims 153, wherein any or all of said steps are carried out in a closed container system.

168. The process of claim 167, wherein said closed container system comprises an illumination source and a detection device or unit.

169. A composition of matter that comprises two parts, wherein the first part is a nucleic acid strand comprising two segments, the first segment comprising a nucleic acid primer or nucleic acid construct, and the second segment comprises a primer-extended sequence, and

wherein the second part comprises a nucleic acid binding agent, wherein said nucleic acid primer or nucleic acid construct comprises one or more fluorescent first energy transfer elements and wherein said nucleic acid binding agent comprises one or more second energy transfer elements.

170. The composition of claim 169, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

171. The composition of claim 169, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

172. The composition of claim 169, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

173. The composition of claim 172, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

174. The composition of claim 169, wherein said nucleic acid binding agent comprises a protein or a polypeptide.

175. The composition of claim 174, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein or antibodies.

176. The composition of claim 169, wherein said nucleic acid binding agent comprises a single strand nucleic acid binding dye.

177. The composition of claim 169, wherein said nucleic acid strand is fixed or immobilized to a solid support.

178. The composition of claim 177, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

179. The composition of claim 177, wherein said fixation or immobilization is direct or indirect.

180. A composition of matter that comprises

(a) two nucleic acid strands, wherein at least one of said strands comprises two segments, the first segment comprising a nucleic acid primer or nucleic acid construct, and the second segment comprising a primer-extended sequence, and

(b) a nucleic acid binding agent, wherein said nucleic acid primer or nucleic acid construct comprises one or more fluorescent first energy transfer elements and wherein said nucleic acid binding agent comprises one or more second energy transfer elements.

181. The composition of claim 180, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

182. The composition of claim 180, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

183. The composition of claim 180, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

184. The composition of claim 183, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

185. The composition of claim 180, wherein said second strand comprises two segments, the first segment comprising a second nucleic acid primer or nucleic acid construct, and the second segment comprising a primer-extended sequence.

186. The composition of claim 185, wherein said second primer or nucleic acid construct comprises one or more first energy transfer elements.

187. The composition of claim 180, wherein said nucleic acid binding agent comprises a protein or a polypeptide.

188. The composition of claim 187, wherein said protein or polypeptide comprises histones or antibodies.

190. The composition of claim 180, wherein said nucleic acid binding agent comprises an intercalator.

191. The composition of claim 190, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

192. The composition of claim 180, wherein at least one of said nucleic acid strands is fixed or immobilized to a solid support.

193. The composition of claim 192, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

194. The composition of claim 192, wherein said fixation or immobilization is direct or indirect.

195. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a nucleic acid primer or nucleic acid construct that comprises

(A) a nucleic acid sequence complementary to at least a portion of said nucleic acid of interest; and

(B) one or more fluorescent first energy transfer elements;

(iii) a nucleic acid binding agent comprising one or more second energy transfer elements;

(iv) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii) and (iv) above;

(c) contacting under hybridization conditions said nucleic acid primer in said composition (ii) with said nucleic acid of interest;

(d) extending said nucleic acid primer or nucleic acid construct to form a primer-extended sequence;

(e) binding said nucleic acid binding agent (iii) to said primer-extended sequence or to a complex comprising said nucleic acid of interest and said primer-extended sequence; and

(f) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

196. The process of claim 195, wherein said providing step (a), the nucleic acid binding agent (iii) comprises a protein or a polypeptide.

197. The process of claim 196, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein, histones or antibodies.

198. The process of claim 195, wherein said providing step (a), the nucleic acid binding agent (iii) comprises a single strand nucleic acid binding dye.

199. The process of claim 195, wherein said providing step (a), the nucleic acid binding agent (iii) comprises an intercalator.

200. The process of claim 199, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

201. The process of claim 195, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

202. The process of claim 195, wherein said primer-extended sequence formed in said extending step (d) has been rendered single-stranded prior to said binding step (e).

203. The process of claim 195, wherein prior to the detecting step (f), said process further comprises the step of (b′

) separating said extended nucleic acid from the nucleic acid of interest and repeating the contacting step (c), the extending step (d) and the binding step (e).

204. The process of claim 203, wherein said separating step (b′

), said contacting step (c), said extending step (d) and said binding step (e) are repeated one or more times.

205. The process of claim 195, wherein in the providing step (a), said reagents (iv) comprises a thermostable DNA polymerase.

206. The process of claims 202, 203 or 204, wherein said rendering or separating step is carried out by thermal denaturation or strand displacement.

207. The process of claim 195, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

208. The process of claim 195, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

209. The process of claim 208, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

210. The process of claim 195, wherein said nucleic acid primer or said primer-extended sequence is fixed or immobilized to a solid support.

211. The process of claim 210, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

212. The process of claim 210, wherein said fixation or immobilization is direct or indirect.

213. The process of claims 195, 202, 203 or 204, wherein any or all of said steps are carried out in a closed container system.

214. The process of claim 213, wherein said closed container system comprises an illumination source and a detection device or unit.

215. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a first nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of one strand of said nucleic acid of interest;

(iii) a second nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence identical to at least a portion of said one strand;

(iv) a nucleic acid binding agent comprising one or more first energy transfer elements; and

(v) reagents for carrying out nucleic acid strand extension;

wherein (ii), (iii) or both (ii) and (iii) comprise one or more fluorescent second energy transfer elements;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if the complementary strand is present;

(e) binding said nucleic acid binding agent (iv) to a primer-extended nucleic acid sequence or to a complex comprising said nucleic acid of interest and a primer-extended sequence; and

(f) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between a second energy transfer element in said first nucleic acid primer, said second nucleic acid primer, or both, and a first energy element in said nucleic acid binding agent (iv).

216. The process of claim 215, wherein in said providing step (a), the nucleic acid binding agent (iv) comprises a protein or a polypeptide.

217. The process of claim 216, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein, histones or antibodies.

218. The process of claim 215, wherein said providing step (a), the nucleic acid binding agent (iv) comprises a single strand nucleic acid binding dye.

219. The process of claim 215, wherein said providing step (a), the nucleic acid binding agent (iii) comprises an intercalator.

220. The composition of claim 219, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

221. The process of claim 215, further comprising:

(b′

) separating said first primer-extended nucleic acid sequence from said nucleic acid of interest and separating said second primer-extended nucleic acid sequence from said complementary strand of said nucleic acid of interest if present;

(c′

) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (b′

), if said second strand is present, and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with said first primer-extended nucleic acid sequence from step (b′

); and

repeating said extending step (d) and said binding step (e) thereafter.

222. The process of claim 221, further comprising the step (b″

) of separating said first primer-extended nucleic acid sequence from said second primer-extended nucleic acid sequence, and the step (c″

) of contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (b″

), and contacting under hybridization conditions said second nucleic acid primer in said composition (iii) with said first primer-extended nucleic acid sequence from step (b″

); and

repeating said extending step (d) and said binding step (e) thereafter.

223. The process of claim 222, wherein said separating step (b″

), said contacting step (c″

), said extending step (d) and said binding step (e) are repeated.

224. The process of claim 215, wherein said complementary strand of the nucleic acid of interest is present.

225. The process of claims 215, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

226. The process of claims 215, 221, 222 or 223, wherein said binding step (e) is carried out after a separation or denaturation step.

227. The process of any of claims 215, 221, 222, or 223, wherein said detecting step (e) is carried out at specific intervals during or after any binding step (e).

228. The process of claim 215, wherein in the providing step (a), said reagents (v) comprise a thermostable DNA polymerase.

229. The process of claim 215, 221, 222, or 223, wherein said separating step is carried out by thermal denaturation or strand displacement.

230. The process of claim 215, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

231. The process of claim 215, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

232. The process of claim 231, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

233. The process of claim 215, wherein at least one of said first or second nucleic acid primers or constructs or any primer-extended nucleic acid sequence is fixed or immobilized to a solid support.

234. The process of claim 233, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

235. The process of claim 233, wherein said fixation or immobilization is direct or indirect.

236. The process of claims 215, 221, 222, or 223, wherein any or all of said steps are carried out in a closed container system.

237. The process of claim 236, wherein said closed container system comprises an illumination source and a detection device or unit.

238. A composition of matter that comprises

(a) a nucleic acid strand comprising two segments, said first segment comprising a primer or a nucleic acid construct;

and said second segment comprising a primer-extended sequence; and

(b) a nucleic acid binding agent;

wherein said primer-extended sequence comprises one or more first energy transfer elements, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements.

239. The composition of claim 238, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

240. The composition of claim 238, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

241. The composition of claim 238, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

242. The composition of claim 241, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

243. The composition of claim 238, wherein said nucleic acid binding agent (b) comprises a protein or a polypeptide.

244. The composition of claim 231, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein or antibodies.

245. The composition of claim 238, wherein said nucleic acid binding agent (b) comprises a single strand nucleic acid binding dye.

246. The composition of claim 238, wherein said nucleic acid strand (a) is fixed or immobilized to a solid support.

247. The composition of claim 246, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

248. The composition of claim 246, wherein said fixation or immobilization is direct or indirect.

249. A composition of matter that comprises

(a) two nucleic acid strands, wherein at least one of said strands comprises two segments, the first segment comprising a nucleic acid primer or nucleic acid construct, and the second segment comprising a primer-extended sequence, and

(b) a nucleic acid binding agent, wherein said primer-extended sequence comprises one or more first energy transfer elements, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements.

250. The composition of claim 249, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

251. The composition of claim 249, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

252. The composition of claim 249, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

253. The composition of claim 252, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

254. The composition of claim 249, wherein said nucleic acid binding agent (b) comprises a protein or a polypeptide.

255. The composition of claim 254, wherein said protein or polypeptide comprises histones or antibodies.

256. The composition of claim 249, wherein said nucleic acid binding agent (b) comprises an intercalator.

257. The composition of claim 256, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

258. The composition of claim 249, wherein both nucleic acid strands (a) comprise two segments, the first segment comprising a nucleic acid primer or a nucleic acid construct, and the second segment comprising a primer-extended sequence.

259. The composition of claim 258, wherein said primer-extended sequences comprise first energy transfer elements.

260. The composition of claim 249, wherein at least one of said nucleic acid strands (a) is fixed or immobilized to a solid support.

261. The composition of claim 260, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

262. The composition of claim 260, wherein said fixation or immobilization is direct or indirect.

263. The composition of claim 249, wherein said nucleic acid primer or nucleic acid construct further comprises a quencher.

264. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) at least one nucleic acid primer or nucleic acid construct complementary to at least a portion of said nucleic acid of interest;

(iii) labeled nucleotide or nucleotides comprising a first energy transfer element;

(iv) a nucleic acid binding agent comprising one or more second energy transfer elements; and

(v) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said nucleic acid primer in said composition (ii) with said nucleic acid of interest;

(d) extending said nucleic acid primer, thereby incorporating said labeled nucleotide or nucleotides;

(e) binding said nucleic acid binding agent to said primer-extended sequence; and

(f) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

265. The process of claim 264, wherein said providing step (a), there is at least other nucleic acid primer or nucleic acid construct complementary to a different portion of said nucleic acid of interest.

266. The process of claim 264, wherein said providing step (a), the nucleic acid binding agent (iv) comprises a protein or a polypeptide.

267. The process of claim 266, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein, histones or antibodies.

268. The process of claim 264, wherein said providing step (a), the nucleic acid binding agent (iv) comprises a single strand nucleic acid binding dye.

269. The process of claim 264, wherein said providing step (a), the nucleic acid binding agent (iv) comprises an intercalator.

270. The process of claim 269, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

271. The process of claim 264, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

272. The process of claim 264, wherein prior to the detecting step (f), said process further comprises the step of (b′

) separating said extended nucleic acid from the nucleic acid of interest and repeating the contacting step (c), the extending step (d) and the binding step (e).

273. The process of claim 264, wherein said separating step (b′

), said contacting step (c), said extending step (d) and said binding step (e) are repeated one or more times.

274. The process of claims 264, 272 or 273, wherein said primer-extended sequence formed in said extending step (d) has been rendered single-stranded prior to said binding step (e).

275. The process of claim 264, wherein in the providing step (a), said reagents (v) comprises a thermostable DNA polymerase.

276. The process of claims 272 or 273, wherein said separating step is carried out by thermal denaturation or strand displacement.

277. The process of claim 264, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

278. The process of claim 264, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

279. The process of claim 278, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

280. The process of claim 264, wherein said nucleic acid primer, said nucleic acid construct or said primer-extended sequence is fixed or immobilized to a solid support.

281. The process of claim 280, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

282. The process of claim 280, wherein said fixation or immobilization is direct or indirect.

283. The process of claims 264, 272 or 273, wherein any or all of said steps are carried out in a closed container system.

284. The process of claim 283, wherein said closed container system comprises an illumination source and a detection device or unit.

285. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing;

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a first nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of one strand of said nucleic acid of interest;

(iii) a second nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence identical to at least a portion of said one strand;

(iv) one or more labeled nucleotides comprising a first energy transfer element;

(v) a nucleic acid binding agent comprising one or more second energy transfer elements; and

(vi) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv), (v) and (vi) above;

(c) contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer or nucleic acid construct (iii) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if the complementary strand is present, thereby incorporating said labeled nucleotide or nucleotides;

(e) binding said nucleic acid binding agent (v) to said first primer-extended nucleic acid sequence, and to said second primer-extended nucleic acid sequence if the complementary strand is present; and

(f) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

286. The process of claim 285, wherein in said providing step (a), the nucleic acid binding agent (v) comprises a protein or a polypeptide.

287. The process of claim 286, wherein said protein or polypeptide comprises T4 gene 32 protein,.SSB protein, histones or antibodies.

288. The process of claim 285, wherein said providing step (a), the nucleic acid binding agent (v) comprises a single strand nucleic acid binding dye.

289. The process of claim 285, wherein said providing step (a), the nucleic acid binding agent (v) comprises an intercalator.

290. The composition of claim 289, wherein said intercalator comprises SYBR green I, ethidium bromide, a homodimer or a heterodimer that comprises ethidium bromide or derivatives.

291. The process of claim 285, further comprising:

(b′

) separating said first primer-extended nucleic acid sequence from said nucleic acid of interest and separating said second primer-extended nucleic acid sequence from said complementary strand of said nucleic acid of interest if present;

(c′

) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (b′

), if said second strand is present, and contacting under hybridization conditions said second nucleic acid primer or nucleic acid construct (iii) with said first primer-extended nucleic acid sequence from step (b′

); and

repeating said extending step (d) and said binding step (e) thereafter.

292. The process of claim 291, further comprising the step (b″

) of separating said first primer-extended nucleic acid sequence from said second primer-extended nucleic acid sequence, and the step (c″

) of contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with said second primer-extended nucleic acid sequence from step (b″

), and contacting under hybridization conditions said second nucleic acid primer or nucleic acid construct (iii) with said first primer-extended nucleic acid sequence from step (b″

); and

repeating said extending step (d) and said binding step (e) thereafter.

293. The process of claim 292, wherein said separating step (b″

), said contacting step (c″

), said extending step (d) and said binding step (e) are repeated.

294. The process of claim 285, wherein said complementary strand of the nucleic acid of interest is present.

295. The process of claims 285, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

296. The process of any of claims 285, 291, 292 or 293, wherein said detecting step (e) is carried out at specific intervals during or after any binding step (e).

297. The process of claim 285, wherein in the providing step (a), said reagents (v) comprise a thermostable DNA polymerase.

298. The process of claim 291, 292 or 293, wherein said separating step is carried out by thermal denaturation or strand displacement.

299. The process of claim 285, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

300. The process of claim 285, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

301. The process of claim 300, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

302. The process of claim 285, wherein at least one of said first or second nucleic acid primers or constructs or any primer-extended nucleic acid sequence is fixed or immobilized to a solid support.

303. The process of claim 302, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

304. The process of claim 302, wherein said fixation or immobilization is direct or indirect.

305. The process of claims 285, 291, 292 or 293, wherein any or all of said steps are carried out in a closed container system.

306. The process of claim 305, wherein said closed container system comprises an illumination source and a detection device or unit.

307. A composition of matter that comprises:

(i) a nucleic acid strand, said strand comprising one or more ribonucleotides, wherein at least one ribonucleotide comprises a first energy transfer element; and

(ii) a nucleic acid binding agent comprising one or more second energy transfer elements.

308. The composition of claim 307, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

309. The composition of claim 307, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

310. The composition of claim 307, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

311. The composition of claim 310, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

312. The composition of claim 307, wherein said nucleic acid binding agent (ii) comprises a protein or a polypeptide.

313. The composition of claim 307, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein or antibodies.

314. The composition of claim 307, wherein said nucleic acid binding agent (ii) comprises a single strand nucleic acid binding dye.

315. The composition of claim 307, wherein said nucleic acid strand is fixed or immobilized indirectly to a solid support.

316. The composition of claim 315, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

317. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) at least one first nucleic acid primer or nucleic acid construct and optionally, a second nucleic acid primer or nucleic acid construct, wherein either the first nucleic acid primer or nucleic acid construct, or said optional second nucleic acid primer or nucleic acid construct comprises an RNA promoter sequence;

(iii) one or more labeled ribonucleotides comprising a first energy transfer element;

(iv) a nucleic acid binding agent comprising a second energy transfer element;

(v) reagents for carrying out nucleic acid strand extension and RNA transcription;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with one strand of said nucleic acid of interest;

(d) extending said nucleic acid primer to form a primer-extended nucleic acid sequence;

(e) synthesizing a second nucleic acid strand complementary to said primer-extended nucleic acid sequence or a portion thereof, thereby forming a double-stranded nucleic acid;

(f) transcribing said double-stranded nucleic acid formed in step (e) to incorporate said labeled ribonucleotides (iii) into labeled transcripts;

(g) binding said nucleic acid binding agent (iv) to said labeled transcripts;

(h) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element;

wherein said transcribing step (f) is carried out by an RNA promoter in either the primer-extended nucleic acid sequence or the second nucleic acid strand synthesized in step (e).

318. The process of claim 317, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of RNA fragments produced by the action of RNase H.

319. The process of claim 317, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of said optional second nucleic acid primer or nucleic acid construct.

320. The process of claim 317, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by terminal addition or terminal ligation to said primer-extended nucleic acid sequence, which terminal addition or ligation is followed by contacting said terminally added or ligated sequences with one or more second nucleic acid primers or constructs complementary to said terminally added or ligated sequences, followed by extension of said second nucleic acid primers or constructs.

321. The process of claim 317, wherein said RNA promoter comprises a T3 promoter, a T7 promoter or an SP6 promoter.

322. The process of claim 317, wherein said transcribing step (f) is carried out by a cognate RNA polymerase.

323. The process of claims 317, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

324. The process of claim 317, wherein said detecting step (h) is carried out one or more times or at specific intervals.

325. The process of claim 317, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

326. The process of claim 317, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

327. The process of claim 326, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

328. The process of claim 317, wherein in said providing step (a), the nucleic acid binding agent (iv) comprises a protein or a polypeptide.

329. The process of claim 328, wherein said protein or polypeptide comprises T4 gene 32 protein, SSB protein or antibodies.

330. The process of claim 317, wherein said providing step (a), the nucleic acid binding agent (v) comprises a single strand nucleic acid binding dye.

331. The process of claim 317, wherein said transcripts obtained in step (f) are fixed or immobilized to a solid support.

332. The process of claim 331, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

333. The process of claim 331, wherein said fixation or immobilization is direct or indirect.

334. The process of claims 317, wherein any or all of said steps are carried out in a closed container system.

335. The process of claim 334, wherein said closed container system comprises an illumination source and a detection device or unit.

336. A composition of matter that comprises a hybridized first and second nucleic acids,

said first strand comprising two segments, the first segment comprising a primer or a nucleic acid construct;

and the second segment comprising a primer-extended sequence,

said second strand comprising a nucleic acid probe hybridized to said primer-extended sequence or a portion thereof, and

wherein said primer-extended sequence comprises one or more first energy transfer elements, and wherein said nucleic acid probe comprises one or more second energy transfer elements.

337. The composition of claim 336, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

338. The composition of claim 336, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

339. The composition of claim 336, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

340. The composition of claim 339, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

341. The composition of claim 336, wherein at least one of said nucleic acid strands is fixed or immobilized to a solid support.

342. The composition of claim 341, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

343. The composition of claim 341, wherein said fixation or immobilization is direct or indirect.

344. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a nucleic acid primer or nucleic acid construct complementary to at least a portion of said nucleic acid of interest;

(iii) labeled nucleotide or nucleotides comprising a first energy transfer element;

(iv) a nucleic acid probe comprising one or more second energy transfer elements; and

(v) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said nucleic acid primer in said composition (ii) with said nucleic acid of interest;

(d) extending said nucleic acid primer, thereby incorporating said labeled nucleotide or nucleotides;

.

(e) separating said primer-extended sequence from said nucleic acid of interest (i);

(f) hybridizing said nucleic acid probe to said primer-extended sequence; and

(g) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

345. The process of claim 344, wherein said nucleic acid probe (iv) comprises modified nucleotides or nucleotide analogs.

346. The process of claim 344, wherein said nucleic acid probe (iv) comprises ribonucleotides or deoxyribonucleotides, or both.

347. The process of claim 344, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

348. The process of claim 344, wherein prior to the detecting step (g), said process further comprises repeating the contacting step (c), the extending step (d), the separating step (e) and the hybridizing step (f).

349. The process of claim 348, wherein said contacting step (c), said extending step (d), said separating step (e) and said hybridizing step (f) are repeated one or more times.

350. The process of claim 344, wherein in the providing step (a), said reagents (v) comprises a thermostable DNA polymerase.

351. The process of claims 348 or 349, wherein said separating step is carried out by thermal denaturation or strand displacement.

352. The process of claim 344, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

353. The process of claim 344, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

354. The process of claim 353, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

355. The process of claim 354, wherein said primer-extended sequence or said probe is fixed or immobilized to a solid support.

356. The process of claim 355, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

357. The process of claim 355, wherein said fixation or immobilization is direct or indirect.

358. The process of claims 344, 348 or 349, wherein any or all of said steps are carried out in a closed container system.

359. The process of claim 358, wherein said closed container system comprises an illumination source and a detection device or unit.

360. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing;

(i) a sample suspected of containing said nucleic acid of interest;

(ii) a first nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence complementary to at least a portion of one strand of said nucleic acid of interest;

(iii) a second nucleic acid primer or nucleic acid construct that comprises a nucleic acid sequence identical to at least a portion of said one strand;

(iv) one or more labeled nucleotides comprising a first energy transfer element;

(v) a nucleic acid probe comprising one or more second energy transfer elements; and

(vi) reagents for carrying out nucleic acid strand extension;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv), (v) and (vi) above;

(c) contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with one strand of said nucleic acid of interest and contacting under hybridization conditions said second nucleic acid primer or nucleic acid construct (iii) with the complementary strand of said nucleic acid of interest if present;

(d) extending said first nucleic acid primer and said second nucleic acid primer to form a first primer-extended nucleic acid sequence and a second primer-extended nucleic acid sequence if the complementary strand is present, thereby incorporating said labeled nucleotide or nucleotides;

(e) separating said first primer-extended nucleic acid sequence and said second primer-extended nucleic acid sequence if produced in step (d);

(f) hybridizing said nucleic acid probe (v) to said first primer-extended nucleic acid sequence, or to said second primer-extended nucleic acid sequence; and

(g) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element.

361. The process of claim 360, wherein said nucleic acid probe (v) comprises modified nucleotides or nucleotide analogs.

362. The process of claim 360, wherein said nucleic acid probe (v) comprises ribonucleotides or deoxyribonucleotides, or both.

363. The process of claim 360, wherein said complementary strand of the nucleic acid of interest is present.

364. The process of claim 363, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

365. The process of claim 360, further comprising:

(c′

) contacting under hybridization conditions said first nucleic acid primer in said composition (ii) with said second primer-extended nucleic acid sequence from step (e), if said second strand is present, and contacting under hybridization conditions said second nucleic acid primer or nucleic acid construct (iii) with said first primer-extended nucleic acid sequence from step (e); and

repeating said extending step (d), said separating step (e) and said hybridizing step (f) thereafter.

366. The process of claim 365, further comprising repeating said contacting step (c′

), said extending step (d), said separating step (e) and said hybridizing step (f) thereafter.

367. The process of any of claims 360, 365 or 366, wherein said detecting step (g) is carried out at specific intervals during or after any hybridizing step (f).

368. The process of claim 360, wherein in the providing step (a), said reagents (v) comprise a thermostable DNA polymerase.

369. The process of claim 360, 365 or 366, wherein said separating step (e) is carried out by thermal denaturation or strand displacement.

370. The process of claim 360, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

371. The process of claim 360, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

372. The process of claim 371, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

373. The process of claim 360, wherein said primer-extended nucleic acid sequence or said nucleic acid probe is fixed or immobilized to a solid support.

374. The process of claim 373, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

375. The process of claim 373, wherein said fixation or immobilization is direct or indirect.

376. The process of claims 360, 365 or 366, wherein any or all of said steps are carried out in a closed container system.

377. The process of claim 376, wherein said closed container system comprises an illumination source and a detection device or unit.

378. A composition of matter that comprises a hybridized first and second nucleic acids, said first strand comprising at least one ribonucleotide, wherein said at least one ribonucleotide comprises a first energy transfer element;

said second strand comprising;

a nucleic acid probe hybridized to said first strand or a portion thereof, wherein said nucleic acid probe comprises one or more second energy transfer elements.

379. The composition of claim 378, wherein said nucleic acid probe comprises modified nucleotides or nucleotide analogs.

380. The composition of claim 378, wherein said nucleic acid probe comprises ribonucleotides or deoxyribonucleotides, or both.

381. The composition of claim 378, wherein said first energy transfer element is an energy donor and wherein said second energy transfer element is an energy acceptor.

382. The composition of claim 378, wherein said first energy transfer element is an energy acceptor and wherein said second energy transfer element is an energy donor.

383. The composition of claim 378, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

384. The composition of claim 383, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

385. The composition of claim 378, wherein said first strand or said nucleic acid probe is fixed or immobilized indirectly to a solid support.

386. The composition of claims 384, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

387. A process for detecting qualitatively or quantitatively the presence of a single-stranded or double-stranded nucleic acid of interest in a sample, said process comprising the steps of:

(a) providing

(i) a sample suspected of containing said nucleic acid of interest;

(ii) at least one first nucleic acid primer or nucleic acid construct and optionally, a second nucleic acid primer or nucleic acid construct, wherein either the first nucleic acid primer or nucleic acid construct, or said optional second nucleic acid primer or nucleic acid construct comprises an RNA promoter sequence;

(iii) one or more labeled ribonucleotides comprising a first energy transfer element;

(iv) a nucleic acid binding probe comprising a second energy transfer element;

(v) reagents for carrying out nucleic acid strand extension and RNA transcription;

(b) forming a reaction mixture comprising (i), (ii), (iii), (iv) and (v) above;

(c) contacting under hybridization conditions said first nucleic acid primer or nucleic acid construct (ii) with one strand of said nucleic acid of interest;

(d) extending said nucleic acid primer to form a primer-extended nucleic acid sequence;

(e) synthesizing a second nucleic acid strand complementary to said primer-extended nucleic acid sequence or a portion thereof, thereby forming a double-stranded nucleic acid;

(f) transcribing said double-stranded nucleic acid formed in step (e) to incorporate said labeled ribonucleotides (iii) into labeled transcripts;

(g) hybridizing said nucleic acid probe (iv) to said labeled transcripts;

(h) detecting the presence or quantity of said nucleic acid of interest by means of energy transfer between said first energy transfer element and said second energy transfer element;

wherein said transcribing step (f) is carried out by an RNA promoter in either the primer-extended nucleic acid sequence or the second nucleic acid strand synthesized in step (e).

388. The process of claim 387, wherein said nucleic acid probe (iv) comprises modified nucleotides or nucleotide analogs.

389. The process of claim 387, wherein said nucleic acid probe (iv) comprises ribonucleotides or deoxyribonucleotides, or both.

390. The process of claim 387, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of RNA fragments produced by the action of RNase H.

391. The process of claim 387, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by primer extension of said optional second nucleic acid primer or nucleic acid construct.

392. The process of claim 387, wherein in said synthesizing step (e), the second nucleic acid strand is synthesized by terminal addition or terminal ligation to said primer-extended nucleic acid sequence, which terminal addition or ligation is followed by contacting said terminally added or ligated sequences with one or more second nucleic acid primers or constructs complementary to said terminally added or ligated sequences, followed by extension of said second nucleic acid primers or constructs.

393. The process of claim 387, wherein said RNA promoter comprises a T3 promoter, a T7 promoter or an SP6 promoter.

394. The process of claim 387, wherein said transcribing step (f) is carried out by a cognate RNA polymerase.

395. The process of claim 387, wherein said nucleic acid of interest (i) has been rendered single stranded before or during said reaction mixture forming step (b).

396. The process of claim 387, wherein said detecting step (h) is carried out one or more times or at specific intervals.

397. The process of claim 387, wherein in said providing step (a), either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

398. The process of claim 387, wherein in said providing step (a), said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

399. The process of claim 398, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

400. The process of claim 387, wherein said transcripts obtained in step (f) or said nucleic acid probes are fixed or immobilized to a solid support.

401. The process of claim 400, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

402. The process of claim 400, wherein said fixation or immobilization is direct or indirect.

403. The process of claim 387, wherein any or all of said steps are carried out in a closed container system.

404. The process of claim 403, wherein said closed container system comprises an illumination source and a detection device or unit.

405. A chimeric nucleic acid construct comprising at least two segments, the first segment comprising five or more universal bases and the second segment comprising a nucleic acid template for synthesizing a discrete nucleic acid sequence.

406. The construct of claim 405, wherein said discrete nucleic acid sequence comprises at least one primer binding sequence or promoter sequence.

407. The construct of claim 406, wherein said primer binding sequence is homopolymeric or heteropolymeric.

408. The construct of claim 407, wherein said:

homopolymeric sequence comprises poly T, poly U, poly G, poly C or poly A.

409. The construct of claim 407, wherein said heteropolymeric sequence comprises an RNA promoter sequence.

410. The construct of claim 409, wherein said RNA promoter sequence comprises a T3 promoter, a T7 promoter or an SP6 promoter.

411. The construct of claim 412, wherein said first segment comprises from about eight to about fifteen universal bases.

412. The construct of claim 405, wherein said universal bases comprise inosine, 5-nitroindole or 3-nitropyrrole.

413. The construct of claim 405, wherein the 5′

end of said first segment is attached to the 3′

end of said second segment.

414. A process for incorporating a desirable nucleic acid sequence into an analyte or a library of analytes, said process comprising the steps of:

a) providing

(i) said analyte or library of analytes;

(ii) a chimeric nucleic acid construct comprising at least two segments, the first segment comprising five or more universal bases and the second segment comprising a template for synthesizing said desirable nucleic acid sequence; and

(iii) reagents for carrying out hybridization and template-dependent strand extension;

b) binding or hybridizing said chimeric nucleic acid construct (ii) to said analyte or library of analytes (i); and

c) extending the 3′

end of said analyte or library of analytes;

wherein said second segment is a template for said extending step (c) when said second segment is in proximity to the 3′

end of said analyte or library of analytes.

415. The construct of claim 414, wherein the 5′

end of said first segment is attached to the 3′

end of said second segment.

416. The process of claim 414, wherein said desirable nucleic acid sequence comprises at least one primer binding sequence or promoter sequence.

417. The process of claim 416, wherein said primer binding sequence is homopolymeric or heteropolymeric.

418. The process of claim 417, wherein said homopolymeric sequence comprises poly T, poly U, poly G, poly C or poly A.

419. The process of claim 417, wherein said heteropolymeric sequence comprises an RNA promoter sequence.

420. The process of claim 419, wherein said RNA promoter sequence comprises a T3 promoter, a T7 promoter or an SP6 promoter.

421. The process of claim 414, wherein in said providing step (a), the analyte or library of analytes (i) comprise DNA or RNA.

422. The process of claim 421, wherein said DNA comprises chromosomal DNA, episomal DNA or viral DNA.

423. The process of claim 421, wherein said RNA comprises mRNA, hRNA, snRNA, rRNA, tRNA or viral RNA.

424. The process of claim 414, wherein in said providing step (a), the DNA or RNA is or has been fragmented.

425. The process of claim 424, wherein said fragmentation has been carried out by a chemical, physical or enzymatic process.

426. The process of claim 425, wherein said enzymatic process is carried out by an endonuclease.

427. The process of claim 414, wherein in said providing step (a) the first segment comprises from about eight to about fifteen universal bases.

428. The process of claim 414, wherein in said providing step (a) the universal bases comprise inosine, 5-nitroindole or 3-nitropyrrole.

429. The process of claim 414, wherein in said providing step (a) the reagents (iii) comprise polymerases or ligases.

430. The process of claim 429, wherein said polymerases comprise reverse transcriptases, DNA Pol I or Klenow fragment of Pol I.

431. The process of claim 429, wherein said ligases comprise T4 DNA ligase.

432. The process of claim 414, wherein said reagents (iii) comprise one or more labeled nucleotides or oligonucleotides.

433. The process of claim 414, wherein said binding or hybridizing step (b) is carried at or near a temperature and under conditions sufficient to form a stable complex or hybrid between said chimeric nucleic acid construct (ii) and said analyte or library of analytes (i).

434. The process of claim 414, further comprising the step (a′

) of pretreating said analyte or library of analytes with a phosphatase.

435. The process of claim 414, wherein said providing step (a), the chimeric nucleic acid construct (ii) is incapable of strand extension.

436. A composition comprising a set of chimeric nucleic acid constructs, each such construct comprising at least three segments, the first segment comprising four or more universal bases, the second segment comprising permutations of from one to eight nucleotides, the third segment comprising a template for synthesizing a desirable nucleic acid sequence,

wherein in said second segment, the permutations of from one to eight nucleotides comprise

(N)_n

wherein N independently comprises G, A, T or C, and wherein n is an integer from one to eight.

437. The composition of claim 436, wherein in each such construct, the 5′

end of said first segment is attached to the 3′

end of said second segment, and the 5′

end of said second segment is attached to the 3′

end of said third segment.

438. The composition of claim 436, wherein said desirable nucleic acid sequence comprises at least one primer binding sequence or promoter sequence.

439. The composition of claim 438, wherein said primer binding sequence is homopolymeric or heteropolymeric.

440. The composition of claim 439, wherein said homopolymeric sequence comprises poly T, poly U, poly G, poly C or poly A.

441. The composition of claim 439, wherein said heteropolymeric sequence comprises an RNA promoter sequence.

442. The composition of claim 441, wherein said RNA promoter sequence comprises a T3 promoter, a T7 promoter or an SP6 promoter.

443. The composition of claim 436, wherein said first segment comprises from about six to about fifteen universal bases.

444. The composition of claim 436, wherein said first segment comprises four universal bases and n is 4.

445. The composition of claim 436, wherein said first segment comprises four universal bases and n is 6.

446. The composition of claim 436, wherein the universal bases in said first segment comprise inosine, 5-nitroindole or 3-nitropyrrole.

447. The composition of claim 436, wherein said chimeric nucleic acid constructs are incapable of strand extension.

448. A process for incorporating a desirable nucleic acid sequence into an analyte or a library of analytes, said process comprising the steps of:

a) providing

(i) said analyte or library of analytes;

(ii) a set of chimeric nucleic acid constructs, each such construct comprising at least three segments, the first segment comprising four or more universal bases, the second segment comprising permutations of from one to eight nucleotides, the third segment comprising a template for synthesizing said desirable nucleic acid sequence,

wherein in said second segment, the permutations of from one to eight nucleotides comprise

(N)_n

wherein N independently comprises G, A, T or C, and wherein n is an integer from one to eight; and

(iii) reagents for carrying out hybridization and template-dependent strand extension;

b) binding or hybridizing said chimeric nucleic acid construct (ii) to said analyte or library of analytes (i); and

c) extending the 3′

end of said analyte or library of analytes;

wherein said third segment is a template for said extending step (c) when said second segment is hybridized to the 3′

end of said analyte or library of analytes.

449. The process of claim 448, wherein in said providing step (a), each such construct, the 5′

end of said first segment is attached to the 3′

end of said second segment, and the 5′

end of said second segment is attached to the 3′

end of said third segment.

450. The process of claim 448, wherein said desirable nucleic acid sequence comprises at least one primer binding sequence or promoter sequence.

451. The process of claim 450, wherein said primer binding sequence is homopolymeric or heteropolymeric.

452. The process of claim 451, wherein said homopolymeric sequence comprises poly T, poly U, poly G, poly C or poly A.

453. The process of claim 451, wherein said heteropolymeric sequence comprises an RNA promoter sequence.

454. The process of claim 453, wherein said RNA promoter sequence comprises a T3 promoter, a T7 promoter or an SP6 promoter.

455. The process of claim 448, wherein in said providing step (a), the analyte or library of analytes (i) comprise DNA or RNA.

456. The process of claim 455, wherein said DNA comprises chromosomal DNA, episomal DNA or viral DNA.

457. The process of claim 455, wherein said RNA comprises mRNA, hRNA, snRNA, rRNA, tRNA or viral RNA.

458. The process of claim 448, wherein in said providing step (a), the DNA or RNA is or has been fragmented.

459. The process of claim 458, wherein said fragmentation has been carried out by a chemical, physical or enzymatic process.

460. The process of claim 459, wherein said enzymatic process is carried out by an endonuclease.

461. The process of claim 448, wherein in said providing step (a) the first segment comprises from about six to about fifteen universal bases.

462. The process of claim 448, wherein in said providing step (a) the first segment comprises four universal bases and n is 4.

463. The process of claim 436, wherein in said providing step (a) the first segment comprises four universal bases and n is 6.

464. The process of claim 448, wherein in said providing step (a) the universal bases comprise inosine, 5-nitroindole or 3-nitropyrrole.

465. The process of claim 448, wherein in said providing step (a) the reagents (iii) comprise polymerases or ligases.

466. The process of claim 465, wherein said polymerases comprise reverse transcriptases, DNA Pol I or Klenow fragment of Pol I.

467. The process of claim 466, wherein said ligases comprise T4 DNA ligase.

468. The process of claim 448, wherein said reagents (iii) comprise one or more labeled nucleotides or oligonucleotides.

469. The process of claim 448, wherein said binding or hybridizing step (b) is carried at or near a temperature and under conditions sufficient to form a stable complex or hybrid between said chimeric nucleic acid construct (ii) and said analyte or library of analytes (i).

470. The process of claim 448, further comprising the step (a′

) of pretreating said analyte or library of analytes with a phosphatase.

471. The process of claim 448, wherein said providing step (a), the chimeric nucleic acid construct (ii) is or has been rendered incapable of strand extension.

472. A chimeric nucleic acid construct that comprises at least two segments, a first segment comprising four or more universal bases;

and

a second segment which is complementary to a discrete nucleic acid sequence of interest;

wherein the 5′

end of said first segment is attached to the 3′

end of said second segment, and the 5′

end of said second segment is attached to the 3′

end of said third segment.

1. A composition of matter comprising at least two parts:

a first part comprising at least one first nucleic acid primer or nucleic acid construct that comprises

(i) at least one first energy transfer element; and

(ii) nucleic acid sequences which are complementary to sequences in at least a portion of a nucleic acid of interest;

a second part comprising at least one second nucleic acid primer or nucleic acid construct that comprises;

(i) at least one second energy transfer element; and

(ii) nucleic acid sequences which are identical to nucleic acid sequences in at least a portion of said nucleic acid of interest;

wherein said first nucleic acid primer or nucleic acid construct does not comprise said second energy transfer element, and wherein said second nucleic acid primer or nucleic acid construct does not comprise said first energy transfer element.

2. The composition of claim 1, wherein either said first energy transfer element is an energy donor and said second energy transfer element is an energy acceptor, or said first energy transfer element is an energy acceptor and said second energy transfer element is an energy donor.

3. The composition of claim 1, wherein said first nucleic acid primer or construct comprises more than one first energy transfer element.

4. The composition of claim 1, wherein said second nucleic acid primer or construct comprises more than one second energy transfer element.

5. The composition of claim 1, wherein said first part comprises more than one nucleic acid primer or nucleic acid construct, or said second part comprises more than one nucleic acid primer or nucleic acid construct, or both said first part and said second part comprise more than one nucleic acid primer or nucleic acid construct.

6. The composition of claim 5, wherein said more than one nucleic acid primer or nucleic acid construct comprise identical or different nucleic acid sequences.

7. The composition of claim 1, wherein said first energy element and said second energy element independently comprise fluorescein, fluorescein isothiocyanate (FITC), 6-carboxyfluorescein (6-FAM), naphthofluorescein, rhodamine, rhodamine 6G, rhodamine X, rhodol, sulforhodamine 101, tetramethylrhodamine (TAMRA), tetramethylrhodamineisothiocyanate (TRITC), 4,7-dichlororhodamine, eosin, eosinisothiocyanate (EITC), dansyl, hydroxycoumarin, methoxycoumarin or p-(Dimethyl aminophenylazo) benzoic acid (DABCYL), cyanine dyes, or derivatives of any of the foregoing.

8. The composition of claim 7, wherein said cyanine dyes or derivatives comprises Cy3 or Cy5.

9. The composition of claim 1, wherein at least one of said nucleic acid primers or constructs is fixed or immobilized to a solid support.

10. The composition of claim 9, wherein said solid support comprises beads, tubes, microtiter plates, glass slides, plastic slides, microchip arrays, wells or depressions.

11. The composition of claim 1, wherein said fixation or immobilization is direct or indirect.

486. A process for cleaving an analyte or a library of analytes at selected sites or sequences, said process comprising the steps of:

(a) providing;

(i) said analyte or library of analytes;

(ii) the composition of claim 472;

(iii) a specific endonuclease;

(iv) reagents for hybridization and endonucleolytic digestion;

(b) hybridizing said composition (ii) with said analyte or library of analytes (i) to form hybrids between said second segment and said selected sites or sequences in said analyte or library of analyte (i); and

(c) cleaving endonucleolytically said hybrids.

487. The process of claim 486, wherein in said providing step (a), the universal bases in said composition (ii) comprise inosine, 5-nitroindole or 3-nitropyrrole.

488. The process of claim 486, wherein in said providing step (a), the second segment in the composition (ii) comprises a recognition sequence for a restriction enzyme.

489. The process of claim 488, wherein in said providing step (a), the second segment in the composition (ii) comprises modified nucleotides that render said second segment resistant to said restriction enzyme.

490. The process of claim 486, wherein in said providing step (a), the composition (ii) further comprises a third segment comprising a desirable nucleic acid sequence.

491. The process of claim 490, wherein said desirable nucleic acid sequence comprises comprises at least one primer binding sequence or promoter sequence.

492. The process of claim 486, wherein in said providing step (a) the composition (ii) is or has been rendered incapable of strand extension.

493. The process of claim 486, further comprising the step (d) of treating with a phosphatase.

494. The process of claim 486, wherein said providing step (a) reagents for strand extension are also provided.

495. The process of claim 494, further comprising the step of extending a 3′

end in the remaining analyte or library of analytes, said 3′

end having been produced by said endonucleolytic cleaving step (c).

496. The process of claim 495, wherein said extending step is carried out in the presence of one or more labeled nucleotides or oligonucleotides.

473. The construct of claim 472, wherein said universal bases comprise inosine, 5-nitroindole or 3-nitropyrrole.

474. The construct of claim 472, wherein said first segment comprises from about six to ten universal bases.

475. The construct of claim 472, wherein said second segment comprises at least four nucleotides or nucleotide analogs.

476. The construct of claim 472, wherein said second segment comprises a recognition sequence for a restriction enzyme.

477. The construct of claim 472, wherein said second segment comprises modified nucleotides that render said second segment resistant to said restriction enzyme.

478. The construct of claim 472, further comprising a third segment that comprises at least four universal bases.

479. The construct of claim 472, further comprising a third segment that comprises a desirable nucleic acid sequence.

480. The construct of claim 479, wherein said desirable nucleic acid sequence comprises comprises at least one primer binding sequence or promoter sequence.

481. The construct of claim 480, wherein said primer binding sequence is homopolymeric or heteropolymeric.

482. The construct of claim 481, wherein said homopolymeric sequence comprises poly T, poly U, poly G, poly C or poly A.

483. The construct of claim 481, wherein said heteropolymeric sequence comprises an RNA promoter sequence.

484. The construct of claim 483, wherein said RNA promoter sequence comprises a T3 promoter, a T7 promoter or an SP6 promoter.

485. The construct of claim 472, wherein said chimeric nucleic acid constructs are incapable of strand extension.

486-1. A process for cleaving an analyte or a library of analytes at selected sites or sequences, said process comprising the steps of:

(a) providing;

(i) said analyte or library of analytes;

(ii) the composition of claim 472;

(iii) a specific endonuclease;

(iv) reagents for hybridization and endonucleolytic digestion;

(b) hybridizing said composition (ii) with said analyte or library of analytes (i) to form hybrids between said second segment and said selected sites or sequences in said analyte or library of analyte (i); and

(c) cleaving endonucleolytically said hybrids.

487-2. The process of claim 486, wherein in said providing step (a), the universal bases in said composition (ii) comprise inosine, 5-nitroindole or 3-nitropyrrole.

488-3. The process of claim 486, wherein in said providing step (a), the second segment in the composition (ii) comprises a recognition sequence for a restriction enzyme.

489-4. The process of claim 488, wherein in said providing step (a), the second segment in the composition (ii) comprises modified nucleotides that render said second segment resistant to said restriction enzyme.

490-5. The process of claim 486, wherein in said providing step (a), the composition (ii) further comprises a third segment comprising a desirable nucleic acid sequence.

491-6. The process of claim 490, wherein said desirable nucleic acid sequence comprises comprises at least one primer binding sequence or promoter sequence.

492-7. The process of claim 486, wherein in said providing step (a) the composition (ii) is or has been rendered incapable of strand extension.

493-8. The process of claim 486, further comprising the step (d) of treating with a phosphatase.

494-9. The process of claim 486, wherein said providing step (a) reagents for strand extension are also provided.

495-10. The process of claim 494, further comprising the step of extending a 3′

end in the remaining analyte or library of analytes, said 3′

end having been produced by said endonucleolytic cleaving step (c).

496-11. The process of claim 495, wherein said extending step is carried out in the presence of one or more labeled nucleotides or oligonucleotides.

497. A process for incorporating a desirable nucleic acid sequence into an analyte or a library of analytes, said process comprising the steps of:

(a) providing;

(i) said analyte or library of analytes;

(ii) a chimeric nucleic acid construct comprising at least two segments, wherein the first of said two segments is complementary to a first analyte nucleic acid sequence and wherein the second of said two segments is complementary to a second analyte nucleic acid sequence;

(iii) reagents for hybridization and endonucleolytic digestion;

(iv) an endonuclease; and

(v) reagents for strand extension;

(b) forming a mixture comprising (i), (ii), (iii) and (iv);

(c) hybridizing said chimeric nucleic acid construct (ii) with said analyte or library of analytes (i), thereby forming a first complex between said first segment and said first analyte nucleic acid sequence, and a second complex between said second segment and said second analyte nucleic acid sequence;

wherein said first complex is resistant to digestion by said endonuclease, and wherein said second complex comprises one or more sites sensitive to endonucleolytic digestion;

(d) digesting said second complex with said endonuclease (iv); and

(e) extending the 3′

-end of said second analyte nucleic acid sequence, said 3′

-end having been generated by said endonuclease (iv), wherein said extending step (e) is carried out by template dependent polymerization or ligation.

497-543. -543. (canceled)

498. The process of claim 497, wherein in the providing step (a), said analyte or library of analytes (i) comprise DNA, RNA, or a mixture of DNA and RNA.

499. The process of claim 497, wherein in the providing step (a), said first segment, said first analyte nucleic acid sequence comprises RNA, said second segment comprises DNA, said second analyte nucleic acid sequence comprise RNA and said endonuclease (iv) comprises RNase H.

500. The process of claim 497, wherein in the providing step (a), said second segment and said second analyte nucleic acid sequence comprise a recognition sequence for an asymmetric restriction enzyme.

501. The process of claim 500, wherein said asymmetric restriction enzyme comprises N. BstN B I.

502. The process of claim 497, wherein in the providing step (a), said first segment comprises modified nucleotides or nucleotide analogs that confer resistance to digestion by said endonuclease (iv).

503. The process of claim 497, wherein in the forming step (b), (i), (ii) and (iii) are mixed together, and then (iv) and (v) are added after said hybridizing step (c).

504. The process of claim 497, wherein in the forming step (b), (i), (ii), (iii) and (v) are mixed together, and then (iv) is added after said hybridizing step (c).

505. The process of claim 497, wherein said strand extending step (e) also comprises strand displacement.

506. The process of claim 497, further comprising the step (f) of carrying out a dephosphorylation step.

507. The process of claim 497, wherein said chimeric nucleic acid construct (ii) further comprises a third segment complementary to a third analyte nucleic acid sequence, and wherein said hybridizing step (c) further comprises forming a third complex between said third segment and said third analyte nucleic acid sequence, wherein said third complex is resistant to digestion by said endonuclease.

508. The process of claim 507, wherein in the providing step (a) said third segment comprises modified nucleotides or nucleotide analogs which confer resistance to digestion by said endonuclease (iv).

509. The process of claim 497, wherein said chimeric nucleic acid construct (ii) further comprises a third segment non-complementary to said analyte or library of analytes.

510. The process of claim 509, wherein said third segment comprises a primer binding site or an RNA promoter sequence.

511. The process of claim 497, wherein the providing step (a) said analyte or library of analytes (i) have been fragmented.

512. The process of claim 511, wherein said analyte or library of analytes (i) have been fragmented by an endonuclease.

513. The process of claim 512, wherein said endonuclease comprises RNase, DNase, S1 nuclease, mung bean nuclease or a restriction enzyme.

514. The process of claim 497, wherein said reagents for strand extension comprise one or more labeled nucleotides or labeled oligonucleotides.

515. The process of claim 497, wherein said chimeric nucleic acid construct (ii) is or has been rendered incapable of strand extension.

516. A chimeric nucleic acid construct that comprises at least two nucleic acid segments, wherein the first segment and the second segment each comprise sequences complementary to different portions of a homopolymeric sequence in a nucleic acid of interest,

wherein hybridization of said first segment to a first portion of said homopolymeric sequence produces a first complex;

wherein hybridization of said second segment to a second portion of said homopolymeric sequence produces a second complex; and

wherein the second portion of the homopolymeric sequence in said second complex is a substrate for a specific endonuclease, and wherein said first complex is resistant to said specific endonuclease.

517. The construct of claim 516, wherein said at least two nucleic acid segments comprise ribonucleotides, deoxyribonucleotides or combinations thereof.

518. The construct of claim 517, wherein said ribonucleotides or said deoxyribonucleotides comprise modified ribonucleotides, ribonucleotide analogs, modified deoxyribonucleotides, or deoxyribonucleotide analogs.

519. The construct of claim 516, wherein the 5′

end of said first segment is attached to the 3′

end of said second segment.

520. The construct of claim 516, wherein said homopolymeric sequence comprises ribonucleotides.

521. The construct of claim 517, wherein said first segment comprises ribonucleotides and said second segment comprises deoxyribonucleotides.

522. The construct of claim 516, wherein said specific endonuclease comprises Ribonuclease H (RNase H).

523. The construct of claim 517, wherein said homopolymeric sequence comprises ribonucleotides, said first segment comprises ribonucleotides, said second segment comprises deoxyribonucleotides, and said specific endonuclease comprises Ribonuclease H (RNase H).

524. The construct of claim 517, wherein said homopolymeric sequence comprises oligo A or poly A.

525. The construct of claim 516, further comprising a third segment that comprises a desirable nucleic acid sequence.

526. The construct of claim 525, wherein said desirable nucleic acid sequence comprises a primer binding sequence or a promoter sequence.

527. The construct of claim 525, wherein said desirable nucleic acid sequence comprises one or more universal bases.

528. A process for removing a portion of a homopolymeric sequence from an analyte or library of analytes, said process comprising:

(a) providing;

(i) said analyte or library of analytes;

(ii) the construct of claim 1;

(iii) an endonuclease;

(iv) reagents for hybridization and endonucleolytic digestion;

(b) hybridizing the construct (ii) with said analyte or library of analytes (i) to form at least one second complex comprising the second segment in said construct (ii) hybridized to said portion of said homopolymeric sequence, and at least one first complex comprising the first segment in said construct (ii) hybridized to a different portion of said homopolymeric sequence;

(c) removing endonucleolytically said portion of the homopolymeric sequence hybridized to said second segment in the second complex or complexes.

529. The process of claim 528, wherein said at least two nucleic acid segments comprise ribonucleotides, deoxyribonucleotides or combinations thereof.

530. The process of claim 529, wherein said ribonucleotides or said deoxyribonucleotides comprise modified ribonucleotides, ribonucleotide analogs, modified deoxyribonucleotides, or deoxyribonucleotide analogs.

531. The process of claim 528, wherein the 5′

end of said first segment is attached to the 3′

end of said second segment.

532. The process of claim 528, wherein said homopolymeric sequence comprises ribonucleotides.

533. The process of claim 529, wherein said first segment comprises ribonucleotides and said second segment comprises deoxyribonucleotides.

534. The process of claim 528, wherein said specific endonuclease comprises Ribonuclease H (RNase H).

535. The process of claim 528, 529 or 530, wherein said homopolymeric sequence comprises ribonucleotides, said first segment comprises ribonucleotides, said second segment comprises deoxyribonucleotides, and said specific endonuclease comprises Ribonuclease H (RNase H).

536. The process of claim 528, wherein said homopolymeric sequence comprises oligo A or poly A.

537. The process of claim 528, further comprising a third segment that comprises a desirable nucleic acid sequence.

538. The process of claim 537, wherein said desirable nucleic acid sequence comprises a primer binding sequence or a promoter sequence.

539. The process of claim 537, wherein said desirable nucleic acid sequence comprises one or more universal bases.

540. The process of claim 528, further comprising the step (d′

) of treating with a phosphatase.

541. The process of claim 528, wherein said providing step (a) reagents for strand extension are provided.

542. The process of claim 541, further comprising the step (d) of extending a 3′

end in the remaining homopolymeric sequence, said 3′

end having been produced by said endonucleolytic removing step (c).

543. The process of claim 542, wherein said extending step (d) is carried out in the presence of one or more labeled nucleotides or oligonucleotides.