Enzymatic nucleic acid synthesis: compositions and methods for inhibiting pyrophosphorolysis

• US 8,314,216 B2
• Filed: 12/29/2006
• Issued: 11/20/2012
• Est. Priority Date: 12/01/2000
• Status: Active Grant

• Current Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Original Assignee: Life Technologies Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Hardin, Susan H., Gao, Xiaolian, Briggs, James, Willson, Richard, Tu, Shiao-Chun
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US11/648,721
• Publication Number:
  US 20100255464A1
• Time in Patent Office: 2,153 Days
• Field of Search: 536/4.1, 536/23.1, 435/6, 435/91.1
• US Class Current: 536/4.1
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C12N 9/1241 Nucleotidyltransferases (2.7.7)
• CPC Class Codes: C12N 9/1252 DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/113 incorporating modified backbone
• CPC Class Codes: C12Q 2533/101 Primer extension
• CPC Class Codes: C12Q 2565/301 Pyrophosphate (PPi)

Abstract

Nucleotide triphosphate probes containing a molecular and/or atomic tag on a γ and/or β phosphate group and/or a base moiety having a detectable property are disclosed, and kits and method for using the tagged nucleotides in sequencing reactions and various assay. Also, phosphate and polyphosphate molecular fidelity altering agents are disclosed.

Claims

1. A composition comprising a polymerase and at least one compound selected from the group consisting of compounds of the following general formulas:

Z—

OPO₂—

(OP(EE′

)O)_n—

PO₂O—

Z′

 

 

(e)

Z—

OPO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(f)

Z—

PO₂—

(OP(EE′

)O)_nPO₂O—

Z′

 

 

(g)

Z—

PO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(h)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent, E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2.

2. The composition of claim 1, wherein one or more of the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

11. The composition of claim 1, wherein at least one member of the group consisting of:

Z and Z′

includes an optically detectable tag.

12. The composition of claim 11, wherein the composition further includes a tagged nucleotide or analog thereof, the tagged nucleotide or analog including an optically detectable nucleotide tag.

13. The composition claim of claim 12, wherein the nucleotide tag is linked to a portion of the tagged nucleotide or analog that is released upon polymerization of the tagged nucleotide or analog by the polymerase.

14. The composition of claim 13, wherein the nucleotide tag is linked to the beta, gamma or other terminal phosphate of the tagged nucleotide or analog.

15. The composition of claim 13, wherein the polymerase further includes a polymerase tag, where the polymerase tag is optically detectable.

16. The composition of claim 15, wherein the polymerase tag undergoes FRET with the nucleotide tag when the tagged nucleotide or analog is bound to an active site of the polymerase.

17. The composition of claim 15, wherein the polymerase tag is selected from the group consisting of:

a nanocrystal tag, a fluorescent tag and a chromogenic tag.

18. The composition of claim 17, wherein the polymerase tag is a nanocrystal tag including a quantum dot.

19. The composition of claim 18, wherein the polymerase is covalently attached to or otherwise associated with the quantum dot.

20. The composition of claim 19, wherein the quantum dot is a FRET donor that undergoes FRET with the nucleotide tag.

21. The method of claim 20, wherein the nucleotide tag comprises a FRET acceptor that undergoes FRET with the quantum dot.

22. The composition of claim 12, where the nucleotide tag is linked to a terminal phosphate in the polyphosphate chain of the tagged nucleotide or analog, and where polymerization of the tagged nucleotide or analog by the polymerase results in the release of a labeled polyphosphate from the tagged nucleotide or analog.

23. The composition of claim 22, wherein the polymerase further includes a fluorescent polymerase tag.

72. The composition of claim 1, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

73. The composition of claim 72, wherein n is 2.

74. The composition of claim 73, wherein n is at least 3.

75. The composition of claim 73, wherein n is at least 4.

76. The composition of claim 73, wherein n is at least 5.

77. The composition of claim 73, wherein Z is hydrogen and Z′

includes a fluorescent tag.

78. The composition of claim 73, wherein Z includes a nucleoside moiety and Z′

includes a fluorescent tag.

3. A composition comprising a polymerase and at least one compound of the general formula:

Z—

OPO₂—

(OP(EE′

)O)_n—

PO₂O—

Z′

 

 

(e)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent and E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2.

4. The composition of claim 3, wherein one or more of the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

40. The composition of claim 3, wherein at least one member of the group consisting of Z and Z′

includes an optically detectable tag.

41. The composition of claim 40, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

42. The composition of claim 41, wherein n is 2.

43. The composition of claim 41, wherein n is at least 3.

44. The composition of claim 41, wherein n is at least 4.

45. The composition of claim 41, wherein n is at least 5.

46. The composition of claim 41, wherein Z is hydrogen and Z′

includes a fluorescent tag.

47. The composition of claim 41, wherein Z includes a nucleoside moiety and Z′

includes a fluorescent tag.

5. A composition comprising a polymerase and at least one compound of the general formula:

Z—

OPO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(f)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent and E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2.

6. The composition of claim 5, wherein one or more of the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

48. The composition of claim 5, wherein at least one member of the group consisting of Z and Z′

includes an optically detectable tag.

49. The composition of claim 48, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

50. The composition of claim 49, wherein n is 2.

51. The composition of claim 49, wherein n is at least 3.

52. The composition of claim 49, wherein n is at least 4.

53. The composition of claim 49, wherein n is at least 5.

54. The composition of claim 49, wherein Z is hydrogen and Z′

includes a fluorescent tag.

55. The composition of claim 49, wherein Z includes a nucleoside moiety and Z′

includes a fluorescent tag.

7. A composition comprising a polymerase and at least one compound of the general formula:

Z—

PO₂—

(OP(EE′

)O)_nPO₂O—

Z′

 

 

(g)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent and E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2.

8. The composition of claim 7, wherein the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

56. The composition of claim 7, wherein at least one member of the group consisting of Z and Z′

includes an optically detectable tag.

57. The composition of claim 56, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

58. The composition of claim 57, wherein n is 2.

59. The composition of claim 57, wherein n is at least 3.

60. The composition of claim 57, wherein n is at least 4.

61. The composition of claim 57, wherein n is at least 5.

62. The composition of claim 57, wherein Z is hydrogen and Z′

includes a fluorescent tag.

63. The composition of claim 57, wherein Z includes a nucleoside moiety and Z′

includes a fluorescent tag.

9. A composition comprising a polymerase and at least one compound of the general formula:

Z—

PO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(h)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent and E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2.

10. The composition of claim 9, wherein one or more of the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

64. The composition of claim 9, wherein at least one member of the group consisting of Z and Z′

includes an optically detectable tag.

65. The composition of claim 64, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

66. The composition of claim 65, wherein n is 2.

67. The composition of claim 65, wherein n is at least 3.

68. The composition of claim 65, wherein n is at least 4.

69. The composition of claim 65, wherein n is at least 5.

70. The composition of claim 65, wherein Z is hydrogen and Z′

includes a fluorescent tag.

71. The composition of claim 65, wherein Z includes a nucleoside moiety and Z′

includes a fluorescent tag.

24. A method for performing a nucleotide incorporation, comprising:

contacting a polymerase with a template nucleic acid molecule and a tagged nucleotide or analog thereof, the tagged nucleotide or analog including an optically detectable nucleotide tag,

wherein the contacting is performed in the presence of a compound selected from the group consisting of compounds of the following general formulas;

Z—

OPO₂—

(OP(EE′

)O)_n—

PO₂O—

Z′

 

 

(e)

Z—

OPO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(f)

Z—

PO₂—

(OP(EE′

)O)_nPO₂O—

Z′

 

 

(g)

and

Z—

PO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(h)

where Z and Z′

are each independently a hydrogen atom or a thermally stable substituent, E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2, and

incorporating the tagged nucleotide or analog into a nascent nucleic acid molecule in a template-dependent manner using the polymerase.

25. The method of claim 24, where the incorporating further includes:

cleaving the optically detectable nucleotide tag from the tagged nucleotide or analog using the polymerase.

26. The method of claim 25, wherein the nucleotide tag is linked to a β

-phosphate, γ

-phosphate or other terminal phosphate of the tagged nucleotide or analog.

79. The method of claim 24, wherein the thermally stable substituents each independently include one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

80. The method of claim 24, wherein one member of the group consisting of Z and Z′

includes a fluorescent tag, and the other member of the group includes a moiety selected from the group consisting of;

a hydrogen atom and a nucleoside moiety.

81. The method of claim 80, wherein n is 2.

82. The method of claim 80, wherein n is at least 3.

83. The method of claim 80, wherein n is at least 4.

84. The method of claim 80, wherein n is at least 5.

85. The method of claim 80, wherein Z is hydrogen and Z′

includes a fluorescent tag.

86. The method of claim 80, wherein Z includes a nucleoside moiety and Z′

is a fluorescent tag.

87. The method of claim 24, further including:

detecting a signal indicating the template-dependent incorporation of the tagged nucleotide or analog into the nascent nucleic acid molecule by the polymerase.

88. The method of claim 87, wherein detecting the signal further includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.

89. The method of claim 87, wherein the polymerase includes a polymerase tag that is optically detectable.

90. The method of claim 89, wherein the polymerase tag includes a fluorescent resonance energy transfer (FRET) donor and the nucleotide tag includes a FRET acceptor, and wherein the incorporating further includes performing energy transfer between the FRET donor and the FRET acceptor.

91. The method of claim 90, wherein detecting the signal further includes detecting the energy transfer between the FRET donor and the FRET acceptor.

92. The method of claim 91, wherein the polymerase tag includes a quantum dot.

93. The method of claim 92, wherein the polymerase is covalently attached to or otherwise associated with the quantum dot.

94. The method of claim 93, wherein the quantum dot is a FRET donor.

95. The method of claim 90, wherein the performing further includes performing FRET between the nucleotide tag and the quantum dot.

96. The method of claim 24, where the nucleotide tag of the at least one tagged nucleotide or analog is linked to a terminal phosphate in the polyphosphate chain of the at least one tagged nucleotide or analog, and where the reaction results in the production of a labeled polyphosphate that is released from the at least one tagged nucleotide or analog.

27. A method for obtaining sequence information from a template nucleic acid molecule, comprising:

contacting a template nucleic acid molecule with a polymerase and at least one tagged nucleotide or analog thereof, wherein the at least one tagged nucleotide or analog includes an optically detectable nucleotide tag, and where the contacting is performed in the presence of at least one compound selected from the group consisting of compounds of the following general formulas;

Z—

OPO₂—

(OP(EE′

)O)_n—

PO₂O—

Z′

 

 

(e)

Z—

OPO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(f)

Z—

PO₂—

(OP(EE′

)O)_nPO₂O—

Z′

 

 

(g)

and

Z—

PO₂—

(OP(EE′

)O)_nPO₂—

Z′

 

 

(h)

where Z or Z′

are each independently a hydrogen atom or a thermally stable substituent, E and E′

are each independently an oxygen atom or a thermally stable substituent and n is an integer having a value of at least 2;

incorporating the tagged nucleotide or analog into a nascent nucleic acid molecule in a template-dependent manner using the polymerase;

detecting a signal that indicates the incorporation of the at least one tagged nucleotide or analog into the nascent nucleic acid molecule by the polymerase; and

identifying the at least one tagged nucleotide or analog, thereby obtaining sequence information from the template nucleic acid molecule.

28. The method of claim 27, wherein the polymerase includes a polymerase tag.

29. The method of claim 28, wherein the nucleotide tag is linked to a β

-phosphate, γ

-phosphate or other terminal phosphate of the at least one tagged nucleotide or analog and wherein the signal that is detected results from an interaction between the polymerase tag and the nucleotide tag.

30. The method of claim 28, wherein the polymerase tag includes a fluorescent resonance energy transfer (FRET) donor and the nucleotide tag includes a FRET acceptor, and wherein the incorporating further includes performing energy transfer between the FRET donor and the FRET acceptor.

31. The method of claim 30, wherein detecting the signal includes detecting a FRET event between the polymerase tag and the nucleotide tag.

32. The method of claim 31, wherein detecting the signal includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.

33. The method of claim 31, wherein detecting the signal includes detecting a change in the emission intensity, the emission frequency or the emission duration of the polymerase tag.

34. The method of claim 28, wherein the polymerase tag is an optically detectable tag selected from the group consisting of:

a nanocrystal tag, a fluorescent tag and a chromogenic tag.

35. The method of claim 34, wherein the optically detectable tag of the polymerase is a nanocrystal tag including a quantum dot.

36. The method of claim 35, wherein the polymerase is covalently attached to or otherwise associated with the quantum dot.

37. The method of claim 35, wherein the quantum dot is a FRET donor.

38. The method of claim 35, wherein the contacting further includes performing FRET between the nucleotide tag and the quantum dot.

39. The method of claim 27, where the nucleotide tag of the at least one tagged nucleotide or analog is linked to a terminal phosphate in the polyphosphate chain of the at least one tagged nucleotide or analog, and where the reaction results in the production of a labeled polyphosphate that is released from the at least one tagged nucleotide or analog.

97. A composition comprising:

a polymerase; and

a tagged nucleotide or analog thereof, where the tagged nucleotide or analog includes;

(a) a polyphosphate chain including at least four phosphate groups, and

(b) an optically detectable nucleotide label linked to a phosphate group of the polyphosphate chain.

98. The composition of claim 97, wherein the polyphosphate chain includes at least five phosphate groups.

99. The composition of claim 97, wherein the polyphosphate chain includes at least six phosphate groups.

100. The composition of claim 97, wherein the polyphosphate chain includes at least seven phosphate groups.

101. The composition of claim 97, wherein at least one of the phosphate groups is a modified phosphate group including one or more thermally stable substituents, each of the thermally stable substituents independently including one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

102. The composition of claim 97, wherein the optically detectable nucleotide label is linked to a beta phosphate, a gamma phosphate or a terminal phosphate of the polyphosphate chain.

103. The composition of claim 97, wherein the polymerase further includes a polymerase tag that is optically detectable.

104. The composition of claim 103, wherein the tagged nucleotide or analog is bound to an active site of the polymerase and wherein the polymerase tag undergoes FRET with the optically detectable nucleotide label.

105. The composition of claim 103, wherein the polymerase tag includes a quantum dot, and wherein the polymerase is covalently attached to or otherwise associated with the quantum dot.

106. The composition of claim 105, wherein the quantum dot includes a FRET donor that undergoes FRET with the nucleotide label.

107. A composition comprising:

a polymerase;

a tagged nucleotide or analog thereof, where the tagged nucleotide or analog includes an optically detectable nucleotide tag, and

a polyphosphate compound including at least four phosphate groups linked to each other to form a polyphosphate chain.

108. The composition of claim 107, wherein the polyphosphate chain includes at least five phosphate groups.

109. The composition of claim 107, wherein the polyphosphate chain includes at least six phosphate groups.

110. The composition of claim 107, wherein the polyphosphate chain includes at least seven phosphate groups.

111. The composition of claim 107, wherein at least one of the phosphate groups of the polyphosphate chain is a modified phosphate group including one or more thermally stable substituents, each of the thermally stable substituents independently including one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

112. The composition of claim 107, wherein the polyphosphate chain has a first end and a second end, the first end including a first terminal phosphate group and the second end comprising a second terminal phosphate group, and wherein the first terminal phosphate group is linked to an optically detectable label.

113. The composition of claim 112, wherein the second terminal phosphate group is linked to a nucleoside.

114. A method for performing a nucleotide incorporation, comprising:

contacting a polymerase with a template nucleic acid molecule and a tagged nucleotide or analog thereof, where the tagged nucleotide or analog includes;

(i) a polyphosphate chain including at least four phosphate groups, and

(ii) an optically detectable nucleotide tag linked to a phosphate group of the polyphosphate chain; and

incorporating the tagged nucleotide or analog into a nascent nucleic acid molecule in a template-dependent manner using the polymerase.

115. The method of claim 114, wherein the incorporating further includes cleaving the nucleotide tag from the tagged nucleotide or analog using the polymerase.

116. The method of claim 114, further including:

detecting a signal indicating the template-dependent incorporation of the tagged nucleotide or analog into the nascent nucleic acid molecule by the polymerase.

117. The method of claim 116, wherein detecting the signal further includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.

118. The method of claim 114, wherein the polymerase includes a polymerase tag that is optically detectable.

119. The method of claim 118, wherein the polymerase tag includes a fluorescent resonance energy transfer (FRET) donor and the nucleotide tag includes a FRET acceptor, and wherein the incorporating further includes performing energy transfer between the FRET donor and the FRET acceptor.

120. The method of claim 119, wherein detecting the signal further includes detecting the energy transfer between the FRET donor and the FRET acceptor.

121. The method of claim 114, wherein the polyphosphate chain includes at least five phosphate groups.

122. The method of claim 114, wherein at least one of the phosphate groups of the polyphosphate chain is a modified phosphate group including one or more thermally stable substituents, each of the thermally stable substituents independently including one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

123. The method of claim 114, wherein the optically detectable nucleotide tag is linked to a beta phosphate, a gamma phosphate or a terminal phosphate of the polyphosphate chain.

124. The method of claim 116, further including identifying the tagged nucleotide or analog by analyzing the signal.

125. The method of claim 124, where the identifying further includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.

126. A method for performing a nucleotide incorporation, comprising:

contacting a polymerase with a template nucleic acid molecule and a tagged nucleotide or analog thereof and a polyphosphate compound including at least four phosphate groups linked to form a polyphosphate chain, where the tagged nucleotide or analog includes an optically detectable nucleotide tag; and

incorporating the tagged nucleotide or analog into a nascent nucleic acid molecule in a template-dependent manner using the polymerase.

127. The method of claim 126, wherein the incorporating further includes cleaving the nucleotide tag from the tagged nucleotide or analog using the polymerase.

128. The method of claim 126, further including:

detecting a signal indicating the template-dependent incorporation of the tagged nucleotide or analog into the nascent nucleic acid molecule by the polymerase.

129. The method of claim 126, wherein detecting the signal further includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.

130. The method of claim 126, wherein the polymerase includes a polymerase tag that is optically detectable.

131. The method of claim 130, wherein the polymerase tag includes a fluorescent resonance energy transfer (FRET) donor and the nucleotide tag includes a FRET acceptor, and wherein the incorporating further includes performing energy transfer between the FRET donor and the FRET acceptor.

132. The method of claim 131, wherein detecting the signal further includes detecting the energy transfer between the FRET donor and the FRET acceptor.

133. The method of claim 126, wherein the polyphosphate chain includes at least five phosphate groups.

134. The method of claim 126, wherein at least one of the phosphate groups of the polyphosphate chain is a modified phosphate group including one or more thermally stable substituents, each of the thermally stable substituents independently including one or more atoms selected from the group consisting of carbon, nitrogen, oxygen, sulfur and phosphorus.

135. The method of claim 134, wherein the polyphosphate chain has a first end and a second end, the first end including a first terminal phosphate group and the second end comprising a second terminal phosphate group, and wherein the first terminal phosphate group is linked to an optically detectable label.

136. The method of claim 135, wherein the second terminal phosphate group is linked to a nucleoside.

137. The method of claim 128, further including identifying the tagged nucleotide or analog by analyzing the signal.

138. The method of claim 137, where the identifying further includes detecting a change in the emission intensity, the emission frequency or the emission duration of the nucleotide tag.