Real-time nucleic acid detection processes and compositions
First Claim
1. 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 and at least one first energy transfer element, wherein said first energy transfer element is;
(a) an energy donor and (b) covalently attached directly or via a linker arm to said first nucleic acid primer and said second segment comprises a primer-extended nucleic sequence complementary to at least a portion of a nucleic acid target sequence; and
a second part comprising at least two segments,wherein said first segment of said second part comprises a second nucleic acid primer and at least one second energy transfer element, wherein said second energy transfer element is;
(a) an energy acceptor and (b) covalently attached directly or via a linker arm to said first nucleic acid primer; 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 target sequence;
wherein said first nucleic acid primer does not comprise said second energy transfer element, and wherein said second nucleic acid primer does not comprise said first nucleic acid energy element;
wherein said first primer is not complementary to said second primer or nucleic acid in the absence of a target dependent extension step; and
wherein neither of said nucleic acid primers is fixed or immobilized to a solid support.
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Abstract
This invention provides 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.
127 Citations
161 Claims
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1. A composition of matter comprising at least two parts:
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a first part comprising at least two segments, wherein said first segment comprises a first nucleic acid primer and at least one first energy transfer element, wherein said first energy transfer element is;
(a) an energy donor and (b) covalently attached directly or via a linker arm to said first nucleic acid primer and said second segment comprises a primer-extended nucleic sequence complementary to at least a portion of a nucleic acid target sequence; anda second part comprising at least two segments, wherein said first segment of said second part comprises a second nucleic acid primer and at least one second energy transfer element, wherein said second energy transfer element is;
(a) an energy acceptor and (b) covalently attached directly or via a linker arm to said first nucleic acid primer; 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 target sequence;wherein said first nucleic acid primer does not comprise said second energy transfer element, and wherein said second nucleic acid primer does not comprise said first nucleic acid energy element; wherein said first primer is not complementary to said second primer or nucleic acid in the absence of a target dependent extension step; and wherein neither of said nucleic acid primers is fixed or immobilized to a solid support. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12)
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13. A composition of matter that comprises a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer;
- and the second segment comprising a sequence derived from a target-dependent extension of said primer,
wherein said primer comprises a first energy transfer element, wherein said first energy transfer element is;
(a) an energy donor and (b) covalently attached directly or via a linker arm to a nucleotide in said first segment,wherein said primer-extended sequence comprises (i) a second energy transfer element, wherein said second energy transfer element is;
(a) an energy acceptor and (b) covalently attached directly or via a linker arm to a nucleotide in said second segment; and
(ii) sequences derived from enzymatically adding more than one nucleotide to said primer using a nucleic acid target sequence as a template, wherein one of said more than one nucleotide comprises said second energy transfer element. - View Dependent Claims (14, 15, 16, 17, 18, 19, 20, 21)
- and the second segment comprising a sequence derived from a target-dependent extension of said primer,
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22. A composition of matter comprising a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer;
- and the second segment comprising a primer-extended sequence,
wherein said primer-extended sequence comprises (a) sequences derived from enzymatically adding more than one nucleotide using a nucleic acid target sequence as a template wherein said nucleotides comprise energy transfer elements to said primer and (b) one or more first energy transfer elements, wherein said first energy element is;
(i) an energy donor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment and (c) one or more second energy transfer elements wherein said second energy element is;
(i) an energy acceptor and (ii) covalently linked directly or via a linker arm to a nucleotide in said second segment. - View Dependent Claims (23, 24, 25, 26, 27, 28, 29)
- and the second segment comprising a primer-extended sequence,
- 30. A composition of matter that comprises a nucleic acid strand, said strand comprising two or more ribonucleotides, wherein at least one ribonucleotide is covalently attached directly or via a linker arm to a first energy transfer element, wherein said first energy transfer element is an energy donor and wherein at least one other ribonucleotide is covalently attached directly or via a linker arm to a second energy transfer element, wherein said second energy transfer element is an energy acceptor, and wherein said one ribonucleotide and said one other ribonucleotide are different ribonucleotides in the nucleic acid strand.
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35. 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, wherein said nucleic acid primer comprises one or more fluorescent first energy transfer elements, wherein said first energy transfer element is (i) covalent attached directly or via a linker arm to said nucleic acid primer in said first part and (ii) is an energy transfer donor, and the second segment comprises a primer-extended sequence,
wherein the second part comprises a nucleic acid binding agent non-covalently bound to said nucleic acid strand, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer acceptor.
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44. 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, and the second segment comprising a primer-extended sequence, wherein said nucleic acid primer comprises one or more fluorescent first energy transfer elements, wherein said first energy transfer element is (i) covalently attached to said nucleic acid primer and (ii) is an energy transfer donor, and (b) a nucleic acid binding agent non-covalently bound to said two nucleic acid strands, wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer acceptor, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said two nucleic acid strands are hybridized to each other.
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56. A composition of matter that comprises
(a) a nucleic acid strand comprising two segments, said first segment comprising a primer; - and said second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is;
(i) an energy transfer donor and (ii) covatently attached directly or via a linker arm to a nucleotide in said second segment; and(b) a nucleic acid binding agent, non-covalently bound to said nucleic acid strand, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer acceptor. - View Dependent Claims (57, 58, 59, 60, 61, 62, 63, 64)
- and said second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is;
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65. A composition of matter that comprises
(a) two nucleic acid strands hybridized to each other, wherein at least one of said strands comprises two segments, the first segment comprising a nucleic acid primer, and the second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is: - (i) an energy transfer donor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment, and
(b) a nucleic acid binding agent non-covalently bound to said two nucleic acid strands, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer acceptor. - View Dependent Claims (66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77)
- (i) an energy transfer donor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment, and
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78. A composition of matter that comprises:
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(i) a nucleic acid strand, said strand comprising one or more ribonucleotides, wherein at least one ribonucleotide comprises a first energy transfer element, wherein said first energy transfer element is;
(a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said ribonucleotide; and(ii) a nucleic acid binding agent, non-covalently bound to said nucleic acid strand comprising one or more second energy transfer elements, wherein said nucleic acid binding agent is not a nucleic acid and wherein said second energy transfer element is an energy transfer acceptor from said donor. - View Dependent Claims (79, 80, 81, 82, 83, 84, 85)
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86. A composition of matter that comprises a hybridized first and second nucleic acid strand, said first strand comprising an RNA transcript, wherein at least one ribonucleotide of said transcript comprises a first energy transfer element, wherein said first energy transfer element is:
- (a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said ribonucleotide;
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, wherein said second energy transfer element is;
(a) an energy transfer acceptor and (b) covalently attached directly or via a linker arm to said nucleic acid probe,wherein at least one of said nucleic acid strands is fixed or immobilized to a solid support. - View Dependent Claims (87, 88, 89, 90, 91)
- (a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said ribonucleotide;
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92. 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, wherein said nucleic acid primer comprises one or more fluorescent first energy transfer elements, wherein said first energy transfer element is:
- (a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said nucleic acid primer in said first part, and the second segment comprises a primer-extended sequence, and
wherein the second part comprises a nucleic acid binding agent, non-covalently bound to said nucleic acid strand, wherein said nucleic acid binding agent is not a nucleic acid, wherein said nucleic acid binding agent comprises one or more second energy transfer elements, and wherein said second energy transfer element is an energy transfer acceptor and a protein or a polypeptide.
- (a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said nucleic acid primer in said first part, and the second segment comprises a primer-extended sequence, and
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93. A composition of matter that comprises
(a) two nucleic acid strands hybridized to each other, wherein at least one of said strands comprises two segments, the first segment comprising a nucleic acid primer, wherein said nucleic acid primer comprises one or more fluorescent first energy transfer elements, wherein said first energy transfer element is: - (i) an energy transfer donor and (ii) covalently attached to said nucleic acid primer, and the second segment comprising a primer-extended sequence, and
(b) a nucleic acid binding agent non-covalently bound to said two nucleic acid strands, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy acceptor.
- (i) an energy transfer donor and (ii) covalently attached to said nucleic acid primer, and the second segment comprising a primer-extended sequence, and
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94. A composition of matter that comprises:
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(i) a nucleic acid strand, said strand comprising one or more ribonucleotides, wherein at least one ribonucleotide comprises a first energy transfer element covalently attached directly or via a linker arm to said ribonucleotide, wherein said first energy transfer element is an energy transfer donor; and (ii) a nucleic acid binding agent non-covalently bound to said nucleic acid strand, said binding agent comprising a T4 gene 32 protein, an SSB protein, histones or a single strand nucleic acid binding dye and one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer acceptor.
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95. A composition of matter comprising at least two parts:
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a first part comprising at least one first nucleic acid primer that comprises (i) at least one first energy transfer element, wherein said first energy transfer element is;
(a) an energy acceptor and (h) covalently attached directly or via a linker arm to said first nucleic acid primer; and(ii) nucleic acid sequences which are complementary to at least a portion of a nucleic acid target sequence; a second part comprising at least one second nucleic acid primer that comprises; (i) at least one second energy transfer element, wherein said second energy transfer element is (a) an energy donor and (b) covalently attached directly or via a linker arm to said second nucleic acid primer; and (ii) nucleic acid sequences which are identical to nucleic acid sequences in at least a portion of said target nucleic acid sequence; wherein said first nucleic acid primer does not comprise said second energy transfer element and wherein said second nucleic acid primer does not comprise said first energy transfer element; wherein said first primer hybridizes to said target strand and said second primer hybridizes to the complement of said target strand; and wherein either said first nucleic acid primer comprises more than one first energy transfer element, said second nucleic acid primer comprises more than one second energy transfer element or said first nucleic acid primer comprises more than one first energy transfer element and said second nucleic acid primer comprises more than one second energy transfer element. - View Dependent Claims (96, 97, 98, 99, 100, 101, 102)
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103. A composition of matter comprising two nucleic acid strands, wherein the first of said two strands comprises at least one first energy transfer element, wherein said first energy transfer element is:
- (a) an energy acceptor and (b) covalently attached directly or via a linker arm to said first strand, and the second of said two strands comprises at least one second energy transfer element, wherein said second energy transfer element is;
(a) an energy donor and (b) covalently attached directly or via a linker arm to said second strand and wherein said first strand or a portion thereof is hybridized to said second strand or a portion thereof, wherein said first strand lacks said second energy transfer element and said second strand lacks said first energy transfer element; andwherein either said first nucleic acid strand comprises more than one first energy transfer element, said second nucleic acid strand comprises more than one second energy transfer element or said first nucleic acid strand comprises more than one second energy transfer element and said second nucleic acid strand comprises more than one first energy transfer element. - View Dependent Claims (104, 105, 106, 107, 108)
- (a) an energy acceptor and (b) covalently attached directly or via a linker arm to said first strand, and the second of said two strands comprises at least one second energy transfer element, wherein said second energy transfer element is;
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109. A composition of matter that comprises a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer;
- and said second segment comprising an enzymatically added primer-extended sequence
wherein said primer comprises a first energy transfer element, wherein said first energy transfer element is;
(a) an energy acceptor and (b) covalently attached directly or via a linker arm to a nucleotide in said first segment,wherein said primer-extended sequence comprises (i) a second energy transfer element, wherein said second energy transfer element is;
(a) an energy donor and (b) covalently attached directly or via a linker arm to a nucleotide in said second segment and (ii) sequences derived from adding more than one nucleotides to said primer using a nucleic acid target sequence as a template. - View Dependent Claims (110, 111, 112, 113, 114, 115, 116, 117)
- and said second segment comprising an enzymatically added primer-extended sequence
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118. A composition of matter comprising a nucleic acid strand, said strand comprising two segments, the first segment comprising a primer;
- and the second segment comprising a primer-extended sequence,
wherein said primer-extended sequence comprises (a) sequences derived from enzymatically adding more than one nucleotide to said primer using a nucleic acid target sequence as a template and (b) one or more first energy transfer elements, wherein said first energy element is;
(i) an energy acceptor and (ii) covalently attached directly or via a linker arm to a nucleotide on said first segment and (c) one or more second energy transfer elements, wherein said second energy transfer element is;
(i) an energy donor and (ii) covalently linked directly or via a linker arm to a nucleotide on said second segment. - View Dependent Claims (119, 120, 121, 122, 123, 124, 125)
- and the second segment comprising a primer-extended sequence,
- 126. A composition of matter that comprises an RNA transcript, wherein at least one ribonucleotide is covalently attached directly or via a linker arm to a first energy transfer element, wherein said first energy transfer element is an energy acceptor and wherein at least one other ribonucleotide is covalently attached directly or via a linker arm to a second energy transfer element, wherein said second energy transfer element is an energy donor, and wherein said one ribonucleotide and said one other ribonucleotide are different ribonucleotides in the RNA transcript.
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131. A composition of matter that comprises
(a) a nucleic acid strand comprising two segments, said first segment comprising a primer; - and said second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is;
(i) an energy transfer acceptor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment; and(b) a nucleic acid binding agent non-covalently bound to said nucleic acid strand, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer donor. - View Dependent Claims (132, 133, 134, 135, 136, 137, 138, 139)
- and said second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is;
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140. A composition of matter that comprises
(a) two nucleic acid strands hybridized to each other, wherein at least one of said strands comprises two segments, the first segment comprising a nucleic acid primer, and the second segment comprising a primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements, wherein said first energy transfer element is: - (i) an energy transfer acceptor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment, and
(b) a nucleic acid binding agent non-covalently bound to said two nucleic acid strands, wherein said nucleic acid binding agent is not a nucleic acid, and wherein said nucleic acid binding agent comprises one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer donor. - View Dependent Claims (141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152)
- (i) an energy transfer acceptor and (ii) covalently attached directly or via a linker arm to a nucleotide in said second segment, and
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153. A composition of matter that comprises:
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(i) a nucleic acid strand, said strand comprising one or more ribonucleotides, wherein at least one ribonucleotide comprises a first energy transfer element covalently attached directly or via a linker arm to said ribonucleotide, wherein said first energy transfer element is an energy transfer acceptor; and (ii) a nucleic acid binding agent non-covalently bound to said nucleic acid strand, said binding agent comprising a T4 gene 32 protein, an SSB protein, histones or a single strand nucleic acid binding dye and one or more second energy transfer elements, wherein said second energy transfer element is an energy transfer donor.
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154. 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; - and the second segment comprising an enzymatically added primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements wherein said first energy transfer element is;
(a) an energy transfer acceptor and (b) covalently attached directly or via a linker arm to a nucleotide in said primer extended sequence,said second strand comprising a nucleic acid probe hybridized to said primer-extended sequence or a portion thereof, wherein said nucleic acid probe comprises one or more second energy transfer elements, wherein said second energy transfer element is;
(a) an energy transfer donor and (b) covalently attached directly or via a linker arm to a nucleotide in said nucleic acid probe,wherein at least one of said nucleic acid strands is fixed or immobilized to a solid support. - View Dependent Claims (155, 156)
- and the second segment comprising an enzymatically added primer-extended sequence, wherein said primer-extended sequence comprises one or more first energy transfer elements wherein said first energy transfer element is;
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157. A composition of matter that comprises a hybridized first and second nucleic acids, said first strand comprising an RNA transcript, wherein at least one ribonucleotide comprises a first energy transfer element, wherein said first energy transfer element is:
- (a) an energy transfer acceptor and (b) covalently attached directly or via a linker arm to said ribonucleotide;
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, wherein said energy transfer element is;
(a) an energy transfer donor and (b) covalently attached directly or via a linker arm to said nucleic acid probe,wherein said first strand or said nucleic acid probe is fixed or immobilized indirectly to a solid support. - View Dependent Claims (158, 159, 160, 161)
- (a) an energy transfer acceptor and (b) covalently attached directly or via a linker arm to said ribonucleotide;
Specification