Terminal-phosphate-labeled nucleotides
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Accused Products
Abstract
The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.
78 Citations
97 Claims
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1-61. -61. (canceled)
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62. A method of assaying for the rate of an enzyme catalyzed nucleoside monophosphate transfer from a terminal-phosphate-labeled nucleoside polyphosphate to detect the activity of said enzyme or said terminal-phosphate-labeled nucleoside polyphosphate, said method comprising:
a) conducting said enzyme catalyzed nucleoside monophosphate transfer from a terminal-phosphate-labeled nucleoside polyphosphate reaction in reaction buffer comprising a divalent metal ion, thereby increasing the rate of said reaction over the rate of said reaction in the absence of the divalent metal ion. - View Dependent Claims (63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74)
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75. A nucleic acid detection reagent comprising:
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a) one or more terminal-phosphate-labeled nucleotide according to the following formula;
wherein P is a phosphate (PO3) or a derivative thereof, and n is 1 or greater;
Y is an oxygen or sulfur atom;
the base unit (B) is a nitrogen-containing heterocyclic base;
S is a carbocyclic moiety or sugar moiety;
P—
Label moiety (L) is a phosphorylated label with a linker between L and P,wherein L is a label containing a hydroxyl group, a sulfhydryl group, a haloalkyl group or an amino group suitable for forming a phosphate ester, a thioester, an alkylphosphonate or a phosphoramidate linkage at the terminal phosphate of a natural or modified nucleotide;
b) one or more DNA polymerase, RNA polymerase, or reverse transcriptase; and
c) reaction buffer containing a divalent metal ion salt. - View Dependent Claims (76, 80, 81, 82, 83)
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77. A nucleic acid detection reagent comprising:
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a) one or more terminal-phosphate-labeled nucleotide according to the following formula;
wherein P is a phosphate (PO3) or a derivative thereof, and n is 1 or greater;
Y is an oxygen or sulfur atom;
the base unit (B) is a nitrogen-containing heterocyclic base;
S is a carbocyclic moiety or sugar moiety;
P—
Label moiety (L) is a phosphorylated label with a linker between L and P,wherein L is a label containing a hydroxyl group, a sulfhydryl group, a haloalkyl group or an amino group suitable for forming a phosphate ester, a thioester, an alkylphosphonate or a phosphoramidate linkage at the terminal phosphate of a natural or modified nucleotide;
b) one or more DNA polymerase, RNA polymerase, or reverse transcriptase;
c) reaction buffer containing a divalent metal ion; and
d) a metal ion binding buffer. - View Dependent Claims (78, 79)
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- 84. A terminal-phosphate labeled nucleoside polyphosphate of the following formula:
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87. A divalent metal ion complex of a terminal-phosphate labeled nucleoside polyphosphate of following structure:
Label-NPP-(Divalent Metal Ion)x,wherein Label is a detectable moiety connected to NPP with or without a linker;
NPP is a nucleoside polyphosphate with two or more phosphates; and
x is 1 or more.- View Dependent Claims (88, 89, 90, 91, 92)
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93. A nucleic acid detection reagent comprising:
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a) at least one divalent metal ion complex of a terminal-phosphate labeled nucleoside polyphosphate of the following formula;
Label-NPP-(Divalent Metal Ion)x,wherein Label is a detectable moiety linked to NPP with or without a linker;
NPP is a nucleoside polyphosphate with two or more phosphates;
and x is 1 or more; and
b) a nucleic acid polymerase. - View Dependent Claims (94, 97)
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95. A nucleic acid detection reagent comprising:
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a) at least one divalent metal ion complex of a terminal-phosphate labeled nucleoside polyphosphate of the following formula;
Label-NPP-(divalent metal ion)xwherein Label is a detectable moiety linked to NPP with or without a linker;
NPP is a nucleoside polyphosphate with two or more phosphates; and
x is 1 or more;
b) a nucleic acid polymerase; and
c) a metal-ion binding buffer. - View Dependent Claims (96)
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Specification