Reagents for monitoring nucleic acid amplification and methods of using same
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Abstract
Described herein are novel indicator molecules of general formula (1):
wherein Q, F, N, Nuc, X1 and X2 are as defined herein, including their tautomeric forms and their additive salts. The present invention also concerns methods for the use of these molecules to monitor nucleic acid amplification in real time and their applications as diagnostics.
16 Citations
22 Claims
- 1. A molecule comprising the formula (1) shown below
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11. A method of detecting nucleic acid amplification comprising the steps of:
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(a) contacting a polymerase with a primer, a template, nucleobase triphosphates and one or more molecules of the formula (1) shown below in a medium in which said polymerase is active;
wherein;
Nuc represents a nucleobase selected from the group consisting of adenine, cytosine, guanine, thymidine, uracil and analogs thereof;
N represents a number from 1 through 8 indicating the number of phosphate moieties present in said molecule;
X1 and X2 are independently selected from the group H, OH, NH2, O-alkyl, N-alkyl, S-Alkyl, P-alkyl, a halogen, an alkyl, a cyclo-alkyl, and an aromatic containing group, wherein the alkyl and cycloalkyl possess varying degrees of unsaturation and are optionally substituted; and
F and Q comprise a pair of indicators, wherein cleavage of the molecule results in separation of the indicators which, in turn, yields a change in a measurable signal; and
(b) detecting a change a measurable signal. - View Dependent Claims (12)
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13. A method of detecting a polymerase comprising the steps of:
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(a) contacting said polymerase with a primer, a template, nucleobase triphosphates and one or more molecules of the formula (1) shown below in a medium in which said polymerase is active;
wherein;
Nuc represents a nucleobase selected from the group consisting of adenine, cytosine, guanine, thymidine, uracil and analogs thereof;
N represents a number from 1 through 8 indicating the number of phosphate moieties present in said molecule;
X1 and X2 are independently selected from the group H, OH, NH2, O-alkyl, N-alkyl, S-Alkyl, P-alkyl, a halogen, an alkyl, a cyclo-alkyl, and an aromatic containing group, wherein the alkyl and cycloalkyl possess varying degrees of unsaturation and are optionally substituted; and
F and Q comprise a pair of indicators, wherein cleavage of the molecule results in separation of the indicators which, in turn, yields a change in a measurable signal; and
(b) detecting a change said measurable signal. - View Dependent Claims (14, 15, 16, 17)
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18. A method of detecting a phosphodiesterase comprising the steps of:
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(a) contacting one and one or more molecules of the formula (1) shown below with a phosphodiesterase in a medium in which said phosphodiesterase is enzymatically active;
wherein;
Nuc represents a nucleobase selected from the group consisting of adenine, cytosine, guanine, thymidine, uracil and analogs thereof;
N represents a number from 1 through 8 indicating the number of phosphate moieties present in said molecule;
X1 and X2 are independently selected from the group H, OH, NH2, O-alkyl, N-alkyl, S-Alkyl, P-alkyl, a halogen, an alkyl, a cyclo-alkyl, and an aromatic containing group, wherein the alkyl and cycloalkyl possess varying degrees of unsaturation and are optionally substituted; and
F and Q comprise a pair of indicators, wherein cleavage of the molecule results in separation of the indicators which, in turn, yields a change in a measurable signal; and
(b) detecting a change in said measurable signal.
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19. A method of detecting nucleobase cyclase activity comprising the steps of:
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(a) contacting one or more molecules of the formula (1) shown below with said cyclase in a medium in which said cyclase is enzymatically active
wherein;
Nuc represents a nucleobase selected from the group consisting of adenine, cytosine, guanine, thymidine, uracil and analogs thereof;
N represents a number from 1 through 8 indicating the number of phosphate moieties present in said molecule;
X1 and X2 are independently selected from the group H, OH, NH2, O-alkyl, N-alkyl, S-Alkyl, P-alkyl, a halogen, an alkyl, a cyclo-alkyl, and an aromatic containing group, wherein the alkyl and cycloalkyl possess varying degrees of unsaturation and are optionally substituted; and
F and Q comprise a pair of indicators, wherein cleavage of the molecule results in separation of the indicators which, in turn, yields a change in a measurable signal; and
(b) detecting a change in said measurable signal.
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20. An assay for detecting the presence of an active viral polymerase in a sample comprising the following components:
- a polymerase with a primer, a template, nucleobase triphosphates and one or more molecules of the formula (1) shown below;
- View Dependent Claims (21, 22)
- a polymerase with a primer, a template, nucleobase triphosphates and one or more molecules of the formula (1) shown below;
Specification