Length determination of nucleic acid repeat sequences by discontinuous primer extension
First Claim
1. A method for determining the number of repeat units in a repeat region of a target nucleic acid comprising the steps of:
- (a) annealing a primer-complementary portion of a target nucleic acid to a primer thereby forming a target-primer hybrid;
(b) performing a first primer extension reaction using a first primer extension reagent;
(c) separating the target-primer hybrid and unreacted first primer extension reagent;
(d) performing a second primer extension reaction using a second primer extension reagent, wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto;
(e) separating the target-primer hybrid from unreacted second primer extension reagent;
(f) measuring a signal produced by the label;
(g) treating the label so as to render the label undetectable;
(h) repeating a cycle of steps (a) through (g) until the signal is substantially less than a signal detected in a previous cycle; and
(i) determining a number of repeat units in a repeat region of the target nucleic acid.
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Accused Products
Abstract
In a first aspect, the method of the invention includes the steps of annealing a primer to a target nucleic acid; performing a first primer extension reaction using a first primer extension reagent; separating the target-primer hybrid and unreacted first primer extension reagent; performing a second primer extension reaction using a second primer extension reagent, wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto; separating the target-primer hybrid from unreacted second primer extension reagent; measuring a signal produced by the label; treating the label so as to render the label undetectable; and repeating the above steps until the signal is substantially less than a signal detected in a previous cycle. In a second aspect, the method of the invention includes the steps of annealing a primer to a target nucleic acid; performing a first primer extension reaction using a first primer-extension reagent; separating the target-primer hybrid from unreacted first primer extension reagent; performing a second primer extension reaction using a second primer extension reagent and with a primer termination reagent, the primer termination reagent including a nucleotide terminator having a label attached thereto; separating the target-primer hybrid from unreacted second primer extension reagent and unreacted primer termination reagent; measuring a signal produced by the label; and repeating the above steps until a signal is detected indicating incorporation of the nucleotide terminator. The invention further includes kits useful for practicing the above methods.
70 Citations
15 Claims
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1. A method for determining the number of repeat units in a repeat region of a target nucleic acid comprising the steps of:
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(a) annealing a primer-complementary portion of a target nucleic acid to a primer thereby forming a target-primer hybrid; (b) performing a first primer extension reaction using a first primer extension reagent; (c) separating the target-primer hybrid and unreacted first primer extension reagent; (d) performing a second primer extension reaction using a second primer extension reagent, wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto; (e) separating the target-primer hybrid from unreacted second primer extension reagent; (f) measuring a signal produced by the label; (g) treating the label so as to render the label undetectable; (h) repeating a cycle of steps (a) through (g) until the signal is substantially less than a signal detected in a previous cycle; and (i) determining a number of repeat units in a repeat region of the target nucleic acid. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11)
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12. A kit useful for determining the number of repeat units in a repeat region of a target nucleic acid comprising:
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a primer having a sequence complementary to a primer-complementary portion of a target nucleic acid; a first primer extension reagent comprising a set of extendible nucleotides that allow a primer extension reaction to proceed only to the extent that a primer is extended by an amount less than a full repeat unit; and a second primer extension reagent comprising a set of extendible nucleotides that allow a primer extension reaction to proceed only to the extent that the portion of a repeat unit not synthesized by the first primer extension reagent is synthesized; wherein at least one of the first or second primer extension reagents includes an extendible nucleotide having a label attached thereto. - View Dependent Claims (13, 14, 15)
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Specification