Allele specific primer extension
First Claim
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1. A method for detecting an allele-specific base at a predetermined position in a target nucleic acid molecule comprising providing a first and a second hybridization mixture, said first hybridization mixture comprising said target nucleic acid molecule, and a primer that hybridizes to a region of said target nucleic acid molecule and that has a 3′
- -terminus that is complementary to a non-mutated base at said predetermined position, said second hybridization mixture comprising said target nucleic acid molecule, and a primer that hybridizes to a region of said target nucleic acid molecule and that has a 3′
-terminus that is complementary to a mutated base at said predetermined position;
adding a primer extension reaction mixture to each of said first and second hybridization mixtures, said primer extension reaction mixture comprising a DNA polymerase, nucleotides, and a nucleotide degrading enzyme; and
determining primer extension efficiency in each of said first and second mixtures, whereby greater efficiency in the mixture comprising the primer having a 3′
-terminus that is complementary to the mutated base is indicative of the presence of the mutated base in the target nucleic acid, and whereby greater efficiency in the mixture comprising the primer having a 3′
-terminus that is complementary to the non-mutated base is indicative of the presence of the non-mutated base in the target nucleic acid.
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Abstract
The present invention provides methods of allele-specific primer extension useful for detecting mutations and genetic variations.
38 Citations
17 Claims
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1. A method for detecting an allele-specific base at a predetermined position in a target nucleic acid molecule comprising providing a first and a second hybridization mixture, said first hybridization mixture comprising said target nucleic acid molecule, and a primer that hybridizes to a region of said target nucleic acid molecule and that has a 3′
- -terminus that is complementary to a non-mutated base at said predetermined position, said second hybridization mixture comprising said target nucleic acid molecule, and a primer that hybridizes to a region of said target nucleic acid molecule and that has a 3′
-terminus that is complementary to a mutated base at said predetermined position;
adding a primer extension reaction mixture to each of said first and second hybridization mixtures, said primer extension reaction mixture comprising a DNA polymerase, nucleotides, and a nucleotide degrading enzyme; and
determining primer extension efficiency in each of said first and second mixtures, whereby greater efficiency in the mixture comprising the primer having a 3′
-terminus that is complementary to the mutated base is indicative of the presence of the mutated base in the target nucleic acid, and whereby greater efficiency in the mixture comprising the primer having a 3′
-terminus that is complementary to the non-mutated base is indicative of the presence of the non-mutated base in the target nucleic acid. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8)
- -terminus that is complementary to a non-mutated base at said predetermined position, said second hybridization mixture comprising said target nucleic acid molecule, and a primer that hybridizes to a region of said target nucleic acid molecule and that has a 3′
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9. A method for detecting an allele-specific base at a predetermined position in a target nucleic acid comprising conducting a first and a second allele-specific primer extension reaction using a first and a second primer, respectively that hybridizes to a region of said target nucleic acid, each of said primers having:
- 1) a 3′
-end base that is complementary to the base that is 5′
of the predetermined position in the target;
2) a base one position from the 3′
-end that in the first primer is complementary to a non-mutated based at the predetermined position, and in the second primer is complementary to a mutated base at the predetermined position; and
3) a base two positions from the 3′
-end that is the same as the base that is 3′
of the predetermined position in the target; and
determining primer extension efficiency in said first and second reactions, whereby greater efficiency in said first reaction is indicative of the presence of a non-mutated base at said predetermined position, and whereby greater efficiency in said second reaction is indicative of the presence of a mutated base at said predetermined position. - View Dependent Claims (10, 11, 12, 13, 14, 15, 16, 17)
- 1) a 3′
Specification