Method for determining specific nucleotide variations by primer extension in the presence of mixture of labeled nucleotides and terminators
First Claim
1. A method for determining the identity of a specific nucleotide at one or more defined sites in a target nucleic acid polymer, the method comprising the steps of:
- (a) providing a detectable amount of a target nucleic acid polymer in a single stranded form,(b) hybridizing the detectable amount of the nucleic acid polymer with one or more oligonucleotide primers, wherein each primer has a nucleotide sequence that is complementary to a sequence in the target nucleic acid polymer, such that when the primer is hybridized to the target nucleic acid polymer, the 3'"'"' end of the primer binds to a nucleotide flanking the specific nucleotide at the defined site in the target nucleic acid,(c) exposing the hybridized nucleic acid polymer to a polymerization agent in a mixture containing at least one deoxynucleotide, said deoxynucleotide comprising a detectable label, and one or more chain terminating nucleotide analogues, such that a detectable primer extension product is formed if the labeled deoxynucleotide is complementary to the specific nucleotide at the defined site, and(d) analyzing the polymerization mixture of step (c) for the presence or absence of the primer extension product containing the labeled deoxynucleotide at the 3'"'"' end thereof, whereby the identity of the specific nucleotide at the defined site is determined.
4 Assignments
0 Petitions
Accused Products
Abstract
Detection of variable nucleotide(s) is based on primer extension and incorporation of detectable nucleoside triphosphates. By selecting the detection step primers from the region immediately adjacent to the variable nucleotide, this variation can be detected after incorporation of as few as one nucleoside triphosphate. Labelled nucleoside triphosphates matching the variable nucleotide are added and the incorporation of a label into the detection step primer is measured. The selection of the detection step primer is important to the method according to this invention and is dependent on the nucleotide sequence of interest. The detection step primers are preferably selected so as to span the region immediately toward the 3'"'"' end from the variable nucleotide to be detected. The detection step primers can also be complementary to a sequence beginning several nucleotides removed from the variable nucleotide. The only limitation concerning the position of the detection step primers is that the sequence between the 3'"'"' end of the detection step primer and the variable nucleotide to be detected must not contain a nucleotide residue of the same type as the one to be detected. The detection step primers can equally well be chosen to be complementary to either the coding or non-coding strands of the nucleotide sequence of interest.
353 Citations
26 Claims
-
1. A method for determining the identity of a specific nucleotide at one or more defined sites in a target nucleic acid polymer, the method comprising the steps of:
-
(a) providing a detectable amount of a target nucleic acid polymer in a single stranded form, (b) hybridizing the detectable amount of the nucleic acid polymer with one or more oligonucleotide primers, wherein each primer has a nucleotide sequence that is complementary to a sequence in the target nucleic acid polymer, such that when the primer is hybridized to the target nucleic acid polymer, the 3'"'"' end of the primer binds to a nucleotide flanking the specific nucleotide at the defined site in the target nucleic acid, (c) exposing the hybridized nucleic acid polymer to a polymerization agent in a mixture containing at least one deoxynucleotide, said deoxynucleotide comprising a detectable label, and one or more chain terminating nucleotide analogues, such that a detectable primer extension product is formed if the labeled deoxynucleotide is complementary to the specific nucleotide at the defined site, and (d) analyzing the polymerization mixture of step (c) for the presence or absence of the primer extension product containing the labeled deoxynucleotide at the 3'"'"' end thereof, whereby the identity of the specific nucleotide at the defined site is determined. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
-
Specification