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1. A method of detecting a single nucleotide polymorphism in a target nucleic acid, comprising:
(a) contacting said target nucleic acid with a first allele-specific primer that hybridizes to a portion of the target nucleic acid comprising the single nucleotide polymorphism and a locus-specific primer, wherein the first allele-specific primer comprises a 3′ nucleophile, and the locus-specific primer comprises a 5′ leaving group, wherein the first allele specific primer and the locus-specific primer hybridize to the target nucleic acid such that the 5′ end of the locus-specific primer is adjacent to the 3′ end of the first allele-specific primer, under conditions allowing chemical ligation between the first allele-specific primer and the first locus-specific primer to form a ligated product; and (b) detecting the ligated product.
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