Patent ID: 7378242

Claim:
A limited primer extension (LPE) reaction used to produce short DNA extension products from a targeted template nucleic acid which comprises: annealing a primer consisting of DNA to a site adjacent to the 3′ end of an extension complement sequence (ECS) in the targeted template DNA, which lacks one or more of the four nucleotides over a span of 18 or more contiguous nucleotides; generating extension products having a primer portion and an extension portion, said extension portion being complementary to the ECS; terminating the extension reaction by either i) including only the three deoxyribonucleotides (dNTP) that are complementary to the nucleotides present in said ECS, such that the extension reaction stops at the first occurrence of the nucleotide in the targeted template DNA, which is lacking in the ECS or ii) by incorporation of a nucleotide analog that is complementary to the nucleotide absent in the ECS and incapable of supporting further extension; dissociating the extension products from the targeted template DNA by varying stringency conditions or with DNA helicases; and identifying the extension products by hybridization to a probe immobilized onto a surface followed by detection of the extension product associated to the probe; said probe having sequence identical to, or a subset of, or a superset of, a sequence in the target that includes the ECS.