Nucleic acid analysis by multiplexed hybridization and probe design for multiplexed hybridization analysis

摘要

Disclosed is an analysis method useful in multiplexed mutation analysis or, in hybridization-mediated multiplexed analysis of polymorphisms under conditions permitting competitive hybridization, i.e., wherein single strands of a labeled nucleic acid of interest (“target”) interact with two or more pairs of immobilized degenerate capture probes. In one embodiment, one member of each pair has a sequence that is complementary to the normal (“wild-type”) sequence in a designated location of the target, while the other member of each pair has a sequence that is complementary to an anticipated variant (“mutant” or “polymorph”) sequence in that location of the target. The methods herein permit the selection of two or more probe pairs such that, for each pair of probes interacting with a given target strand, the interaction of the target with a preferred member of the probe pair is optimized. Also disclosed is a method of interpreting results obtained by multiplexed hybridization of the target to two or more pairs of probes under conditions permitting competitive hybridization.