Guidelines for incorporating non-perfectly matched oligonucleotides into target-specific hybridization probes for a DNA microarray.

ABSTRACT: Sequence-specific oligonucleotide probes play a crucial role in hybridization techniques including PCR, DNA microarray and RNA interference. Once the entire genome becomes the search space for target genes/genomic sequences, however, cross-hybridization to non-target sequences becomes a problem. Large gene families with significant similarity among family members, such as the P450s, are particularly problematic. Additionally, accurate single nucleotide polymorphism (SNP) detection depends on probes that can distinguish between nearly identical sequences. Conventional oligonucleotide probes that are perfectly matched to target genes/genomic sequences are often unsuitable in such cases. Carefully designed mismatches can be used to decrease cross-hybridization potential, but implementing all

SUBMITTER: Lee I 

PROVIDER: S-EPMC373323 | biostudies-literature | 2004

REPOSITORIES: biostudies-literature