Design and analysis of mismatch probes for long oligonucleotide microarrays.

ABSTRACT:

Background

Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes.

Results

Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 degrees C). In general, the probes with evenly distributed mismatches were more

SUBMITTER: Deng Y 

PROVIDER: S-EPMC2576263 | biostudies-literature | 2008 Oct

REPOSITORIES: biostudies-literature