Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental applications

Liebich, J.; Rhee, S.-K.; Chong, S. C.; Schadt, C. W.; He, Z.; Zhou, J.-H.

doi:10.1128/AEM.72.2.1688-1691.2006

Journal Article

PreJuSER-50473

Improvement of Oligonucleotide Probe Design Criteria for Functional Gene Microarrays in Environmental applications

Liebich, J.FZJ* ; Schadt, C. W. ; Chong, S. C. ; He, Z. ; Rhee, S.-K. ; Zhou, J.-H.

2006
Soc. Washington, DC [u.a.]

Applied and environmental microbiology 72, 1688 - 1691 (2006) [10.1128/AEM.72.2.1688-1691.2006]

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Please use a persistent id in citations: http://hdl.handle.net/2128/796 doi:10.1128/AEM.72.2.1688-1691.2006

Abstract: To optimize oligonucleotide probe design criteria, PCR products with different similarities to probes were hybridized to a functional gene microarray designed to detect homologous genes from different organisms. In contrast to more restrictive probe designs based on a single criterion, simultaneous consideration of the percent similarity (< or =90%), the length of identical sequence stretches (< or =20 bases), and the binding free energy (> or =-35 kcal mol(-1)) was found to be predictive of probe specificity.

Keyword(s): Base Sequence (MeSH) ; Drug Design (MeSH) ; Environmental Microbiology (MeSH) ; Nucleic Acid Hybridization (MeSH) ; Oligonucleotide Array Sequence Analysis: methods (MeSH) ; Oligonucleotide Array Sequence Analysis: statistics & numerical data (MeSH) ; Oligonucleotide Probes: chemistry (MeSH) ; Oligonucleotide Probes: genetics (MeSH) ; Polymerase Chain Reaction (MeSH) ; Thermodynamics (MeSH) ; Oligonucleotide Probes ; J