Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications

Appl Environ Microbiol. 2006 Feb;72(2):1688-91. 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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Base Sequence
  • Drug Design
  • Environmental Microbiology*
  • Nucleic Acid Hybridization
  • Oligonucleotide Array Sequence Analysis / methods*
  • Oligonucleotide Array Sequence Analysis / statistics & numerical data
  • Oligonucleotide Probes* / chemistry
  • Oligonucleotide Probes* / genetics
  • Polymerase Chain Reaction
  • Thermodynamics

Substances

  • Oligonucleotide Probes