title: Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications.
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.
authors.affiliation: Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
authors.forename: Jost
authors.initials: J
authors.lastname: Liebich
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Schadt
authors.forename: Song C
authors.initials: SC
authors.lastname: Chong
authors.forename: Zhili
authors.initials: Z
authors.lastname: He
authors.forename: Sung-Keun
authors.initials: SK
authors.lastname: Rhee
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
mesh_terms: D001483:Base Sequence; D015195:Drug Design; D004783:Environmental Microbiology; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D015345:Oligonucleotide Probes / Q000737:chemistry / Q000235:genetics; D016133:Polymerase Chain Reaction; D013816:Thermodynamics
chemical_list: D015345:Oligonucleotide Probes