Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications.
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.
Liebich
Jost
J
Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA.
Schadt
Christopher W
CW
Chong
Song C
SC
He
Zhili
Z
Rhee
Sung-Keun
SK
Zhou
Jizhong
J
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
D015345:Oligonucleotide Probes