Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets
Journal Article
·
· Applied and Environmental Microbiology
OSTI ID:860356
Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via anoligonucleotide array that contained perfect match (PM) and mismatch probes (50-mers and 70-mers) based upon four genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were tested. Little hybridization was observed at a probe-target identity of 85 percent for both 50-mer and 70-mer probes. PM signal intensities (33 to 48 percent) were detected at a probe-target identity of 94 percent for 50-meroligonucleotides and 43 to 55 percent for 70-mer probes at a probe-target identity of 96 percent. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15bases) contributed an additional 9 percent of the PM signal intensity compared to a nonstretch probe (15 bases) at the same identity level. Cross-hybridization increased as the length of continuous stretch increased. A 35-base stretch for 50-mer probes or a 50-base stretch for 70-mer probes had approximately 55 percent of the PM signal. Little cross-hybridization was observed for probes with a minimal binding free energy greater than 30 kcal/mol for 50-mer probes or 40 kcal/mol for 70-mer probes. Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and the experimentally established criteria should provide valuable information for new software and algorithms for microarray-based studies.
- Research Organization:
- OLLABORATION - Oak Ridge NationalLaboratory
- DOE Contract Number:
- AC02-05CH11231
- OSTI ID:
- 860356
- Report Number(s):
- LBNL--58739
- Journal Information:
- Applied and Environmental Microbiology, Journal Name: Applied and Environmental Microbiology Journal Issue: 7 Vol. 71; ISSN AEMIDF; ISSN 0099-2240
- Country of Publication:
- United States
- Language:
- English
Similar Records
Empirical Establishment of Oligonucleotide Probe Design Criteria; Use of Microarrays with Different Probe Sizes for Monitoring Gene Expression; Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion
Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions
Design and analysis of mismatch probes for long oligonucleotide microarrays
Journal Article
·
Fri Jul 15 00:00:00 EDT 2005
· Applied and Environmental Microbiology
·
OSTI ID:927688
Final Report Construction of Whole Genome Microarrays, and Expression Analysis of Desulfovibrio vulgaris cells in Metal-Reducing Conditions
Technical Report
·
Thu May 15 00:00:00 EDT 2008
·
OSTI ID:929541
Design and analysis of mismatch probes for long oligonucleotide microarrays
Journal Article
·
Fri Aug 15 00:00:00 EDT 2008
· BMC Genomics
·
OSTI ID:957036