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Title: Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets

Abstract

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 criteriamore » 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.« less

Authors:
; ; ; ;
Publication Date:
Research Org.:
OLLABORATION - Oak Ridge NationalLaboratory
OSTI Identifier:
860356
Report Number(s):
LBNL-58739
Journal ID: ISSN 0099-2240; AEMIDF; TRN: US200524%%109
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Journal Article
Journal Name:
Applied and Environmental Microbiology
Additional Journal Information:
Journal Volume: 71; Journal Issue: 7; Related Information: Journal Publication Date: July, 2005; Journal ID: ISSN 0099-2240
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ALGORITHMS; DESIGN; FREE ENERGY; GENES; HYBRIDIZATION; OLIGONUCLEOTIDES; PROBES; SPECIFICITY; TARGETS

Citation Formats

He, Z, Wu, L, Li, X, Fields, M, and Zhou, J -Z. Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets. United States: N. p., 2004. Web.
He, Z, Wu, L, Li, X, Fields, M, & Zhou, J -Z. Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets. United States.
He, Z, Wu, L, Li, X, Fields, M, and Zhou, J -Z. Thu . "Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets". United States.
@article{osti_860356,
title = {Empirical establishment of oligonucleotide probe design criteriausing perfect match and mismatch probes and artificial targets},
author = {He, Z and Wu, L and Li, X and Fields, M and Zhou, J -Z},
abstractNote = {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.},
doi = {},
url = {https://www.osti.gov/biblio/860356}, journal = {Applied and Environmental Microbiology},
issn = {0099-2240},
number = 7,
volume = 71,
place = {United States},
year = {2004},
month = {9}
}