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

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

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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 »« less

Authors:: He, Z; Wu, L; Li, X; Fields, M; Zhou, J -Z

Publication Date:: 2004-09-16

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

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                    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. 
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                    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.

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                    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.

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@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}

}

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