MersV1, Main, Exploration, bibRecord, 002F11

Empirical establishment of oligonucleotide probe design criteria.

Identifieur interne : 002F11 ( Main/Exploration ); précédent : 002F10; suivant : 002F12

Empirical establishment of oligonucleotide probe design criteria.

Auteurs : Zhili He [États-Unis] ; Liyou Wu ; Xingyuan Li ; Matthew W. Fields ; Jizhong Zhou

Source :

Applied and environmental microbiology [ 0099-2240 ] ; 2005.

RBID : pubmed:16000786

Descripteurs français

KwdFr :
- Hybridation d'acides nucléiques, Mésappariement de bases, Plan de recherche (normes), Shewanella (génétique), Sondes oligonucléotidiques (génétique), Spécificité d'espèce, Séquençage par oligonucléotides en batterie.
MESH :
- génétique : Shewanella, Sondes oligonucléotidiques.
- normes : Plan de recherche.
- Hybridation d'acides nucléiques, Mésappariement de bases, Spécificité d'espèce, Séquençage par oligonucléotides en batterie.

English descriptors

KwdEn :
- Base Pair Mismatch, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oligonucleotide Probes (genetics), Research Design (standards), Shewanella (genetics), Species Specificity.
MESH :
- chemical , genetics : Oligonucleotide Probes.
- genetics : Shewanella.
- standards : Research Design.
- Base Pair Mismatch, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Species Specificity.

Abstract

Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide 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 < or =85% for both 50-mer and 70-mer probes. PM signal intensities (33 to 48%) were detected at a probe-target identity of 94% for 50-mer oligonucleotides and 43 to 55% for 70-mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a nonstretch probe (< or =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% 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: 10.1128/AEM.71.7.3753-3760.2005
PubMed: 16000786

Affiliations:

Le document en format XML

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<front><div type="abstract" xml:lang="en">Criteria for the design of gene-specific and group-specific oligonucleotide probes were established experimentally via an oligonucleotide 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 < or =85% for both 50-mer and 70-mer probes. PM signal intensities (33 to 48%) were detected at a probe-target identity of 94% for 50-mer oligonucleotides and 43 to 55% for 70-mer probes at a probe-target identity of 96%. When the effects of sequence identity and continuous stretch were considered independently, a stretch probe (>15 bases) contributed an additional 9% of the PM signal intensity compared to a nonstretch probe (< or =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% 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.</div>
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Empirical establishment of oligonucleotide probe design criteria.

Empirical establishment of oligonucleotide probe design criteria.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki

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