Empirical establishment of oligonucleotide probe design criteria.
Identifieur interne : 002211 ( PubMed/Checkpoint ); précédent : 002210; suivant : 002212Empirical establishment of oligonucleotide probe design criteria.
Auteurs : Zhili He [États-Unis] ; Liyou Wu ; Xingyuan Li ; Matthew W. Fields ; Jizhong ZhouSource :
- Applied and environmental microbiology [ 0099-2240 ] ; 2005.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- 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
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Fields</name></author><author><name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name></author></analytic><series><title level="j">Applied and environmental microbiology</title><idno type="ISSN">0099-2240</idno><imprint><date when="2005" type="published">2005</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pair Mismatch</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Oligonucleotide Probes (genetics)</term><term>Research Design (standards)</term><term>Shewanella (genetics)</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Hybridation d'acides nucléiques</term><term>Mésappariement de bases</term><term>Plan de recherche (normes)</term><term>Shewanella (génétique)</term><term>Sondes oligonucléotidiques (génétique)</term><term>Spécificité d'espèce</term><term>Séquençage par oligonucléotides en batterie</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotide Probes</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Shewanella</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Shewanella</term><term>Sondes oligonucléotidiques</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Plan de recherche</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Research Design</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pair Mismatch</term><term>Nucleic Acid Hybridization</term><term>Oligonucleotide Array Sequence Analysis</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Hybridation d'acides nucléiques</term><term>Mésappariement de bases</term><term>Spécificité d'espèce</term><term>Séquençage par oligonucléotides en batterie</term></keywords></textClass></profileDesc></teiHeader><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></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16000786</PMID><DateCompleted><Year>2005</Year><Month>09</Month><Day>13</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0099-2240</ISSN><JournalIssue CitedMedium="Print"><Volume>71</Volume><Issue>7</Issue><PubDate><Year>2005</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Applied and environmental microbiology</Title><ISOAbbreviation>Appl. Environ. Microbiol.</ISOAbbreviation></Journal><ArticleTitle>Empirical establishment of oligonucleotide probe design criteria.</ArticleTitle><Pagination><MedlinePgn>3753-60</MedlinePgn></Pagination><Abstract><AbstractText>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. 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Box 2008, Oak Ridge, TN 37831-6038, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wu</LastName><ForeName>Liyou</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Xingyuan</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Fields</LastName><ForeName>Matthew W</ForeName><Initials>MW</Initials></Author><Author ValidYN="Y"><LastName>Zhou</LastName><ForeName>Jizhong</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D023362">Evaluation Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Appl Environ 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Fields</name><name sortKey="Li, Xingyuan" sort="Li, Xingyuan" uniqKey="Li X" first="Xingyuan" last="Li">Xingyuan Li</name><name sortKey="Wu, Liyou" sort="Wu, Liyou" uniqKey="Wu L" first="Liyou" last="Wu">Liyou Wu</name><name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name></noCountry><country name="États-Unis"><region name="Tennessee"><name sortKey="He, Zhili" sort="He, Zhili" uniqKey="He Z" first="Zhili" last="He">Zhili He</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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