Design and analysis of mismatch probes for long oligonucleotide microarrays.
Identifieur interne : 002001 ( PubMed/Checkpoint ); précédent : 002000; suivant : 002002Design and analysis of mismatch probes for long oligonucleotide microarrays.
Auteurs : Ye Deng [États-Unis] ; Zhili He ; Joy D. Van Nostrand ; Jizhong ZhouSource :
- BMC genomics [ 1471-2164 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Oligonucleotide Probes.
- methods : Oligonucleotide Array Sequence Analysis.
- Base Pair Mismatch, Models, Theoretical, Temperature.
Abstract
Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes.
DOI: 10.1186/1471-2164-9-491
PubMed: 18928550
Affiliations:
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Van Nostrand</name></author><author><name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2008">2008</date><idno type="RBID">pubmed:18928550</idno><idno type="pmid">18928550</idno><idno type="doi">10.1186/1471-2164-9-491</idno><idno type="wicri:Area/PubMed/Corpus">002067</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002067</idno><idno type="wicri:Area/PubMed/Curation">002067</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002067</idno><idno type="wicri:Area/PubMed/Checkpoint">002001</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002001</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Design and analysis of mismatch probes for long oligonucleotide microarrays.</title><author><name sortKey="Deng, Ye" sort="Deng, Ye" uniqKey="Deng Y" first="Ye" last="Deng">Ye Deng</name><affiliation wicri:level="2"><nlm:affiliation>Institute for Environmental Genomics, Department of Botany and Microbiology, the University of Oklahoma, Norman, OK 73019, USA. dengye@ou.edu</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Institute for Environmental Genomics, Department of Botany and Microbiology, the University of Oklahoma, Norman, OK 73019</wicri:regionArea><placeName><region type="state">Oklahoma</region></placeName></affiliation></author><author><name sortKey="He, Zhili" sort="He, Zhili" uniqKey="He Z" first="Zhili" last="He">Zhili He</name></author><author><name sortKey="Van Nostrand, Joy D" sort="Van Nostrand, Joy D" uniqKey="Van Nostrand J" first="Joy D" last="Van Nostrand">Joy D. Van Nostrand</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">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2008" type="published">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Pair Mismatch</term><term>Models, Theoretical</term><term>Oligonucleotide Array Sequence Analysis (methods)</term><term>Oligonucleotide Probes (chemistry)</term><term>Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Modèles théoriques</term><term>Mésappariement de bases</term><term>Sondes oligonucléotidiques ()</term><term>Séquençage par oligonucléotides en batterie ()</term><term>Température</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Oligonucleotide Probes</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Oligonucleotide Array Sequence Analysis</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pair Mismatch</term><term>Models, Theoretical</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Modèles théoriques</term><term>Mésappariement de bases</term><term>Sondes oligonucléotidiques</term><term>Séquençage par oligonucléotides en batterie</term><term>Température</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18928550</PMID><DateCompleted><Year>2008</Year><Month>11</Month><Day>18</Day></DateCompleted><DateRevised><Year>2019</Year><Month>12</Month><Day>10</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>9</Volume><PubDate><Year>2008</Year><Month>Oct</Month><Day>17</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Design and analysis of mismatch probes for long oligonucleotide microarrays.</ArticleTitle><Pagination><MedlinePgn>491</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-9-491</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Nonspecific hybridization is currently a major concern with microarray technology. One of most effective approaches to estimating nonspecific hybridizations in oligonucleotide microarrays is the utilization of mismatch probes; however, this approach has not been used for longer oligonucleotide probes.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Here, an oligonucleotide microarray was constructed to evaluate and optimize parameters for 50-mer mismatch probe design. A perfect match (PM) and 28 mismatch (MM) probes were designed for each of ten target genes selected from three microorganisms. The microarrays were hybridized with synthesized complementary oligonucleotide targets at different temperatures (e.g., 42, 45 and 50 degrees C). In general, the probes with evenly distributed mismatches were more distinguishable than those with randomly distributed mismatches. MM probes with 3, 4 and 5 mismatched nucleotides were differentiated for 50-mer oligonucleotide probes hybridized at 50, 45 and 42 degrees C, respectively. Based on the experimental data generated from this study, a modified positional dependent nearest neighbor (MPDNN) model was constructed to adjust the thermodynamic parameters of matched and mismatched dimer nucleotides in the microarray environment. The MM probes with four flexible positional mismatches were designed using the newly established MPDNN model and the experimental results demonstrated that the redesigned MM probes could yield more consistent hybridizations.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">This study provides guidance on the design of MM probes for long oligonucleotides (e.g., 50 mers). The novel MPDNN model has improved the consistency for long MM probes, and this modeling method can potentially be used for the prediction of oligonucleotide microarray hybridizations.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Deng</LastName><ForeName>Ye</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Institute for Environmental Genomics, Department of Botany and Microbiology, the University of Oklahoma, Norman, OK 73019, USA. dengye@ou.edu</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>He</LastName><ForeName>Zhili</ForeName><Initials>Z</Initials></Author><Author ValidYN="Y"><LastName>Van Nostrand</LastName><ForeName>Joy D</ForeName><Initials>JD</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="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>10</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015345">Oligonucleotide Probes</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D020137" MajorTopicYN="Y">Base Pair Mismatch</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008962" MajorTopicYN="N">Models, Theoretical</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020411" 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Van Nostrand</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="Oklahoma"><name sortKey="Deng, Ye" sort="Deng, Ye" uniqKey="Deng Y" first="Ye" last="Deng">Ye Deng</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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