Design and analysis of mismatch probes for long oligonucleotide microarrays
Identifieur interne : 001400 ( Pmc/Checkpoint ); précédent : 001399; suivant : 001401Design and analysis of mismatch probes for long oligonucleotide microarrays
Auteurs : Ye Deng [États-Unis] ; Zhili He [États-Unis] ; Joy D. Van Nostrand [États-Unis] ; Jizhong Zhou [États-Unis]Source :
- BMC Genomics [ 1471-2164 ] ; 2008.
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.
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°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°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.
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.
Url:
DOI: 10.1186/1471-2164-9-491
PubMed: 18928550
PubMed Central: 2576263
Affiliations:
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Results</title>
<p>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°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°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.</p>
</sec>
<sec><title>Conclusion</title>
<p>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.</p>
</sec>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Genomics</journal-id>
<journal-title>BMC Genomics</journal-title>
<issn pub-type="epub">1471-2164</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
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<article-meta><article-id pub-id-type="pmid">18928550</article-id>
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<article-id pub-id-type="doi">10.1186/1471-2164-9-491</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
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<title-group><article-title>Design and analysis of mismatch probes for long oligonucleotide microarrays</article-title>
</title-group>
<contrib-group><contrib id="A1" contrib-type="author"><name><surname>Deng</surname>
<given-names>Ye</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>dengye@ou.edu</email>
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<contrib id="A2" corresp="yes" contrib-type="author"><name><surname>He</surname>
<given-names>Zhili</given-names>
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<email>zhili.he@ou.edu</email>
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<contrib id="A3" contrib-type="author"><name><surname>Van Nostrand</surname>
<given-names>Joy D</given-names>
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<email>Joy.VanNostrand@ou.edu</email>
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<contrib id="A4" corresp="yes" contrib-type="author"><name><surname>Zhou</surname>
<given-names>Jizhong</given-names>
</name>
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<email>jzhou@ou.edu</email>
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<aff id="I1"><label>1</label>
Institute for Environmental Genomics, Department of Botany and Microbiology, the University of Oklahoma, Norman, OK 73019, USA</aff>
<pub-date pub-type="collection"><year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>17</day>
<month>10</month>
<year>2008</year>
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<volume>9</volume>
<fpage>491</fpage>
<lpage>491</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2164/9/491"></ext-link>
<history><date date-type="received"><day>21</day>
<month>5</month>
<year>2008</year>
</date>
<date date-type="accepted"><day>17</day>
<month>10</month>
<year>2008</year>
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<permissions><copyright-statement>Copyright © 2008 Deng et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2008</copyright-year>
<copyright-holder>Deng et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Deng
Ye
dengye@ou.edu
Design and analysis of mismatch probes for long oligonucleotide microarrays
2008 BMC Genomics 9(1): 491-. (2008) 1471-2164(2008)9:1<491> urn:ISSN:1471-2164 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>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.</p>
</sec>
<sec><title>Results</title>
<p>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°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°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.</p>
</sec>
<sec><title>Conclusion</title>
<p>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.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Oklahoma</li>
</region>
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<name sortKey="He, Zhili" sort="He, Zhili" uniqKey="He Z" first="Zhili" last="He">Zhili He</name>
<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>
<name sortKey="Zhou, Jizhong" sort="Zhou, Jizhong" uniqKey="Zhou J" first="Jizhong" last="Zhou">Jizhong Zhou</name>
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