A Phenomenological Model for Predicting Melting Temperatures of DNA Sequences
Identifieur interne : 002652 ( Main/Exploration ); précédent : 002651; suivant : 002653A Phenomenological Model for Predicting Melting Temperatures of DNA Sequences
Auteurs : Garima Khandelwal [Inde] ; Jayaram Bhyravabhotla [Inde]Source :
- PLoS ONE [ 1932-6203 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- chemical , genetics : DNA.
- chemistry : Escherichia coli, Oryza.
- genetics : Escherichia coli, Oryza.
- Base Pairing, Base Sequence, Internet, Models, Chemical, Nucleic Acid Conformation, Temperature, Transition Temperature.
Abstract
We report here a novel method for predicting melting temperatures of DNA sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of DNA. The model presented here attempts to quantify the energetic components stabilizing the structure of DNA such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. The model gives a Pearson product-moment correlation coefficient (r) of ∼0.98 between experimental and predicted melting temperatures for over 300 sequences of varying lengths ranging from 15-mers to genomic level and at different salt concentrations. The approach is implemented as a web tool (
Url:
DOI: 10.1371/journal.pone.0012433
PubMed: 20865157
PubMed Central: 2928768
Affiliations:
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India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation></author><author><name sortKey="Bhyravabhotla, Jayaram" sort="Bhyravabhotla, Jayaram" uniqKey="Bhyravabhotla J" first="Jayaram" last="Bhyravabhotla">Jayaram Bhyravabhotla</name><affiliation wicri:level="1"><nlm:aff id="aff1"><addr-line>Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India</addr-line></nlm:aff><country xml:lang="fr">Inde</country><wicri:regionArea>Department of Chemistry, Indian Institute of Technology Delhi, New Delhi</wicri:regionArea><wicri:noRegion>New Delhi</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="aff2"><addr-line>Supercomputing Facility for Bioinformatics and Computational Biology, Indian Institute of Technology Delhi, New Delhi, 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(genetics)</term><term>Escherichia coli (chemistry)</term><term>Escherichia coli (genetics)</term><term>Internet</term><term>Models, Chemical</term><term>Nucleic Acid Conformation</term><term>Oryza (chemistry)</term><term>Oryza (genetics)</term><term>Temperature</term><term>Transition Temperature</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (génétique)</term><term>Appariement de bases</term><term>Conformation d'acide nucléique</term><term>Escherichia coli ()</term><term>Escherichia coli (génétique)</term><term>Internet</term><term>Modèles chimiques</term><term>Oryza ()</term><term>Oryza (génétique)</term><term>Séquence nucléotidique</term><term>Température</term><term>Température de transition</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Escherichia coli</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term><term>Oryza</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>Escherichia coli</term><term>Oryza</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Pairing</term><term>Base Sequence</term><term>Internet</term><term>Models, Chemical</term><term>Nucleic Acid Conformation</term><term>Temperature</term><term>Transition Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Appariement de bases</term><term>Conformation d'acide nucléique</term><term>Escherichia coli</term><term>Internet</term><term>Modèles chimiques</term><term>Oryza</term><term>Séquence nucléotidique</term><term>Température</term><term>Température de transition</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>We report here a novel method for predicting melting temperatures of DNA sequences based on a molecular-level hypothesis on the phenomena underlying the thermal denaturation of DNA. The model presented here attempts to quantify the energetic components stabilizing the structure of DNA such as base pairing, stacking, and ionic environment which are partially disrupted during the process of thermal denaturation. The model gives a Pearson product-moment correlation coefficient (r) of ∼0.98 between experimental and predicted melting temperatures for over 300 sequences of varying lengths ranging from 15-mers to genomic level and at different salt concentrations. The approach is implemented as a web tool (<ext-link ext-link-type="uri" xlink:href="http://www.scfbio-iitd.res.in/chemgenome/Tm_predictor.jsp">www.scfbio-iitd.res.in/chemgenome/Tm_predictor.jsp</ext-link>) for the prediction of melting temperatures of DNA sequences.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Cantor, Cr" uniqKey="Cantor C">CR Cantor</name></author><author><name sortKey="Schimmel, Pr" uniqKey="Schimmel P">PR Schimmel</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Doktycz, Mj" uniqKey="Doktycz M">MJ Doktycz</name></author><author><name sortKey="Morris, Md" uniqKey="Morris M">MD Morris</name></author><author><name sortKey="Dormady, Sj" uniqKey="Dormady S">SJ Dormady</name></author><author><name sortKey="Beattie, Kl" uniqKey="Beattie K">KL Beattie</name></author><author><name sortKey="Jacobson, Kb" uniqKey="Jacobson K">KB 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uniqKey="Dutta S">S Dutta</name></author><author><name sortKey="Singhal, P" uniqKey="Singhal P">P Singhal</name></author><author><name sortKey="Agrawal, P" uniqKey="Agrawal P">P Agrawal</name></author><author><name sortKey="Tomer, R" uniqKey="Tomer R">R Tomer</name></author><author><name sortKey="Kritee" uniqKey="Kritee">Kritee</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Singhal, P" uniqKey="Singhal P">P Singhal</name></author><author><name sortKey="Jayaram, B" uniqKey="Jayaram B">B Jayaram</name></author><author><name sortKey="Dixit, Sb" uniqKey="Dixit S">SB Dixit</name></author><author><name sortKey="Beveridge, Dl" uniqKey="Beveridge D">DL Beveridge</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lisser, S" uniqKey="Lisser S">S Lisser</name></author><author><name sortKey="Margalit, H" uniqKey="Margalit H">H Margalit</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wada, A" uniqKey="Wada A">A Wada</name></author><author><name sortKey="Suyama, A" uniqKey="Suyama A">A Suyama</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Inde</li></country></list><tree><country name="Inde"><noRegion><name sortKey="Khandelwal, Garima" sort="Khandelwal, Garima" uniqKey="Khandelwal G" first="Garima" last="Khandelwal">Garima Khandelwal</name></noRegion><name sortKey="Bhyravabhotla, Jayaram" sort="Bhyravabhotla, Jayaram" uniqKey="Bhyravabhotla J" first="Jayaram" last="Bhyravabhotla">Jayaram Bhyravabhotla</name><name sortKey="Bhyravabhotla, Jayaram" sort="Bhyravabhotla, Jayaram" uniqKey="Bhyravabhotla J" first="Jayaram" last="Bhyravabhotla">Jayaram Bhyravabhotla</name><name sortKey="Bhyravabhotla, Jayaram" sort="Bhyravabhotla, Jayaram" uniqKey="Bhyravabhotla J" first="Jayaram" last="Bhyravabhotla">Jayaram Bhyravabhotla</name><name sortKey="Khandelwal, Garima" sort="Khandelwal, Garima" uniqKey="Khandelwal G" first="Garima" last="Khandelwal">Garima Khandelwal</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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