Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.
Identifieur interne : 000774 ( Ncbi/Merge ); précédent : 000773; suivant : 000775Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.
Auteurs : Ernesto Carrillo-Nava [Allemagne] ; Ludger Busch ; Yamilet Mejía-Radillo ; Kristian Boehm ; Hans-Jürgen HinzSource :
- The journal of physical chemistry. B [ 1520-5207 ] ; 2010.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Oligonucleotides.
- Algorithms, Calorimetry, Calorimetry, Differential Scanning, Thermodynamics.
Abstract
Recently, we reported the kinetics of hybridization of cDNA dodecamers (Carrillo-Nava, E., Mejía-Radillo, Y., and Hinz, H.-J. Biochemistry 2008, 47, 13153-13157). In this study, we provide the thermodynamic reaction parameters of those dodecamers as well as a comparison with parameters for 24-mers designed from two identical dodecamers in tandem arrangement. The thermodynamic properties were determined by isothermal titration calorimetry (ITC), differential scanning microcalorimetry (DSC), and UV melting studies. On the basis of the results from our kinetic studies, fitting algorithms of DSC and UV melting profiles employed the two-state assumption for the duplex to a single strand dissociation reaction. The formation of both 12-mer and 24-mer duplexes is strongly enthalpy driven at all temperatures. At identical temperatures, the hybridization enthalpy of the 24-mer is within error limits twice that of the 12-mer. Duplex formation is always associated with a significant negative heat capacity change, ΔC(p), which, on a mass basis, is comparable to that observed for protein folding. Only a small part of the favorable reaction enthalpy appears as a standard Gibbs free energy change due to large compensating negative entropy changes linked to duplex formation. On the basis of the results of the present studies, it appears to be absolutely essential for a proper analysis of thermodynamic parameters of oligonucleotide hybridization reactions to combine low temperature ITC measurements of binding enthalpies with DSC and UV melting studies to obtain an accurate assessment of standard Gibbs energy changes or, equivalently, hybridization constants over a broad temperature range. The experimental thermodynamic parameters were compared with theoretical estimates based on nearest-neighbor approximations employing temperature-independent enthalpies. Good agreement between experimental and predicted ΔG° values is observed at ambient temperatures (20-30 °C), as long as helix formation is associated with small molar heat capacity changes. If the experimental ΔC(p) values determined by ITC are taken into account, significant deviations occur.
DOI: 10.1021/jp100412a
PubMed: 20839824
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 001F37
- to stream PubMed, to step Curation: 001F37
- to stream PubMed, to step Checkpoint: 001E46
Links to Exploration step
pubmed:20839824Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.</title><author><name sortKey="Carrillo Nava, Ernesto" sort="Carrillo Nava, Ernesto" uniqKey="Carrillo Nava E" first="Ernesto" last="Carrillo-Nava">Ernesto Carrillo-Nava</name><affiliation wicri:level="3"><nlm:affiliation>Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Münster</region><settlement type="city">Münster</settlement></placeName></affiliation></author><author><name sortKey="Busch, Ludger" sort="Busch, Ludger" uniqKey="Busch L" first="Ludger" last="Busch">Ludger Busch</name></author><author><name sortKey="Mejia Radillo, Yamilet" sort="Mejia Radillo, Yamilet" uniqKey="Mejia Radillo Y" first="Yamilet" last="Mejía-Radillo">Yamilet Mejía-Radillo</name></author><author><name sortKey="Boehm, Kristian" sort="Boehm, Kristian" uniqKey="Boehm K" first="Kristian" last="Boehm">Kristian Boehm</name></author><author><name sortKey="Hinz, Hans Jurgen" sort="Hinz, Hans Jurgen" uniqKey="Hinz H" first="Hans-Jürgen" last="Hinz">Hans-Jürgen Hinz</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2010">2010</date><idno type="RBID">pubmed:20839824</idno><idno type="pmid">20839824</idno><idno type="doi">10.1021/jp100412a</idno><idno type="wicri:Area/PubMed/Corpus">001F37</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001F37</idno><idno type="wicri:Area/PubMed/Curation">001F37</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001F37</idno><idno type="wicri:Area/PubMed/Checkpoint">001E46</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001E46</idno><idno type="wicri:Area/Ncbi/Merge">000774</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.</title><author><name sortKey="Carrillo Nava, Ernesto" sort="Carrillo Nava, Ernesto" uniqKey="Carrillo Nava E" first="Ernesto" last="Carrillo-Nava">Ernesto Carrillo-Nava</name><affiliation wicri:level="3"><nlm:affiliation>Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster</wicri:regionArea><placeName><region type="land" nuts="1">Rhénanie-du-Nord-Westphalie</region><region type="district" nuts="2">District de Münster</region><settlement type="city">Münster</settlement></placeName></affiliation></author><author><name sortKey="Busch, Ludger" sort="Busch, Ludger" uniqKey="Busch L" first="Ludger" last="Busch">Ludger Busch</name></author><author><name sortKey="Mejia Radillo, Yamilet" sort="Mejia Radillo, Yamilet" uniqKey="Mejia Radillo Y" first="Yamilet" last="Mejía-Radillo">Yamilet Mejía-Radillo</name></author><author><name sortKey="Boehm, Kristian" sort="Boehm, Kristian" uniqKey="Boehm K" first="Kristian" last="Boehm">Kristian Boehm</name></author><author><name sortKey="Hinz, Hans Jurgen" sort="Hinz, Hans Jurgen" uniqKey="Hinz H" first="Hans-Jürgen" last="Hinz">Hans-Jürgen Hinz</name></author></analytic><series><title level="j">The journal of physical chemistry. B</title><idno type="eISSN">1520-5207</idno><imprint><date when="2010" type="published">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Calorimetry</term><term>Calorimetry, Differential Scanning</term><term>DNA (chemistry)</term><term>Oligonucleotides (chemistry)</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Algorithmes</term><term>Calorimétrie</term><term>Calorimétrie différentielle à balayage</term><term>Oligonucléotides ()</term><term>Thermodynamique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Oligonucleotides</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Calorimetry</term><term>Calorimetry, Differential Scanning</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Algorithmes</term><term>Calorimétrie</term><term>Calorimétrie différentielle à balayage</term><term>Oligonucléotides</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recently, we reported the kinetics of hybridization of cDNA dodecamers (Carrillo-Nava, E., Mejía-Radillo, Y., and Hinz, H.-J. Biochemistry 2008, 47, 13153-13157). In this study, we provide the thermodynamic reaction parameters of those dodecamers as well as a comparison with parameters for 24-mers designed from two identical dodecamers in tandem arrangement. The thermodynamic properties were determined by isothermal titration calorimetry (ITC), differential scanning microcalorimetry (DSC), and UV melting studies. On the basis of the results from our kinetic studies, fitting algorithms of DSC and UV melting profiles employed the two-state assumption for the duplex to a single strand dissociation reaction. The formation of both 12-mer and 24-mer duplexes is strongly enthalpy driven at all temperatures. At identical temperatures, the hybridization enthalpy of the 24-mer is within error limits twice that of the 12-mer. Duplex formation is always associated with a significant negative heat capacity change, ΔC(p), which, on a mass basis, is comparable to that observed for protein folding. Only a small part of the favorable reaction enthalpy appears as a standard Gibbs free energy change due to large compensating negative entropy changes linked to duplex formation. On the basis of the results of the present studies, it appears to be absolutely essential for a proper analysis of thermodynamic parameters of oligonucleotide hybridization reactions to combine low temperature ITC measurements of binding enthalpies with DSC and UV melting studies to obtain an accurate assessment of standard Gibbs energy changes or, equivalently, hybridization constants over a broad temperature range. The experimental thermodynamic parameters were compared with theoretical estimates based on nearest-neighbor approximations employing temperature-independent enthalpies. Good agreement between experimental and predicted ΔG° values is observed at ambient temperatures (20-30 °C), as long as helix formation is associated with small molar heat capacity changes. If the experimental ΔC(p) values determined by ITC are taken into account, significant deviations occur.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">20839824</PMID><DateCompleted><Year>2011</Year><Month>04</Month><Day>01</Day></DateCompleted><DateRevised><Year>2010</Year><Month>12</Month><Day>14</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1520-5207</ISSN><JournalIssue CitedMedium="Internet"><Volume>114</Volume><Issue>49</Issue><PubDate><Year>2010</Year><Month>Dec</Month><Day>16</Day></PubDate></JournalIssue><Title>The journal of physical chemistry. B</Title><ISOAbbreviation>J Phys Chem B</ISOAbbreviation></Journal><ArticleTitle>Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.</ArticleTitle><Pagination><MedlinePgn>16087-98</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1021/jp100412a</ELocationID><Abstract><AbstractText>Recently, we reported the kinetics of hybridization of cDNA dodecamers (Carrillo-Nava, E., Mejía-Radillo, Y., and Hinz, H.-J. Biochemistry 2008, 47, 13153-13157). In this study, we provide the thermodynamic reaction parameters of those dodecamers as well as a comparison with parameters for 24-mers designed from two identical dodecamers in tandem arrangement. The thermodynamic properties were determined by isothermal titration calorimetry (ITC), differential scanning microcalorimetry (DSC), and UV melting studies. On the basis of the results from our kinetic studies, fitting algorithms of DSC and UV melting profiles employed the two-state assumption for the duplex to a single strand dissociation reaction. The formation of both 12-mer and 24-mer duplexes is strongly enthalpy driven at all temperatures. At identical temperatures, the hybridization enthalpy of the 24-mer is within error limits twice that of the 12-mer. Duplex formation is always associated with a significant negative heat capacity change, ΔC(p), which, on a mass basis, is comparable to that observed for protein folding. Only a small part of the favorable reaction enthalpy appears as a standard Gibbs free energy change due to large compensating negative entropy changes linked to duplex formation. On the basis of the results of the present studies, it appears to be absolutely essential for a proper analysis of thermodynamic parameters of oligonucleotide hybridization reactions to combine low temperature ITC measurements of binding enthalpies with DSC and UV melting studies to obtain an accurate assessment of standard Gibbs energy changes or, equivalently, hybridization constants over a broad temperature range. The experimental thermodynamic parameters were compared with theoretical estimates based on nearest-neighbor approximations employing temperature-independent enthalpies. Good agreement between experimental and predicted ΔG° values is observed at ambient temperatures (20-30 °C), as long as helix formation is associated with small molar heat capacity changes. If the experimental ΔC(p) values determined by ITC are taken into account, significant deviations occur.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Carrillo-Nava</LastName><ForeName>Ernesto</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Institut für Physikalische Chemie der Westfälischen Wilhelms-Universität Münster, Corrensstrasse 30, 48149 Münster, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Busch</LastName><ForeName>Ludger</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Mejía-Radillo</LastName><ForeName>Yamilet</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Boehm</LastName><ForeName>Kristian</ForeName><Initials>K</Initials></Author><Author ValidYN="Y"><LastName>Hinz</LastName><ForeName>Hans-Jürgen</ForeName><Initials>HJ</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2010</Year><Month>09</Month><Day>14</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Phys Chem B</MedlineTA><NlmUniqueID>101157530</NlmUniqueID><ISSNLinking>1520-5207</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002151" MajorTopicYN="N">Calorimetry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002152" MajorTopicYN="N">Calorimetry, Differential Scanning</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="Y">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2010</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2010</Year><Month>9</Month><Day>16</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>4</Month><Day>2</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">20839824</ArticleId><ArticleId IdType="doi">10.1021/jp100412a</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Allemagne</li></country><region><li>District de Münster</li><li>Rhénanie-du-Nord-Westphalie</li></region><settlement><li>Münster</li></settlement></list><tree><noCountry><name sortKey="Boehm, Kristian" sort="Boehm, Kristian" uniqKey="Boehm K" first="Kristian" last="Boehm">Kristian Boehm</name><name sortKey="Busch, Ludger" sort="Busch, Ludger" uniqKey="Busch L" first="Ludger" last="Busch">Ludger Busch</name><name sortKey="Hinz, Hans Jurgen" sort="Hinz, Hans Jurgen" uniqKey="Hinz H" first="Hans-Jürgen" last="Hinz">Hans-Jürgen Hinz</name><name sortKey="Mejia Radillo, Yamilet" sort="Mejia Radillo, Yamilet" uniqKey="Mejia Radillo Y" first="Yamilet" last="Mejía-Radillo">Yamilet Mejía-Radillo</name></noCountry><country name="Allemagne"><region name="Rhénanie-du-Nord-Westphalie"><name sortKey="Carrillo Nava, Ernesto" sort="Carrillo Nava, Ernesto" uniqKey="Carrillo Nava E" first="Ernesto" last="Carrillo-Nava">Ernesto Carrillo-Nava</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000774 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd -nk 000774 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Merge
|type= RBID
|clé= pubmed:20839824
|texte= Experiment and prediction: a productive symbiosis in studies on the thermodynamics of DNA oligomers.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Merge/RBID.i -Sk "pubmed:20839824" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Merge/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |