Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss.
Identifieur interne : 002087 ( PubMed/Checkpoint ); précédent : 002086; suivant : 002088Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss.
Auteurs : Rambod Daneshfar [Canada] ; John S. KlassenSource :
- Journal of the American Society for Mass Spectrometry [ 1044-0305 ] ; 2006.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (), Cinétique, Concentration en ions d'hydrogène, Données de séquences moléculaires, Gaz (), Modèles chimiques, Oligonucléotides (), Simulation numérique, Solvants (), Spectrométrie de masse ESI (), Spectroscopie infrarouge à transformée de Fourier (), Séquence nucléotidique, Température, Température élevée, Thymidine (), Transition de phase, Électricité statique.
- MESH :
- Analyse de séquence d'ADN, Cinétique, Concentration en ions d'hydrogène, Données de séquences moléculaires, Gaz, Modèles chimiques, Oligonucléotides, Simulation numérique, Solvants, Spectrométrie de masse ESI, Spectroscopie infrarouge à transformée de Fourier, Séquence nucléotidique, Température, Température élevée, Thymidine, Transition de phase, Électricité statique.
English descriptors
- KwdEn :
- Base Sequence, Computer Simulation, Gases (chemistry), Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Models, Chemical, Molecular Sequence Data, Oligonucleotides (chemistry), Phase Transition, Sequence Analysis, DNA (methods), Solvents (chemistry), Spectrometry, Mass, Electrospray Ionization (methods), Spectroscopy, Fourier Transform Infrared (methods), Static Electricity, Temperature, Thymidine (chemistry).
- MESH :
- chemical , chemistry : Gases, Oligonucleotides, Solvents, Thymidine.
- methods : Sequence Analysis, DNA, Spectrometry, Mass, Electrospray Ionization, Spectroscopy, Fourier Transform Infrared.
- Base Sequence, Computer Simulation, Hot Temperature, Hydrogen-Ion Concentration, Kinetics, Models, Chemical, Molecular Sequence Data, Phase Transition, Static Electricity, Temperature.
Abstract
Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).
DOI: 10.1016/j.jasms.2006.05.002
PubMed: 16782356
Affiliations:
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Klassen</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16782356</idno><idno type="pmid">16782356</idno><idno type="doi">10.1016/j.jasms.2006.05.002</idno><idno type="wicri:Area/PubMed/Corpus">002251</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002251</idno><idno type="wicri:Area/PubMed/Curation">002251</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002251</idno><idno type="wicri:Area/PubMed/Checkpoint">002087</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002087</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss.</title><author><name sortKey="Daneshfar, Rambod" sort="Daneshfar, Rambod" uniqKey="Daneshfar R" first="Rambod" last="Daneshfar">Rambod Daneshfar</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Chemistry, University of Alberta, Edmonton, Alberta</wicri:regionArea><wicri:noRegion>Alberta</wicri:noRegion></affiliation></author><author><name sortKey="Klassen, John S" sort="Klassen, John S" uniqKey="Klassen J" first="John S" last="Klassen">John S. Klassen</name></author></analytic><series><title level="j">Journal of the American Society for Mass Spectrometry</title><idno type="ISSN">1044-0305</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Computer Simulation</term><term>Gases (chemistry)</term><term>Hot Temperature</term><term>Hydrogen-Ion Concentration</term><term>Kinetics</term><term>Models, Chemical</term><term>Molecular Sequence Data</term><term>Oligonucleotides (chemistry)</term><term>Phase Transition</term><term>Sequence Analysis, DNA (methods)</term><term>Solvents (chemistry)</term><term>Spectrometry, Mass, Electrospray Ionization (methods)</term><term>Spectroscopy, Fourier Transform Infrared (methods)</term><term>Static Electricity</term><term>Temperature</term><term>Thymidine (chemistry)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Cinétique</term><term>Concentration en ions d'hydrogène</term><term>Données de séquences moléculaires</term><term>Gaz ()</term><term>Modèles chimiques</term><term>Oligonucléotides ()</term><term>Simulation numérique</term><term>Solvants ()</term><term>Spectrométrie de masse ESI ()</term><term>Spectroscopie infrarouge à transformée de Fourier ()</term><term>Séquence nucléotidique</term><term>Température</term><term>Température élevée</term><term>Thymidine ()</term><term>Transition de phase</term><term>Électricité statique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Gases</term><term>Oligonucleotides</term><term>Solvents</term><term>Thymidine</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term><term>Spectrometry, Mass, Electrospray Ionization</term><term>Spectroscopy, Fourier Transform Infrared</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Base Sequence</term><term>Computer Simulation</term><term>Hot Temperature</term><term>Hydrogen-Ion Concentration</term><term>Kinetics</term><term>Models, Chemical</term><term>Molecular Sequence Data</term><term>Phase Transition</term><term>Static Electricity</term><term>Temperature</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Cinétique</term><term>Concentration en ions d'hydrogène</term><term>Données de séquences moléculaires</term><term>Gaz</term><term>Modèles chimiques</term><term>Oligonucléotides</term><term>Simulation numérique</term><term>Solvants</term><term>Spectrométrie de masse ESI</term><term>Spectroscopie infrarouge à transformée de Fourier</term><term>Séquence nucléotidique</term><term>Température</term><term>Température élevée</term><term>Thymidine</term><term>Transition de phase</term><term>Électricité statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16782356</PMID><DateCompleted><Year>2007</Year><Month>07</Month><Day>03</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1044-0305</ISSN><JournalIssue CitedMedium="Print"><Volume>17</Volume><Issue>9</Issue><PubDate><Year>2006</Year><Month>Sep</Month></PubDate></JournalIssue><Title>Journal of the American Society for Mass Spectrometry</Title><ISOAbbreviation>J. Am. Soc. Mass Spectrom.</ISOAbbreviation></Journal><ArticleTitle>Thermal decomposition of multiply charged T-rich oligonucleotide anions in the gas phase. Influence of internal solvation on the arrhenius parameters for neutral base loss.</ArticleTitle><Pagination><MedlinePgn>1229-38</MedlinePgn></Pagination><Abstract><AbstractText>Arrhenius activation parameters (E(a), A) for the loss of neutral nucleobases from a series of T-rich, doubly and triply deprotonated 15- and 20-mer oligodeoxynucleotides (ODN) containing a single reactive base (X = A or C) with the sequence, XT14, XT19 and T19X, have been determined using the blackbody infrared radiative dissociation technique. The A-containing anions are significantly more reactive (> or =3000 times) than the C-containing ions over the temperature range investigated. Importantly, the Arrhenius parameters for the loss of AH exhibit a strong dependence on size of the ODN and, to some extent, the charge state; the Arrhenius parameters increase with size and charge (Ea = 29-39 kcal mol(-1), A = 10(15)-10(20) s(-1)). In contrast, the parameters for the loss of CH are much less sensitive to size (Ea = 35-39 kcal mol(-1), A = 10(14)-10(17) s(-1)). The results are consistent with a greater contribution from the internal solvation of the reactive base to the Arrhenius parameters for the loss of A, compared with C, from the 15- and 20-mers. To further probe differences in internal solvation of A and C, hydrogen/deuterium exchange was carried out on AT19(-3), T19A(-3), CT19(-3) and T19C(-3) using D2O as the exchange reagent. However, the H/D exchange results did not reveal any differences in internal solvation within the ODN anions. Arrhenius parameters for the dissociation of noncovalent complexes of T20(-3) and the neutral nucleobase AH or CH have also been determined. Differences in the parameters indicate differences in the nature of the intermolecular interactions. It is proposed that neutral A-T interactions (i.e., base-base), which originate in solution, dominate in the case of (T20 + AH)(-3), while charge solvation, involving CH and a deprotonated phosphate group, is present for (T20 + CH)(-3).</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Daneshfar</LastName><ForeName>Rambod</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Klassen</LastName><ForeName>John S</ForeName><Initials>JS</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>2006</Year><Month>06</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>J Am Soc Mass Spectrom</MedlineTA><NlmUniqueID>9010412</NlmUniqueID><ISSNLinking>1044-0305</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005740">Gases</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012997">Solvents</NameOfSubstance></Chemical><Chemical><RegistryNumber>VC2W18DGKR</RegistryNumber><NameOfSubstance UI="D013936">Thymidine</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D003198" MajorTopicYN="N">Computer 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MajorTopicYN="N">Temperature</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013936" MajorTopicYN="N">Thymidine</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2005</Year><Month>11</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2006</Year><Month>05</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2006</Year><Month>05</Month><Day>05</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>6</Month><Day>20</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>7</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>6</Month><Day>20</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16782356</ArticleId><ArticleId IdType="pii">S1044-0305(06)00480-6</ArticleId><ArticleId IdType="doi">10.1016/j.jasms.2006.05.002</ArticleId></ArticleIdList><ReferenceList><Reference><Citation>Chem Biol. 1995 Nov;2(11):709-12</Citation><ArticleIdList><ArticleId IdType="pubmed">9383477</ArticleId></ArticleIdList></Reference><Reference><Citation>Biochemistry. 1973 Dec 4;12(25):5151-4</Citation><ArticleIdList><ArticleId IdType="pubmed">4600811</ArticleId></ArticleIdList></Reference><Reference><Citation>J Am Chem Soc. 2002 May 22;124(20):5902-13</Citation><ArticleIdList><ArticleId IdType="pubmed">12010066</ArticleId></ArticleIdList></Reference><Reference><Citation>J Am Soc Mass Spectrom. 1999 Nov;10 (11):1095-104</Citation><ArticleIdList><ArticleId 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Klassen</name></noCountry><country name="Canada"><noRegion><name sortKey="Daneshfar, Rambod" sort="Daneshfar, Rambod" uniqKey="Daneshfar R" first="Rambod" last="Daneshfar">Rambod Daneshfar</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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