Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.
Identifieur interne : 002111 ( Ncbi/Merge ); précédent : 002110; suivant : 002112Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.
Auteurs : Stefanie Ickert [Allemagne] ; Timm Schwaar [Allemagne] ; Andreas Springer [Allemagne] ; Márk Grabarics [Allemagne] ; Jens Riedel [Allemagne] ; Sebastian Beck [Allemagne] ; Kevin Pagel [Allemagne] ; Michael W. Linscheid [Allemagne]Source :
- Journal of mass spectrometry : JMS [ 1096-9888 ] ; 2019.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Oligonucleotides.
- Base Sequence, Models, Molecular, Nucleic Acid Conformation, Spectrometry, Mass, Electrospray Ionization, Thermodynamics.
Abstract
DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.
DOI: 10.1002/jms.4344
PubMed: 30771235
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wicri:level="3"><nlm:affiliation>Federal Institute for Materials Research and Testing, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Federal Institute for Materials Research and Testing, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Springer, Andreas" sort="Springer, Andreas" uniqKey="Springer A" first="Andreas" last="Springer">Andreas Springer</name><affiliation wicri:level="3"><nlm:affiliation>Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name 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of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Linscheid, Michael W" sort="Linscheid, Michael W" uniqKey="Linscheid M" first="Michael W" last="Linscheid">Michael W. Linscheid</name><affiliation wicri:level="3"><nlm:affiliation>Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author></analytic><series><title level="j">Journal of mass spectrometry : JMS</title><idno type="eISSN">1096-9888</idno><imprint><date when="2019" type="published">2019</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>DNA (chemistry)</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Oligonucleotides (chemistry)</term><term>Spectrometry, Mass, Electrospray Ionization</term><term>Thermodynamics</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Oligonucléotides ()</term><term>Spectrométrie de masse ESI</term><term>Séquence nucléotidique</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>Base Sequence</term><term>Models, Molecular</term><term>Nucleic Acid Conformation</term><term>Spectrometry, Mass, Electrospray Ionization</term><term>Thermodynamics</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Conformation d'acide nucléique</term><term>Modèles moléculaires</term><term>Oligonucléotides</term><term>Spectrométrie de masse ESI</term><term>Séquence nucléotidique</term><term>Thermodynamique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30771235</PMID><DateCompleted><Year>2019</Year><Month>08</Month><Day>14</Day></DateCompleted><DateRevised><Year>2019</Year><Month>08</Month><Day>14</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1096-9888</ISSN><JournalIssue CitedMedium="Internet"><Volume>54</Volume><Issue>5</Issue><PubDate><Year>2019</Year><Month>May</Month></PubDate></JournalIssue><Title>Journal of mass spectrometry : JMS</Title><ISOAbbreviation>J Mass Spectrom</ISOAbbreviation></Journal><ArticleTitle>Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.</ArticleTitle><Pagination><MedlinePgn>402-411</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1002/jms.4344</ELocationID><Abstract><AbstractText>DNA and locked nucleic acid (LNA) were characterized as single strands, as well as double stranded DNA-DNA duplexes and DNA-LNA hybrids using tandem mass spectrometry with collision-induced dissociation. Additionally, ion mobility spectrometry was carried out on selected species. Oligonucleotide duplexes of different sequences-bearing mismatch positions and abasic sites of complementary DNA 15-mers-were investigated to unravel general trends in their stability in the gas phase. Single-stranded LNA oligonucleotides were also investigated with respect to their gas phase behavior and fragmentation upon collision-induced dissociation. In contrast to the collision-induced dissociation of DNA, almost no base loss was observed for LNAs. Here, backbone cleavages were the dominant dissociation pathways. This finding was further underlined by the need for higher activation energies. Base losses from the LNA strand were also absent in fragmentation experiments of the investigated DNA-LNA hybrid duplexes. While DNA-DNA duplexes dissociated easily into single stranded fragments, the high stability of DNA-LNA hybrids resulted in predominant fragmentation of the DNA part rather than the LNA, while base losses were only observed from the DNA single strand of the hybrid.</AbstractText><CopyrightInformation>© 2019 John Wiley & Sons, Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ickert</LastName><ForeName>Stefanie</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Federal Institute for Materials Research and Testing, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Schwaar</LastName><ForeName>Timm</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Federal Institute for Materials Research and Testing, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Springer</LastName><ForeName>Andreas</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grabarics</LastName><ForeName>Márkó</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Riedel</LastName><ForeName>Jens</ForeName><Initials>J</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-5273-6605</Identifier><AffiliationInfo><Affiliation>Federal Institute for Materials Research and Testing, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Beck</LastName><ForeName>Sebastian</ForeName><Initials>S</Initials><Identifier Source="ORCID">https://orcid.org/0000-0001-6440-693X</Identifier><AffiliationInfo><Affiliation>Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pagel</LastName><ForeName>Kevin</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Chemistry and Biochemistry, Freie Universitaet Berlin, Berlin, Germany.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Linscheid</LastName><ForeName>Michael W</ForeName><Initials>MW</Initials><Identifier Source="ORCID">https://orcid.org/0000-0002-8902-1734</Identifier><AffiliationInfo><Affiliation>Department of Chemistry, Humboldt-Universitaet zu Berlin, Berlin, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>J Mass Spectrom</MedlineTA><NlmUniqueID>9504818</NlmUniqueID><ISSNLinking>1076-5174</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D009841">Oligonucleotides</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C477371">locked nucleic acid</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><MeshHeadingList><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D008958" MajorTopicYN="N">Models, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009690" MajorTopicYN="N">Nucleic Acid Conformation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009841" MajorTopicYN="N">Oligonucleotides</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D021241" MajorTopicYN="N">Spectrometry, Mass, Electrospray Ionization</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013816" MajorTopicYN="N">Thermodynamics</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">collision induced dissociation (CID)</Keyword><Keyword MajorTopicYN="N">double strands</Keyword><Keyword MajorTopicYN="N">ion mobility spectrometry</Keyword><Keyword MajorTopicYN="N">locked nucleic acids</Keyword><Keyword MajorTopicYN="N">oligonucleotide fragmentation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>09</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2019</Year><Month>02</Month><Day>08</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2019</Year><Month>02</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2019</Year><Month>2</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>8</Month><Day>15</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2019</Year><Month>2</Month><Day>17</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30771235</ArticleId><ArticleId 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