Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.
Identifieur interne : 000653 ( Main/Exploration ); précédent : 000652; suivant : 000654Comparison 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
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000643
- to stream PubMed, to step Curation: 000643
- to stream PubMed, to step Checkpoint: 000630
- to stream Ncbi, to step Merge: 002111
- to stream Ncbi, to step Curation: 002111
- to stream Ncbi, to step Checkpoint: 002111
- to stream Main, to step Merge: 000656
- to stream Main, to step Curation: 000653
Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.</title><author><name sortKey="Ickert, Stefanie" sort="Ickert, Stefanie" uniqKey="Ickert S" first="Stefanie" last="Ickert">Stefanie Ickert</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><author><name sortKey="Schwaar, Timm" sort="Schwaar, Timm" uniqKey="Schwaar T" first="Timm" last="Schwaar">Timm Schwaar</name><affiliation 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 sortKey="Grabarics, Mark" sort="Grabarics, Mark" uniqKey="Grabarics M" first="Márk" last="Grabarics">Márk Grabarics</name><affiliation wicri:level="3"><nlm:affiliation>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Riedel, Jens" sort="Riedel, Jens" uniqKey="Riedel J" first="Jens" last="Riedel">Jens Riedel</name><affiliation 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="Beck, Sebastian" sort="Beck, Sebastian" uniqKey="Beck S" first="Sebastian" last="Beck">Sebastian Beck</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><author><name sortKey="Pagel, Kevin" sort="Pagel, Kevin" uniqKey="Pagel K" first="Kevin" last="Pagel">Kevin Pagel</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 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></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2019">2019</date><idno type="RBID">pubmed:30771235</idno><idno type="pmid">30771235</idno><idno type="doi">10.1002/jms.4344</idno><idno type="wicri:Area/PubMed/Corpus">000643</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000643</idno><idno type="wicri:Area/PubMed/Curation">000643</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000643</idno><idno type="wicri:Area/PubMed/Checkpoint">000630</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000630</idno><idno type="wicri:Area/Ncbi/Merge">002111</idno><idno type="wicri:Area/Ncbi/Curation">002111</idno><idno type="wicri:Area/Ncbi/Checkpoint">002111</idno><idno type="wicri:Area/Main/Merge">000656</idno><idno type="wicri:Area/Main/Curation">000653</idno><idno type="wicri:Area/Main/Exploration">000653</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.</title><author><name sortKey="Ickert, Stefanie" sort="Ickert, Stefanie" uniqKey="Ickert S" first="Stefanie" last="Ickert">Stefanie Ickert</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><author><name sortKey="Schwaar, Timm" sort="Schwaar, Timm" uniqKey="Schwaar T" first="Timm" last="Schwaar">Timm Schwaar</name><affiliation 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 sortKey="Grabarics, Mark" sort="Grabarics, Mark" uniqKey="Grabarics M" first="Márk" last="Grabarics">Márk Grabarics</name><affiliation wicri:level="3"><nlm:affiliation>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Riedel, Jens" sort="Riedel, Jens" uniqKey="Riedel J" first="Jens" last="Riedel">Jens Riedel</name><affiliation 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="Beck, Sebastian" sort="Beck, Sebastian" uniqKey="Beck S" first="Sebastian" last="Beck">Sebastian Beck</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><author><name sortKey="Pagel, Kevin" sort="Pagel, Kevin" uniqKey="Pagel K" first="Kevin" last="Pagel">Kevin Pagel</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 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><affiliations><list><country><li>Allemagne</li></country><region><li>Berlin</li></region><settlement><li>Berlin</li></settlement></list><tree><country name="Allemagne"><region name="Berlin"><name sortKey="Ickert, Stefanie" sort="Ickert, Stefanie" uniqKey="Ickert S" first="Stefanie" last="Ickert">Stefanie Ickert</name></region><name sortKey="Beck, Sebastian" sort="Beck, Sebastian" uniqKey="Beck S" first="Sebastian" last="Beck">Sebastian Beck</name><name sortKey="Grabarics, Mark" sort="Grabarics, Mark" uniqKey="Grabarics M" first="Márk" last="Grabarics">Márk Grabarics</name><name sortKey="Linscheid, Michael W" sort="Linscheid, Michael W" uniqKey="Linscheid M" first="Michael W" last="Linscheid">Michael W. Linscheid</name><name sortKey="Pagel, Kevin" sort="Pagel, Kevin" uniqKey="Pagel K" first="Kevin" last="Pagel">Kevin Pagel</name><name sortKey="Riedel, Jens" sort="Riedel, Jens" uniqKey="Riedel J" first="Jens" last="Riedel">Jens Riedel</name><name sortKey="Schwaar, Timm" sort="Schwaar, Timm" uniqKey="Schwaar T" first="Timm" last="Schwaar">Timm Schwaar</name><name sortKey="Springer, Andreas" sort="Springer, Andreas" uniqKey="Springer A" first="Andreas" last="Springer">Andreas Springer</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000653 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 000653 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= pubmed:30771235
|texte= Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:30771235" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |