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Comparison of the fragmentation behavior of DNA and LNA single strands and duplexes

  • 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-LNADNA 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.zeige mehrzeige weniger

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Autor*innen:Stefanie Ickert, Timm Schwaar, A. Springer, M. Grabarics, Jens RiedelORCiD, S. Beck, K. Pagel, M. W. Linscheid
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):Journal of Mass Spectrometry
Jahr der Erstveröffentlichung:2019
Organisationseinheit der BAM:1 Analytische Chemie; Referenzmaterialien
1 Analytische Chemie; Referenzmaterialien / 1.5 Proteinanalytik
Verlag:Wiley
Jahrgang/Band:54
Ausgabe/Heft:5
Erste Seite:402
Letzte Seite:411
DDC-Klassifikation:Naturwissenschaften und Mathematik / Chemie / Analytische Chemie
Freie Schlagwörter:Collision induced dissociation (CID); Double strands; Ion mobility spectrometry; Locked nucleic acids; Oligonucleotide fragmentation
Themenfelder/Aktivitätsfelder der BAM:Chemie und Prozesstechnik
DOI:10.1002/jms.4344
Verfügbarkeit des Dokuments:Datei im Netzwerk der BAM verfügbar ("Closed Access")
Datum der Freischaltung:06.03.2019
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:06.03.2019
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