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Influence of metal ion complexation on the metastable fragmentation of DNA hexamers

  • Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0–6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0–3 alkaline earth metal ions (Mg2+ and Ca2+), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C–O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C–O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C–O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases.Here, we study the metastable decay of 5'-d(TTGCTT) in the presence of 0–6 alkaline metal ions (Li+, Na+, K+, Rb+) and 0–3 alkaline earth metal ions (Mg2+ and Ca2+), which replace the corresponding number of protons in the oligonucleotide. We find that all ions studied here stabilize the oligonucleotide with respect to simple 3'-C–O backbone cleavage, but at the same time these metal ions promote a central oligonucleotide deletion accompanied by a concomitant recombination of the terminal d(TT) groups. We find that the quenching of the 3'-C–O backbone cleavage is not ion specific, since it is due to the removal of the phosphate protons upon replacement with the respective metal ions. The central nucleotide deletion competes with the 3'-C–O backbone cleavage channels and is thus promoted through the replacement of the exchangeable protons against metal ions. However, with increasing positive charge density of the metal ions the yield of the central nucleotide deletion further increases. We attribute this effect to the necessity of sufficient proximity of the terminal d(TT) group to allow for their recombination on this reaction path. Hence, the formation of a reactive conformer is mediated by the metal ions.zeige mehrzeige weniger

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Metadaten
Autor*innen:A. Piecarczyk, Ilko Bald, H.D. Flossadóttir, B. Ómarsson, A. Lafosse, O. Ingólfsson
Dokumenttyp:Zeitschriftenartikel
Veröffentlichungsform:Verlagsliteratur
Sprache:Englisch
Titel des übergeordneten Werkes (Englisch):The European physical journal D
Jahr der Erstveröffentlichung:2014
Verlag:Springer
Verlagsort:Berlin
Jahrgang/Band:68
Erste Seite:146, 1
Letzte Seite:7
Freie Schlagwörter:DNA oligonucleotides; Mass spectrometry; Matrix-assisted laser desorption/ionization; Metastable decay
DOI:10.1140/epjd/e2014-40838-7
ISSN:1434-6060
Verfügbarkeit des Dokuments:Datei im Netzwerk der BAM verfügbar ("Closed Access")
Datum der Freischaltung:20.02.2016
Referierte Publikation:Ja
Datum der Eintragung als referierte Publikation:13.08.2014
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