oru.sePublications
Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Distinct Hydroxy-Radical-Induced Damage of 3-Uridine Monophosphate in RNA: A Theoretical Study
Beijing Intitute of Technology.
Örebro University, School of Science and Technology.
2009 (English)In: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, no 10, p. 2394-2402Article in journal (Refereed) Published
Abstract [en]

Cutting ties: Strand scission and base release in hydroxy-radical adducts of 3-uridine monophosphate (UMP) have been explored by using density functional theory. The presence of the ribose 2-OH group and the resultant formation of low-barrier hydrogen bonds with oxygen atoms of the 3-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions (see picture).RNA strand scission and base release in 3-uridine monophosphate (UMP), induced by OH radical addition to uracil, is studied at the DFT B3LYP/6-31+G(d,p) level in the gas phase and in solution. In particular, the mechanism of hydrogen-atom transfer subsequent to radical formation, from C2 on the sugar to the C6 site on the base, is explored. The barriers of (C2-)H2a abstraction by the C6 radical site range from 11.2 to 20.0 kcal mol-1 in the gas phase and 14.1 to 21.0 kcal mol-1 in aqueous solution, indicating that the local surrounding governs the hydrogen-abstraction reaction in a stereoselective way. The calculated N1C1 (N1-glycosidic bond) and -phosphate bond strengths show that homolytic and heterolytic bond-breaking processes are largely favored in each case, respectively. The barrier for -phosphate bond rupture is approximately 3.2-4.0 kcal mol-1 and is preferred by 8-12 kcal mol-1 over N1-glycosidic bond cleavage in both the gas phase and solution. The -phosphate bond-rupture reactions are exothermal in the gas phase and solution, whereas N1C1 bond-rupture reactions require both solvation and thermal corrections at 298 K to be energetically favored. The presence of the ribose 2-OH group and its formation of low-barrier hydrogen bonds with oxygen atoms of the 3-phosphate linkage are highly important for hydrogen transfer and the subsequent bond-breakage reactions.

Place, publisher, year, edition, pages
Weinheim: Wiley-VCH Verlagsgesellschaft, 2009. Vol. 15, no 10, p. 2394-2402
National Category
Natural Sciences Chemical Sciences
Research subject
Chemistry
Identifiers
URN: urn:nbn:se:oru:diva-6320DOI: 10.1002/chem.200801654ISI: 000264029500021PubMedID: 19156657Scopus ID: 2-s2.0-62349138274OAI: oai:DiVA.org:oru-6320DiVA, id: diva2:212305
Available from: 2009-04-21 Created: 2009-04-21 Last updated: 2017-12-13Bibliographically approved

Open Access in DiVA

No full text in DiVA

Other links

Publisher's full textPubMedScopus

Authority records BETA

Eriksson, Leif A.

Search in DiVA

By author/editor
Eriksson, Leif A.
By organisation
School of Science and Technology
In the same journal
Chemistry - A European Journal
Natural SciencesChemical Sciences

Search outside of DiVA

GoogleGoogle Scholar

doi
pubmed
urn-nbn

Altmetric score

doi
pubmed
urn-nbn
Total: 33 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf