Jump to main content
Jump to site search

Issue 9, 2006
Previous Article Next Article

Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Author affiliations

Abstract

Oxidized cytosine product 5-hydroxyuracil has been shown to be the major chemical precursor for the GC to AT transition, the most frequent substitution mutation observed in aerobic organisms. We have calculated the interaction energy of base-pair formation involving uracil or 5-hydroxyuracil, which is formed in cells by oxidative deamination of cytosine, bound to any of the natural DNA bases, A, C, G, and T, and discuss the effects of the hydroxyl group in this respect. The base-pair geometries and energies were calculated using the 6-311G(dp) basis set under four conditions: using density functional theory (DFT) without out basis set super-position error (BSSE) correction, using DFT with BSSE correction of geometries and energies, using Møller–Plesset second order perturbation theory (MP2) without BSSE correction, and using MP2 with BSSE geometry and energy correction. We find that the hydroxyl group of 5-HO-U (relative to U) has little effect on the base-pairs with A, C or one conformation of T, while making a substantial energy difference in base-pairs involving G or a different conformation of T. For most of the complexes studied, the BSSE-corrected energies at the DFT and MP2 levels of theory agreed to within 0.5 kcal.

Graphical abstract: Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels

Back to tab navigation

Supplementary files

Article information


Submitted
15 Feb 2006
Accepted
10 Mar 2006
First published
30 Mar 2006

Org. Biomol. Chem., 2006,4, 1741-1745
Article type
Paper

Ab initio base-pairing energies of uracil and 5-hydroxyuracil with standard DNA bases at the BSSE-free DFT and MP2 theory levels

D. E. Volk, V. Thiviyanathan, A. Somasunderam and D. G. Gorenstein, Org. Biomol. Chem., 2006, 4, 1741
DOI: 10.1039/B602263D

Social activity

Search articles by author

Spotlight

Advertisements