Ab initio base-pairing energies of an oxidized thymine product, 5-formyluracil, with standard DNA bases at the BSSE-free DFT and MP2 theory levels.
Oxidation of the thymine methyl group produces two stable products, non-mutagenic 5-hydroxymethyluracil and highly mutagenic 5-formyluracil. We have calculated the interaction energy of base-pair formation involving 5-formyluracil bound to the natural DNA bases adenine (A), cytosine (C), guanine (G), and thymine (T), and discuss the effects of the 5-formyl group with respect to similar base-pairs containing uracil, 5-hydroxyuracil, thymine (5-methyluracil), and 5-hydroxycytosine. The interaction geometries and energies were calculated four ways: (a) using density functional theory (DFT) without basis set super-position error (BSSE) corrections, (b) using DFT with BSSE correction of geometries and energies, (c) using Møller-Plesset second order perturbation theory (MP2) without BSSE correction, and (d) using MP2 with BSSE geometry and energy correction. All calculations used the 6-311G(d,p) basis set. Notably, we find that the A:5-formyluracil base-pair is more stable than the precursor A:T base-pair. The relative order of base-pair stabilities is A:5-Fo-U > G:5-Fo-U > C:5-Fo-U > T:5-Fo-U.
Volk
David E
DE
Sealy Center for Structural Biology and Molecular Biophysics, Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555-1157, USA.
Thiviyanathan
Varatharasa
V
Somasunderam
Anoma
A
Gorenstein
David G
DG
D020029:Base Pairing; D002138:Calibration; D004247:DNA / Q000737:chemistry*; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008962:Models, Theoretical; D009153:Mutagens; D009690:Nucleic Acid Conformation; D010100:Oxygen / Q000737:chemistry; D012984:Software; D013816:Thermodynamics; D013936:Thymidine / Q000737:chemistry*; D013941:Thymine / Q000737:chemistry; D014498:Uracil / Q000031:analogs & derivatives* / Q000737:chemistry / Q000494:pharmacology
D009153:Mutagens; C007777:5-formyluracil; D014498:Uracil; D004247:DNA; D013941:Thymine; D010100:Oxygen; D013936:Thymidine