Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment

C. Fonseca Guerra, F.M. Bickelhaupt, J.G. Snijders, E.J. Baerends

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Abstract

Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson - Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine - thymine (AT) and guanine - cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A - T and G - C bond enthalpies (-12.1 and -21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields -11.8 and -23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5'- deoxyribose monophosphate as the substituents at N9 and N1 of the purine and pyrimidine bases, respectively. Even the BP86/DZP geometry of the Watson- Crick-type dimer of deoxyadenylyl-3',5'-deoxyuridine including one Na
Original languageEnglish
Pages (from-to)4117-4128
Number of pages11
JournalJournal of the American Chemical Society
Volume122
Issue number17
DOIs
Publication statusPublished - 2000

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