Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair

Journal of Biomolecular Structure & Dynamics
M Meyer, J Sühnel

Abstract

Recent experiments have shown that difluorotoluene (F), a nonpolar isostere for thymine (T), codes efficiently and specifically for adenine (A) in DNA replication. F has almost the same shape as thymine but it is unable to form conventional hydrogen bonds with adenine. Therefore, it has been claimed that not hydrogen bonding but shape complementary may be important for the selection of the correct bases by DNA-replicating enzymes. In order to gain deeper insight into structure, charge distribution and energetics of the A-F and A-T base pairs we have performed quantum-chemical ab initio and density functional calculations at the HF, MP2 and B3LYP levels. The interaction energy of the A-F complex amounts to -3.8 kcal/mol (MP2) and is thus substantially smaller than typical ab initio interaction energies for Watson-Crick or non-canonical base pairs. The A-T and A-F complexes are planar and their overall geometries are similar (root-mean-square deviation: 0.4 A). The calculated donor acceptor atom distances in A-T are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. However, A-F shows a base pair opening as compared to A-T. Even though the interaction energy in the ...Continue Reading

References

Aug 1, 1996·Journal of Biomolecular Structure & Dynamics·J SponerP Hobza

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Citations

Feb 4, 2012·Journal of the American Chemical Society·Omid KhakshoorEric T Kool
Mar 14, 2002·Biopolymers·J Sühnel
Apr 9, 2013·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·A K JissyAyan Datta
Jan 9, 2017·The Journal of Chemical Physics·Vanessa J Bukas, Karsten Reuter
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Jul 26, 2000·Journal of the American Chemical Society·Kevin M GuckianEric T Kool
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Jan 1, 1998·The Journal of Organic Chemistry·Kevin M GuckianEric T Kool
Jul 15, 2006·The Journal of Physical Chemistry. a·Judit E SponerJirí Sponer

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