Theoretical investigation of the coupling between the hydrogen transfer and the base pair opening in the adenine–thymine system (original) (raw)
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Physical Chemistry Chemical Physics, 2013
The effect of the stacking interaction on some properties of the guanine-cytosine (G-C) base pair has been studied. In particular, the strength of the hydrogen bonds, the mechanism of hydrogen transfer and the charge redistribution intra-and inter-base pair have been analyzed in the three canonical dimers. The inclusion of both the stacking interaction and of the hydrogen bond interaction between the bases allows us to study both the local and the long-range phenomena of DNA. The comparison of these results with those of the G-C monomeric system supports the idea that the variations of these properties depend from the exact dimer considered and are different for one or another hydrogen bond.
ChemPhysChem, 2013
Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.
Chemical Physics, 2008
Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementi's double ζ basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO4-, to Na+, and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zürich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO4- groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.
Theoretical investigation of hydrogen transfer mechanism in the guanine–cytosine base pair
Chemical Physics, 2006
We have studied the quantum dynamics of the hydrogen bonds in the adenine-thymine base pair. Due to the position of hydrogen atoms, different tautomers are possible: the stable Watson-Crick A-T, the imino-enol A*-T* and the zwitterionic (the form with charge separation) A + -T À and A À -T + structures. The common idea in the literature is that only A-T exists either because the difference of energy among this tautomer and the others is large or because the other structures are transformed quickly in A-T. Here, we show a detailed theoretical study that suggests the following conclusion: A-T is the stablest tautomer, a partially charged system is important and a small amount of the imino-enol A*-T* tautomer is present at any time. The mechanism of passage from A-T tautomer to the others has also been investigated.
Proton Transfer in DNA Base Pairs
Computational Studies of RNA and DNA, 2006
This chapter reviews the theoretical studies performed on single and double proton transfer reactions in guanine-cytosine and adenine-thymine base pairs. The influence of excitation, ionization, protonation and metal cation binding of base pairs in these processes is explored from the analysis of the potential energy surfaces.
Hydrogen bonding in DNA base pairs: Reconciliation of theory and experiment
Journal of The American Chemical Society, 2000
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 + ion (with 123 atoms our largest model for sodium adenylyl-3′,5′-uridine hexahydrate, the crystal of which had been studied experimentally with the use of X-ray diffraction) still shows this disagreement with experiment. The source of the divergence turns out to be the molecular environment (water, sugar hydroxyl groups, counterions) of the base pairs in the crystals studied experimentally. This has been missing, so far, in all theoretical models. After we had incorporated the major elements of this environment in our model systems, excellent agreement between our BP86/TZ2P geometries and the X-ray crystal structures was achieved.