BIFURCATED HYDROGEN-BONDS IN DNA CRYSTAL-STRUCTURES - AN AB-INITIO QUANTUM-CHEMICAL STUDY

An ab initio quantum chemical analysis is performed on the intrinsic d eformability of the DNA base amino groups and their role in the base s tacking interactions and conformational variability observed in the DN A crystal structures. The present calculations, made at the HF/6-31G ( NH2) and MP2/6-31G levels of theory, lead to results qualitatively dif ferent from the previous empirical potential studies and demonstrate l imited applicability of the commonly used force fields. The amino grou ps of isolated DNA bases are nonplanar, and the deviation of the amino group hydrogens from the DNA base plane amounts to 0.1-0.5 angstrom. The largest amino group nonplanarity is found for guanine. In the case of cytosine containing complexes, modeling the isolated base pair, th e amino group geometry is determined primarily by the intermolecular g eometry of the hydrogen bonds. The flexibility of the amino groups fac ilitates optimization of the interaction energy under condition of non planar geometry of the complex. On the other hand, the DNA base amino groups are significantly nonplanar, if they participate in the interst rand bifurcated hydrogen bonds or in the interstrand contacts of amino groups. Both phenomena are observed in many DNA crystal structures. T he nonplanar amino group geometry improves the interaction energy. It is demonstrated that the widespread idea of the interstrand repulsive amino group clashes in the DNA is not correct, because close contact b etween two amino groups results in an attractive interaction similar t o that in the bifurcated hydrogen bonds. The only exception represents the steps having crystallographically identical base pairs. It is bec ause attractive amino group interaction requires a highly asymmetric a rrangement of the two amino groups, while any geometry with 2-fold sym metry is repulsive. The ab initio calculations are supplemented by an analysis of the contacts of amino groups in the available B-DNA crysta ls to show that the close amino group contacts are very frequent in th e asymmetric steps. These close contacts are, however, absent in the c entral steps of the crystal structures with crystallographically ident ical strands. This finding agrees with the nonempirical calculations a nd shows that conformational variability of the symmetric steps is sig nificantly restricted by the crystal packing forces.