NONPLANAR GEOMETRIES OF DNA BASES - AB-INITIO 2ND-ORDER MOLLER-PLESSET STUDY

Interactions of DNA bases represent a crucial source of DNA conformational variability. Oligonucleotide crystal studies revealed a number of base-base interactions which seem to be stabilized by nonplanar DNA base amino groups. Therefore, an accurate description of the geometry and deformability of the DNA base amino groups is very important. Here, the second-order Moller-Plesset (MP2) 6-31G*-optimized nonplanar geometries of adenine, cytosine, guanine, thymine, and isocytosine are presented. The amino groups of the bases exhibit significant Sp3 pyramidalization. The dihedral angles between the cytosine and adenine rings and their amino group hydrogen atoms range from 10 to 25-degrees, and the nonplanar cytosine and adenine are 0.4 kcal/mol more stable than the planar molecules. Dihedral angles between the two guanine amino group hydrogen atoms and the guanine ring are 43 and 12-degrees, and the nonplanar guanine is 1.6 kcal/mol more stable than the planar molecule. Isocytosine exhibits amino group properties similar to those of guanine. Selected DNA bases were also optimized using larger basis sets of atomic orbitals: 6-31G**, DZP+, and DZ(2d). The MP2/6-31G** calculations yield results very similar to those of the MP2/6-31G* calculations, while the larger DZP+ and DZ(2d) basis sets indicate an even greater amino group nonplanarity.