[Study of the flexibility of complementary dinucleoside phosphates by the Monte-Carlo method]

Monte-Carlo calculations have revealed a significant flexibility of the double stranded dinucleoside phosphates AA: TT, AT: AT, TA: TA, GG: CC, GC: GC and CG: CG within the limits of the B-family of forms. Fluctuations of the dihedral angles and of the phase angle of pseudorotation, P, have been found to be 5-20 degrees and 10-20 degrees respectively. The r.m.s. deviation of the helical winding angle varies from 3 degrees to 6 degrees for different dimers. The G: C-containing dimers proved to be more rigid that the A: T-containing ones, though the methyl groups of thymines take part in stabilization of AA: TT and AT: AT dimers. The propeller angles in A: T and G: C pairs are of opposite sing. The pyrimidine-(3'-5')-purine dinucleoside phosphates demonstrate the least stability. All the dimers proved to be more flexible when opened into both grooves than in perpendicular directions. Due to the greater value of the glycosidic angle in the 3'-monomer the base pairs are opened into the wide groove. A connection between opening of the base pairs and bending of the double helix for different nucleotide sequences has been discussed. This might be important for the DNA package in nucleosomes.