Conformational analysis of polynucleotide chains. Double-stranded structures.

Conformational anal. of double-stranded helical polynucleotides was carried out in terms of internal and external parameters, using semiempirical energy potential functions. The results obtained show that the structures proposed on the basis of the x-ray anal. for A-DNA and RNA's are almost identical to those corresponding to the conformational energy min., whereas that proposed for B-DNA still appears to suffer from conformational strains. On the other hand, the B-DNA structure theor. predicted is stabilized by both van der Waals energy and possible specific interactions with water mols. and counterions. This may explain the stability of the B form with respect to the A form at high relative humidity and ionic strength. A possible role of the A + T fraction in stabilizing the B-type DNA emerges in connection with its preferential ability to bind ions. This agrees with the results on the cryst. structures of GpC and ApU. For RNA's, the occurrence of only A-type structures is explained as being due to the C(3')-endo puckering of ribose in a double helix