USE OF A 3D STRUCTURE DATA-BASE FOR UNDERSTANDING SEQUENCE-DEPENDENT CONFORMATIONAL ASPECTS OF DNA

The roll-twist-slide correlation im the DNA crystal structures that ar e collected in the Nucleic Acid Data Base is analyzed in order to obta in a general understanding of the effects of the nucleotide sequence o n the 3D structure of a dinucleotide step. It is concluded that the di fferences between the pyrimidine bases and the purine bases in terms o f their physical shapes are the major factors that determine the stere ochemical characteristics of the steps through base to backbone and ba se to base interactions. The characteristics are further modulated by the differences between the A:T and G:C base-pairs, Which can be expla ined by enhancement of the purine-pyrimidine asymmetry in the A:T base -pair. (C) 1997 Academic Press Limited.