INTERDEPENDENCE OF CONFORMATIONAL VARIABLES IN DOUBLE-HELICAL DNA

DNA exhibits conformational polymorphism, with the details depending o n the sequence and its environment. To understand the mechanisms of co nformational polymorphism and these transitions, we examine the interr elationships among the various conformational variables of DNA. In par ticular, we examine the stress-strain relation among conformational va riables, describing base-pair morphology and their effects on the back bone conformation, For the calculation of base pairs, we use the metho d previously developed to calculate averages over conformational varia bles of DNA. Here we apply this method to calculate the Boltzmann aver ages of conformational variables for fixed values of one particular co nformational variable, which reflects the strain in the structure resp onding to a particular driving stress, This averaging over all but one driving variable smooths the usual rough energy surface to permit obs ervation of the effects of one conformational variable at a time. The stress-strain analyses of conformational variables of base pair slide, twist, and roll, which exhibit characteristic changes during the conf ormational transition of DNA, have shown that the conformational chang es of base pairs are strongly correlated with one another. Furthermore , the stress-strain relations are not symmetrical with respect to thes e variables, i.e., the response of one coordinate to another is differ ent from the reverse direction, We also examine the effect of conforma tional changes in base-pair variables on the sugar-backbone conformati on by using the minimization method we developed. The conformational c hanges of base pairs affect the sugar pucker and other dihedral angles of the backbone of DNA, but each variable affects the sugar-backbone differently, In particular, twist is found to have the most influence in affecting the sugar pucker and backbone conformation. These calcula ted conformational changes in base pairs and backbone segments are con sistent with experimental observations and serve to validate the calcu lation method.