THE ASSESSMENT OF THE GEOMETRY OF DINUCLEOTIDE STEPS IN DOUBLE-HELICAL DNA - A NEW LOCAL CALCULATION SCHEME

In this paper, we develop a new local Euler-angle-based scheme for ass essing the internal kinematics or geometry of a general dinucleotide s tep in double-helical DNA. The geometry of a dinucleotide step is comp letely defined by: (1) the base-pair parameters that describe the rela tive position and orientation of one base with respect to the other in a standard Watson-Crick base-pair, and (2) the step parameters that d escribe the relative position and orientation of the two base-pairs. T he key feature of our scheme is that it makes use of the concept of a mid-step reference frame, In addition to ensuring that identical value s of step parameters are obtained irrespective of the direction of rec koning of a dinucleotide step (in the 5'-->3' direction along either s trand), this mid-step-triad concept leads to local definitions of the step parameters that render them independent of the overall global con formation of the oligomer in question. In addition to presenting our o wn calculation scheme we also examine critically the most widely used package for the calculation of some of the step and base-pair paramete rs, viz, the NEWHELIX suite of programmes by R. E. Dickerson. Finally, a dodecamer, a decamer and an octamer are arbitrarily selected from a public data-base (N.D.B at Rutgers), and their step parameters are ca lculated by using both NEWHELIX and the proposed scheme. A comparison of the results is given whereby it is shown that for the step paramete rs: Helical Twist and Slide, and the base-pair parameters Propeller an d Buckle, NEWHELIX and our proposed scheme give rather similar values. Substantial differences are seen, however, in the case of Rise. Two a lternative definitions are given by NEWHELIX for the calculation of Ro ll and Tilt. Whereas one definition agrees well with our proposed sche me, the other is substantially different. (C) 1995 Academic Press Limi ted