Conformational analysis of nucleic acid molecules with flexible furanose rings in dihedral angle space

Abstract

ABSTRACT The computational algorithm that works in the coordinate space of dihedral angles (i.e., bond lengths and bond angles are kept fixed and only rotatable dihedral angles are treated as independent variables) is extended to deal with the pseudorotational motion of furanose rings by introducing a variable of pseudorotation. Then, this algorithm is applied to a distance geometry calculation that generates three-dimensional (3D) structures that are consistent with given constraints of interatomic distances. This method efficiently generates 3D structures of an RNA hairpin loop which satisfy a set of experimental NMR data. 0 1996 by John Wiley & Sons, Inc. Introduction C omputational chemistry has made various contributions to conformational analyses of macromolecules. Many computer programs have been developed to analyze their static and/or dy- namic conformations at the atomic level. They can be classified into two types from the viewpoint of independent variables used to describe conforma- tions of macromolecules: one in which Cartesian *Author to whom