A standard reference frame for the description of nucleic acid base-pair geometry

摘要

A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to conflicting interpretations of the same structure. For example, parts of a structure that appear "normal" according to one computational scheme may be highly unusual according to another and vice versa. It is thus difficult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures. In order to resolve these issues, a group of researchers who create and use the different software packages have proposed the standard base reference frames outlined below for nucleic acid conformational analysis. The definitions build upon qualitative guidelines established'previously to specify the arrangements of bases and base-pairs in DNA and RNA structures. Base coordinates are derived from a survey of high-resolution crystal structures of nucleic acid analogs stored in the Cambridge Structural Database (CSD). The coordinate frames are chosen so that complementary bases form an ideal, planar Watson-Crick base-pair in the undistorted reference state with hydrogen bond donor-acceptor distances, C1'...C1' virtual lengths, and purine N9-C1'...C1' and pyrimidine N1-C1'...C1' virtual angles consistent with values observed in the crystal structures of relevant small molecules. Conformational analyses performed in this reference frame lead to interpretations of local helical structure that are essentially independent of computational scheme. A compilation of base-pair parameters from representative A-DNA, B-DNA, and protein-bound DNA structures from the Nucleic Acid Database (NDB)~4 provides useful guidelines for understanding other nucleic acid structures.