Dynamic Structure of Nucleic Acid Duplexes

Abstract

Sequence-dependent structural variations in nucleic acids are important for the protein-nucleic acid and RNA-DNA interactions essential for life. Furthermore, structural variations are important factors in the binding of extrinsic agents, such as mutagens or drugs. While an understanding of these subtle structural variations may have biological significance, the nucleic acid double helix also provides a challenging problem. Since we can fairly readily determine that a double helix is right- (probably) or left-handed, we know a priori the structure nearly as well as one often can determine a protein structure. It is therefore incumbent upon us to determine the structure accurately and to high-resolution if we wish to distinguish the three-dimensional, sequence-dependent structural subtleties. The constraints in constructing a double helix from complementary nucleic acid strands via base-stacking with two or three interbase hydrogen bonds in each base pair also suggests that the double helix should assume a fairly stable structure; modeling indicates that some degree of conformational flexibility may still be present though.KeywordsDouble HelixDistance RestraintConformational EnsembleConformational FluctuationInterproton DistanceThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.