Determination of Three-Dimensional Structures of Nucleic Acids by NMR

The chapter reviews the current status of three-dimensional structure determination for nucleic acids, both DNA and RNA, via nuclear magnetic resonance (NMR). The various methods of preparing oligonucleotides, both unlabeled and labeled with stable isotopes, with utility for structure determination are discussed. Different NMR methods required for making nuclear resonance assignments and generation of structural restraints are presented. In particular, techniques to identify hydrogen bonds, use scalar coupling to provide torsion angle restraints, use nuclear Overhauser effect measurements to either estimate or determine internuclear distances, use chemical shifts to discern chemical environments, and enable residual dipolar coupling measurements to ascertain internuclear vector orientation are presented. Various means of structure refinement utilizing the acquired NMR data are also discussed. Assessment of the quality (accuracy and precision) of the structures is presented along with complications such as conformational averaging and possible ways to investigate the dynamic state of nucleic acids in solution.