P Nmr and Two-dimensional Nmr Spectra of Nucleic Acids and 2d Noesy-constrained Molecular Mechanics Calculations for Structural Solution of Duplex Oligonucleotides*

Nuclear magnetic resonance spectroscopy is now able to provide detailed 3-dimensional structures and dynamics of oligonucleotide duplexes and nucleic acid complexes (1,2). Unfortunately, of the six torsional angles that largely define the backbone structure, only the four involving the deoxyribose ring have been shown to be directly amenable to analysis by NMR techniques. In fact for modest-sized oligonucleotide duplexes, determination of these torsional angles through measurement of three-bond coupling constants is very difficult. Using the time development of cross peak intensities in 2D-N0ESY NMR spectra, a number of workers (3-10) have been able to qualitatively or semi-quantitatively determine whether two protons are within 3-5 ft of each other (11). From these NOESY-derived distances and constrained molecular dynamics or distance geometry (12) calculations, models for these duplexes may be determined. While base pairing and stacking interactions can often be adequately demonstrated, detailed conformational information, especially with regard to the deoxyribose phosphate backbone, is often lacking.