The determination of three--dimensional structures of macromolecules in solution is of central importance to understanding detailed molecular mechanisms of function. This project currently focuses on drug-DNA interaction and the primary and conformational structure of oligosaccharides and polysaccharides and polysaccharides. Two-dimensional NMR methods are used to measure inter-proton distances and scalar coupling constants within complex molecular systems. The coupling constants determine dihedral angles and are translated into distance constraints which, along with NOE distance constraints, are used in distance geometry calculations to generate a three-dimentional structure. The calculations are not unique, and a family of structures is determined; similar to comparisons of multiple molecular dynamics trajectories to completely sample conformational space. For the d(ATATCGTACGATAT)2- Daunomycin system, the free oligonucleotide is seen to adopt a general B- DNA structure; however, there are clear perturbations of the geneic B- structure. The major difficulties in the procedure is the under- determination of the phosphodiester backbone. This may be addressed by new approaches to complete resonance assignment and NOE measurement utilizing heteronuclear techniques, specifically 1-H/13-C HMOC and HMOC-NOESY experiments. Isotopic labeling with 13-C in combination with three-dimensional heteronuclear NMR methods have been developed to overcome long standing structural problems in primary structure determinations of polysaccharides and oligosaccharides by NMR spectroscopy. Conventional H-H correlation techniques suffer from small scalar coupling constants for two crucial residues, e.g. galactosyl and mannosyl. This difficulty may be overcome by uniform labeling of the polysaccharide with 13-C and utilization of new experiments (HCCH TOCSY and HCCH COSY) which take advantage of 1-bond 13-C- 13-C scalar coupling. This coupling is large and conformationally independent. Studies with E, coli polysaccharides K1, K14, and K15 indicate the generality of this approach and the feasibility of extending the methods to more complex carbohydrates and to glycoproteins. Extensions of these methods to measure NOEs in complex carbohydrates is part of collaborative efforts on oligosaccharide conformations within the Laboratory (see W.Egan).
