Investigation of oligonucleotide structures by multi-dimensional nuclear magnetic resonance methods

Interproton distances derived from nuclear Overhauser effect is the major information extracted from NMR spectroscopic data in structure determination of biomolecules. For large biomolecules, severe spectral overlap in 2D NOESY becomes a serious problem by limiting the accurate measurements of NOESY volumes. Spreading the spectral dimension into the third dimension is one way to overcome this problem. Solution structure of a DNA three way junction containing unpaired nucleotides is studied using 3D NOESY-NOESY methods. The Hybrid-Hybrid matrix refinement method described in this thesis provides an accurate and robust means to extract quantitative information from the 3D NOESY-NOESY. This methodology combines the computational efficiency of 2D methods and the spectral dispersion of 3D NOESY-NOESY. Though RNA exhibits variety of secondary structures of biological importance structural information of the RNA structural motifs are limited due to difficulties in synthesizing NMR quantities of oligomers and the lack of spectral dispersion in RNA. The in-vitro transcription method using T7 RNA polyemerase enzyme developed for the synthesis of short RNA oligomers in NMR quantities is described in this thesis. The solution structure of an RNA duplex containing a bulged Adenosine is studied by NMR spectroscopy and relaxation matrix refinement methods