This proposal outlines high resolution NMR studies of the conformation, dynamics and interactions in DNA duplexes and their modified analogs containing one to two turns of helix. The conformation of nucleic acids will be investigated by a distance geometry analysis of all proton-proton distances of less than 5 angstroms evaluated from two dimensional nuclear Overhauser effect measurements. The dynamics of nucleic acids will be probed from inversion recovery kinetic measurements of the resolved and assigned imino protons to measure hydrogen exchange rates and activation barriers in DNA duplexes at the individual base pair level. Our research will focus on the following areas: (1) The sequence dependence of the conformation and dynamics of DNA with special emphasis on differences between alternating (purine-pyrimidine) sequences compared to (purine).(pyrimidine) sequences. (2) The effect of counterion, solvent polarity and temperature on DNA conformational transitions with a priority towards elucidating the unique structure of alternating (dA-dT)n and (dG-dT)n.(dA-dC)n duplexes in saturating CsF solution and in alcohol-water solutions containing divalent ions. (3) The conformational and hydrogen exchange characteristics at the junction between right-handed A and B forms of DNA and between right and left handed DNAs from studies of synthetically tailored duplexes. (4) The structural details of chain folding in hairpin and bulge loop formation and the contributions of base sequence to the stability of loops and their adjoining stem regions. (5) The conformation and dynamics at and adjacent to purine.pyrimidine, purine.purine, and pyrimidine.pyrimidine base pair mismatches, as well as helix interruption sites containing an extra purine or pyrimidine base imbedded in DNA duplexes. (6) The structure of the covalent modification site on incorporation of 06-methyl guanosine into DNA duplexes and the elucidation of the potential pairing of the alkylated guanosine with all other bases to delineate the origin of transition and transversion errors in replication. (7) The conformation of the metabolically active carcinogen N-2-acetyl aminofluorene when covalently bound to guanosine in B-DNA and the elucidation of the details of the insertion-denaturation model for aromatic carcinogen DNA complexes. (8) The structural distortions at the cis-dichloroamine platinum coordination site on adjacent guanosines and at the thymine dimerisation site in a DNA duplex and an estimation of the type and extent of the perturbation in the base pairing and the sugar phosphate on either side of the modification site.
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