SOLUTION STRUCTURE OF 2 DNA OLIGONUCLEOTIDES: HIV

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We are working on solving the solution structure of two DNA oligonucleotides: the Hepatitis B Dr1 fragment, and the gerE recognition fragment. These are the DNA fragments recognized by host cell RNA Polymerase II, and by the Bacillus subtilis protein gerE, respectively. The NOESY and COSY NMR spectra of these oligonucleotides were obtained previously. Subsequently, the resonances were assigned and peak volumes measured. We have refined these data using Amber 4.1 molecular dynamics package and used the graphics model to produce a pdb file which we used to run these molecular dynamics calculations. We have produced movies of trajectories to assess weak portions of the structure, and to determine whether a given run is physically reasonable.