PHYSICAL CHEMISTRY OF RECOMBINATIONAL INTERMEDIATES

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The goals of this project involve the structural, dynamic, thermodynamic and biological characterization of branched nucleic acid structures, the nucleic acid junctions. These structures are central intermediates in the process of recombination, and they or their analogs are also involved in replication, viral integration, and telomere synthesis. These processes are all central to the functioning of DNA living organisms. Recombination, in particular, is the process through which genetic diversity is generated in all living species. This is a particularly sensitive point in the life cycle, since it occurs during meiosis, the generation of gametes for the next generation; any errors at this stage can result in birth defects. The system to be exploited here makes these structures tractable to high resolution physical probes, such as NMR and X-ray Crystallography, for the first time. While naturally occurring nucleic acid junctions are inherantly unstable, due to sequence symmetry, the system utilized here minimizes this symmetry, stabilizing the junctions, without perturbing the molecules chemically. The specific aims for the project period include determining the structure of the junctions by crystallography, solution scattering and NMR, as well as characterizing the twisting and bending dynamics of junctions by ligation closure experiments. We plan intensive exploration of the details of the branch point migratory isomerization process which junctions can undergo, as well as its sensitivity to drugs and environmental chemicals. We intend to investigate the biological role of junctions as substrates for resolvase enzymes, as well as searching for them in cells by immune techniques.