CRYSTALLOGRAPHIC STUDIES OF DNA AND RNA POLYMERASES

Cornell University, Ithaca NY

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Abstract

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. The overall goal of this project is to provide a structural basis for understanding the mechanisms of initiation and elongation by DNA and RNA polymerases, their transitions from initiation to elongation phases, the regulation of polymerases by factors and the mechanisms by which these polymerases assure that the correct nucleotide is inserted. This objective will be achieved by determining the crystal structures of polymerases complexed with functionally associated proteins and bound to appropriate DNA or RNA substrates, as well as by appropriate biochemical experiments. Further, we aim to establish the structures of component assemblies of the replisome. These include a replication fork complex between DNA polymerase III, tau and a forked-DNA substrate, as well as the structure of the primasome that includes Thermus aquaticus DnaB helicase complexed with the DnaG primase bound to their DNA substrate. Additionally, the structure of the DnaB helicase bound to its DNA and nucleotide substrates as well as the helicase binding domain of DnaG and helicase loader protein. The structural basis of the initiation of DNA synthesis by the protein primed phi29 DNA polymerase and the mechanism of its transition to the elongation phase will be determined through a series of structures of intermediate states in this transition. The regulation of transcription initiation by the multi-subunit RNA polymerase from E. coli will be examined from its structures complexed with the gal and lac operon promoter DNAs and the catabolite gene activator protein regulator transcription factor.