Investigating the Catalytic Mechanism of the HDV Ribozyme

University Of Chicago, Chicago IL

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Abstract

Defining the Catalytic Mechanism of the HDV Ribozyme. The hepatitis delta virus (HDV) is a satellite virus of the human pathogen hepatitis B; coinfection with HDV exacerbates the symptoms of hepatitis B. This genome contains the sequence for a ribozyme essential for viral replication. Although our understanding of ribozyme catalysis has advanced enormously in the two and half decades since their discovery, their mechanisms of catalysis remain largely undefined. Although crystal structures for many of these ribozymes have been solved, significant discrepancies between the structural data and functional experiments remain with many ribozyme systems including the HDV ribozyme. In this work, we will combine nucleic acid chemistry with quantitative enzymatic characterization to develop powerful approaches for probing fundamental features of structure, catalysis, and dynamics in the HDV ribozyme. Experiments will be directed at three big questions in the ribozyme field: (1) Do the available structures provide an accurate representation of the catalytic architecture? (2) How does the ribozyme mediate general acid/base catalysis? (3) How do alterations in flexibility (dynamics) of the ribose phosphate backbone affect function? We expect that experiments described herein will not only yield fundamental insights into the HDV ribozyme mechanism, in particular, but will have general implications for all RNAs.