Structural dynamics of retroviral genomes Public Deposited

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  • March 22, 2019
  • Grohman, Jacob K.
    • Affiliation: School of Medicine, Department of Biochemistry and Biophysics
  • Retroviral RNA genomes form myriad structures that are governed by critical interactions with either the nucleocapsid (NC) protein or the nucleocapsid domain of Gag polyprotein. I have pioneered two powerful technologies, based on SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension), to explore interactions between NC and the RNA genomes of the xenotropic murine leukemia virus related virus (XMRV) and the Moloney murine leukemia virus (MuLV). In the first approach, ultra-sensitive SHAPE, I developed a two-color capillary electrophoresis instrument with low attomole (10-18) sensitivity. New analysis approaches and the high sensitivity of this instrument allowed me to obtain unprecedented single-nucleotide resolution structures from authentic RNA genomes of MuLV and XMRV. In the second approach, time-resolved SHAPE, I used a fast acting SHAPE reagent to reveal the structural biogenesis of NC binding to the MuLV retroviral RNA genome. The data generated using these SHAPE-based technologies allow me to propose detailed mechanisms for both the specific RNA binding and the chaperone activities of NC.
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  • ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Biochemistry and Biophysics.
  • Weeks, Kevin

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