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Degree

Doctor of Philosophy, Case Western Reserve University, Chemistry, 2006.

Abstract

HIV-1 reverse transcriptase (RT) is a multifunctional enzyme responsible for production of the integration-competent provirus. Along with RNA- and DNA-dependent DNA synthesis it catalyzes degradation of the RNA template via its RNase H activity. The biologically active form of the enzyme is a heterodimer that consists of p66 and p51 subunits. Besides RT several cis-acting elements have been designated in the RNA template sequence that help orchestrate important steps in the overall reverse transcription mechanism. This work brings attention to the thermodynamic stability of RT and its implications to the enzyme function. It also examines the RT behavior when it encounters substrates containing the central termination sequence (CTS). The existence of two different forms of RT during DNA polymerization is postulated. It is proposed that CTS slows down DNA polymerization by shuffling RT into non-productive form. Productive and non-productive forms are speculated to correspond to the structures of RT with substrate bound at the P- and N-sites. The effects of 2-AP substitutions in the polypurine tract (PPT) sequences on the efficiency and accuracy of the PPT removal was investigated. Differences in the local structures of 2-AP at –8 and –13 positions were indistinguishable by steady-state and time-resolved fluorescence techniques. A new fluorescent probe with suitable photophysical properties is characterized by steady-state and time-resolved fluorescence. It is shown that it can be used as a simple and effective probe of the oligonucleotide hybridization state.

Keywords

HIV-1 reverse transcription; AIDS; RT; Fluorescence; 2-aminopurine; pyrrolo-C; pre-steady-state kinetics; Polypurine tract

Advisor

Mary Dicky Barkley

Pages

162p.

Document number: case1149088883
Permalink: http://rave.ohiolink.edu/etdc/view?acc_num=case1149088883

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