Identifier

etd-11082011-165455

Degree

Doctor of Philosophy (PhD)

Department

Biological Sciences

Document Type

Dissertation

Abstract

RNA recently remained unexploited and is now drawing interest as a potential drug target. The methodology and available drug libraries for RNA targeting/screening are in rudimentary stages. The interactions made by ligands with RNA can be explored for RNA based drug development. The dissertation is composed of 4 chapters. The first chapter focuses on the structural features of RNA and the attempts made to target RNA previously. The second chapter focuses on the development of a small molecule library enriched with substructures derived from RNA binding ligands. For this study a fragment-based approach (fragment based approach is detailed in chapter 2) is used in order to accommodate the conformational flexibility of RNA. The library molecules are used for screening against suitable RNA targets using NMR. We identified at least 5 ligands out of which 2 are novel ligands binding to the ribosomal 16s rRNA. The third chapter is focused on the role of small molecules in inducing conformational changes in an RNA genetic regulatory element called the S-Adenosyl methionine (SAM) SAM-I riboswitch. The mechanistic features of the SAM-I riboswitch to understand the basis for specificity and discrimination and its gene regulation mechanism are reported. To address the conformational dynamics Bacillus subtilis and Thermoanearobacter tencongenesis SAM-I riboswitches in response to SAM binding several conformer mimics are designed, synthesized and characterized using NMR, equilibrium dialysis, and inline probing. The study shows that apart from the conserved residues of the binding pocket, residues downstream of the binding pocket are involved in detecting SAM and assist the binding of SAM to the riboswitch with weak affinity. Our data highlights the capacity of a so-called antiterminator helix from the expression platform to assist the formation of a partial P1 helix of the aptamer domain. A stable P1 is involved in recognition and tight binding of SAM. Our in vitro experiments suggest that the riboswitch could switch from an unbound conformation to tightly SAM bound structure through weakly binding intermediate structures in the presence of the small molecule SAM. The future directions are included in the fourth chapter along with the conclusions.

Date

2011

Document Availability at the Time of Submission

Student has submitted appropriate documentation to restrict access to LSU for 365 days after which the document will be released for worldwide access.

Committee Chair

Aboul-Ela, Fareed

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