Date of Submission

Spring 2013

Academic Program

Chemistry

Project Advisor 1

Swapan Jain

Abstract/Artist's Statement

Riboswitches are RNA molecules that function as direct sensors for intracellular metabolites or metal ions.1 They are most commonly found in the 5 ́-untranslated region (5 ́-UTR) of bacterial mRNAs, but at least one riboswitch class has been discovered in organisms in each of the three domains of life.2 These RNA elements are responsible for the regulation of downstream genes. The binding of specific metabolites or metal ligands to the aptamer region results in a structural conformation that either upregulates (switch turns on) or inhibits (switch turns off) the expression of the downstream gene. The guanine responsive riboswitch (xpt) regulates the expression of genes involved in purine biosynthesis and transport.2 Because of these fundamental associations in certain bacterial pathogens, guanine responsive riboswitches (and other riboswitches) have become targets for the development of antibacterial compounds.2 However two of the concerns with these compounds are their efficiency and their binding ability to these riboswitches. Structural probing of this guanine responsive riboswitch’s secondary structure can enable the investigation of the local structure of the riboswitch in a sequence-dependent manner.1 This allows analysis of any conformational changes due to a ligand, where the rate of spontaneous cleavage due to differences in the riboswitch’s flexibility is measured and the apparent KD can be estimated. This in vitro study examines these structural changes of the guanine responsive riboswitch (xpt), when bound to guanine, and 2,6-dihydrazinopurine (Fig. 4d.) using in-line probing in an effort to estimate their apparent KD values.

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