Talk abstracts

Talk on Saturday 11:00-11:20am submitted by Mina Sumita

Conformationally restricted nucleotides as a biophysical probe of RNA thermodynamics, catalysis, and protein binding

Minako Sumita (Department of Biochemistry and Molecular Biology, Michigan State University), Kristine R. Julien (Department of Biochemistry and Molecular Biology, Michigan State University), Po-Han Chen, Ite Laird-Offringa (Department of Biochemistry and Molecular Biology, University of Southern California), Charles G. Hoogstraten (Department of Biochemistry and Molecular Biology, Michigan State University)

Abstract:
The 2’-OH is a unique character of RNA, and it affects RNA structure and function via the ribose conformation. Ribose conformation has previously been studied with 2’-OH modifications, such as methoxy (2’-OMe), fluorine (2’-F), and amino (2’-NH2) groups. Each modification has a preference of either C2’-endo or C3’-endo conformation; however, it is not 100%. Therefore, we use locked nucleic acid (LNA) to study the functional and thermodynamic effects of sugar conformation. LNA is typically used for antisense RNA chemistry and is locked completely into the C3’-endo conformation via a methylene linkage between 2’-O and 4’-C. We used well studied RNA structures (UUCG tetra loop and leadzyme) as a model. We tested the functional importance of sugar pucker dynamics in leadzyme catalysis. Structural and thermodynamic effects of ribose conformation are examined with the highly stable UUCG tetraloop. Finally, we are undertaking a preliminary analysis of LNA substitution effects on protein recognition of a structured RNA. As a result, LNA is useful as a probe of the functional and stability effects of structured RNA molecules.

Keywords: RNA catalysis, RNA structure, RNA-protein recognition