Dr. Matthew A. Fountain
Assistant Professor of Chemistry and Biology
Biochemistry Program Coordinator
218 Houghton Hall
SUNY College at Fredonia
Fredonia, NY 14063
Tel: (716) 673-3287
Fax: (716) 673 3347
Schedule
Matthew.Fountain@Fredonia.edu

Research

RNA exhibits a variety of biological functions. RNA is used to decode and transport information in the cell and can function as a catalyst, either alone or in conjunction with proteins. Non-canonical structural motifs such as bulges, hairpins, multi branched junctions, and internal loops allow RNA to fold into biologically active macromolecules. Understanding the folding and tertiary structure of RNA will provide a better understanding of how it functions and assist in the development of RNA targeting drugs. I am proposing a thermodynamic and structural study of RNA hairpin loops that focuses on the effect of sequence and loop length on hairpin stability and structure. Naturally occurring hairpin loop sequences obtained from a database of phylogenetically determined secondary structures will be analyzed. Sequence trends observed in this data will be further studied using thermodynamic and structural methods. Thermodynamic studies will reveal the presence of stabilizing interactions within the loop. In addition, the thermodynamic parameters obtained in the study will provide valuable hairpin loop parameters for secondary prediction algorithms (Turner et al. 1988). Structural information like the turning point in the loop, hydrogen bonding, base stacking and sugar geometry will be determined using NMR and molecular modeling methods. These structural features will be used to build a generalized model for RNA hairpin loop structure. This study in conjunction with others will enhance our understanding of RNA structure and eventually lead to the prediction of RNA structure from sequence.