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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.
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