EXAMINATION OF LOCAL AND LONG DISTANCE EFFECTS OF NUCLEOTIDE SUBSTITUTIONS IN SECONDARY RNA STRUCTURES

Researchers are currently designing RNAs for diagnostic and therapeutic applications, and an understanding of the factors that affect stability of these RNAs could inform the design of new RNA constructs. This project involved the use of in silico experiments to investigate the effects of different nucleotide substitutions on the stability of RNAs using EteRNA, a publicly available, online computer modeling software developed by researchers at Carnegie Mellon and Stanford Universities to study RNA folding. It was determined that while many types of single nucleotide substitutions can alter the stability of secondary structures, such as loops, the stability of adjacent structures was not affected.