Date of Award


Document Type

Honors Thesis

Degree Name

Bachelor of Science



Advisor/Committee Chair

Alan Chen


MicroRNAs (miRNA) are a class of small non-coding RNAs that play a key role in gene silencing. miRNAs form an RNA-induced silencing complex (RISC) with the argonaute 2 (AGO2) protein in order to control gene expression through silencing messenger RNAs (mRNA). The ability for a miRNA-mRNA complex to fit into AGO2 and form the RISC is based on the location and characteristics of a central bulge, but the mechanism and interactions that lead to a functional RISC remain unknown. Using available experimental data, we modeled complexes composed of a miRNA (miR-34a) and different mRNA sequences inside of AGO2. The resulting structures were then simulated in all atom molecular dynamics (MD) simulations with and without magnesium ions. To quantify how well the miRNA-mRNA complex fits into AGO2, the bonds between the seed region of the miRNA and mRNA as well as the contacts between the miRNA phosphate backbone and AGO2 were measured over the course of the simulation.

Creative Commons License

Creative Commons Attribution-NonCommercial 4.0 International License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License

Included in

Chemistry Commons