Date of Award
Spring 2025
Language
English
Embargo Period
4-30-2025
Document Type
Master's Thesis
Degree Name
Master of Science (MS)
College/School/Department
Department of Chemistry
Program
Chemistry
First Advisor
Alan Chen
Committee Members
Alan Chen, Michael Yeung, Sweta Vangaveti
Keywords
miRNA, miR-34a, mRNA, argonaute, AGO2, molecular dynamics simulations
Subject Categories
Computational Chemistry
Abstract
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 the miR-34 and NOTCH1 duplex inside of AGO2 with only the seed region base paired. The resulting structure was then simulated in a series of all atom molecular dynamics (MD) simulations with distance restraints being applied to the base pairs after the central bulge to investigate how the supplemental and tail region of the miRNA moves from the P channel to the N channel to bind with the mRNA.
License
This work is licensed under a Creative Commons Attribution 4.0 International License.
Recommended Citation
Karadiakos, Christina MS, "Investigation of the Binding Mechanism Between the Supplemental and Tail Regions of miRNA and mRNA Within Argonaute 2" (2025). Electronic Theses & Dissertations (2024 - present). 164.
https://scholarsarchive.library.albany.edu/etd/164