Date of Award


Document Type

Honors Thesis

Degree Name

Bachelor of Science



Advisor/Committee Chair

Alan Chen


RNA-RNA junctions between hairpin loops are a common feature of RNA retroviruses, accounting for their high mechanical stability. Dimerization of Moloney Murine Leukemia Virus (MMLV) is dependent on H3 stem loop interactions, which are an example of such a junction. H3 in MMLV dimerizes via a two base pair hairpin loop enhanced by two adjacent stacking bases. All atom, explicit solvent molecular dynamics pulling simulations were performed to examine the stability of the junction. Salt concentrations and temperatures were varied and unstacking times of the flanking bases and breaking times of the kissing bonds were calculated. Survival curves revealed that increasing salt concentration, decreasing temperature, decreasing force, and having two adenine stacking bases as opposed to one guanine and one adenine stacking bases stabilizes the flanking bases of the complex. Additionally, breaking of bonds is made faster by increased temperature, pulling force, and two adenine stacking bases over one guanine and one adenine stacking bases. Increased salt decreases the breaking rate, but only at low temperatures. Simulation results were compared with single molecule optical tweezers experiments.

Included in

Chemistry Commons