Date of Award

Spring 2021

Project Type


Program or Major

Chemical Engineering

Degree Name

Doctor of Philosophy

First Advisor

Harish Vashisth

Second Advisor

Harish Vashisth

Third Advisor

Nivedita Gupta


In my thesis work, I conducted molecular simulation studies to explore dynamics and interactions in nucleic acids. I began my work by applying conventional molecular dynamics (MD) simulations to study the local and global dynamics of the transactivation response (TAR) element from the type-1 human immunodeficiency virus (HIV-1) and the effect of binding of ligands on the dynamics of TAR RNA. I determined that the TAR RNA structure was stabilized on binding of ligands due to the decreased flexibility in helices that comprise TAR RNA. This rigidity of the TAR RNA structure was coupled with the decreased flipping of bulge nucleotides. I also observed that different initial conformations of TAR RNA converged to similar conformations in the course of MD simulations. Finally, I observed the formation of binding pockets in unliganded TAR structures that could accommodate ligands of various sizes.

After comprehensively exploring the dynamics of TAR RNA with and without ligands, I conducted more specific studies on the interactions that were formed or broken during the (un)binding process of two ligands, a small molecule inhibitor and a helical peptide, from the viral RNA molecules using non-equilibrium simulations. Firstly, I observed that the dissociation of a small molecule is coupled with a base flipping event which I described using physical variables and thermodynamic properties. Secondly, I observed that the dissociation process of a helical peptide is facilitated by a network of hydrogen bonding and salt bridging interactions which are formed across four distinct dissociation pathways. I also resolved the free-energy profiles for each pathway which revealed metastable states and dissociation barriers. Based on the free-energy profiles, I proposed a preferred dissociation pathway and identified one arginine amino acid that plays an important role in the recognition of the peptide by the viral RNA.

Next, I focused on studying a more complex reaction coordinate (RC) that could describe a base flipping mechanism in a double-stranded RNA (dsRNA) molecule using transition path sampling (TPS) methods. Additionally, I used the likelihood maximization method to determine a refined RC based on an ensemble of 1000 transition trajectories created by the path sampling algorithm. The refined RC consisted of two collective variables (CVs), a distance and a dihedral angle between the neighboring nucleotides and the flipping base. I also projected a free-energy profile along the refined RC which revealed three free-energy minima. I proposed that one of the free-energy minima represented a wobbled conformation of the flipping nucleobase. I also analyzed the reactive trajectories which showed that the base flipping is coupled with global conformational changes in a stem-loop of dsRNA.

Outside of studies involving RNA, I conducted conventional MD simulations to study the dynamics of a porphyrin/DNA nanoassembly which revealed the overall left-handed orientation of the nanoassembly. I characterized the resulting porphyrin/DNA system using various physical variables. Overall, my thesis revealed the local and global dynamics of RNA as well as DNA systems, and perturbations to dynamics originating in binding of ligands of various sizes.