RNA Folding Simulation by Giff Ransom RNA Folding Simulation

Scientific Background RNA molecules are single stranded copies of a segment of a gene in the DNA. Though a DNA strand is locked in a double helix with its partner, making their three dimensional structure predictable and stable, RNA molecules have no such complementary strand. Rather than staying stretched out in a line, RNA molecules tend to fold back on themselves, and the three- dimensional shape formed by a given strand is important for studying its interaction with other molecules.

Scientific Background As an RNA molecule folds, its bases bond with other complementary bases in the strand, similar to DNA. However, since the sequence isn't symmetrical, it will not match perfectly and form a double helix. Exactly which bases line up with their pair determines the most stable structure of the RNA molecule. Most biologists use two- dimensional simulations when they need to find the ideal configuration for a given RNA molecule. However, these do not provide an accurate representation of the three- dimensional dynamics and emerging structure.

3D Simulation Three-dimensional molecular dynamic simulations give a much better glimpse of the RNA molecule's structure, as well as a more accurate prediction of the actual shape. Ideally, each atom of the molecule would be modeled, but this limits the size and scope of the simulation.

Kurt Grunberger, 2002 The molecular structure can be simplified while still fairly accurately predicting the RNA tertiary structure

My Model I intend to create a 3D RNA folding simulation accurate enough to reproduce experimental configurations for small RNA molecules. Rather than implementing an atomic-level molecular dynamics engine, my model will operate on the higher level of bases and sugars. I aim to achieve computational simplicity while retaining the basic forces and angles between key elements.

So Far… Created a basic simulation using the DNA double helix structure as the resting point for my spring constants Implemented bond length and bond angle springs Verlet integration Electrostatic attraction and repulsion in bases Very basic rigid body (i.e. angular forces) dynamics on bases

Yet to Do… It just doesn’t look right yet – needs a good bit of tweaking Use constraints rather than springs on the bond- lengths Implement torsional potential if necessary