1Tools for Simulating and Analyzing RNA Folding

It has recently been found that some RNA functions are determined by the actual folding kinetics and not just the RNA's nucleotide sequence or its native structure. In this poster, we present our new computational tools that can study such functions by simulating the RNA folding kinetics. We present our prediction results of (1) the relative plasmid replication ratesof ColE1 RNAII and its mutants and (2) the relative gene expression rates of MS2 phage RNA and its mutants. These results show that our approach computes the same relative functional rates as seen in experiment. Our computational tools can study RNA folding kinetics such as population kinetics, folding rates, and the folding of particular subsequences. Our method rst builds an ap-proximate map (or model) of the RNA's folding energy landscape. Next, we analyze the population kinetics of the roadmaps by solving the Master Equation. We can also use our new analysis technique, Map-based Monte Carlo (MMC) simulation, to stochastically extract folding pathways from the map. We rst compare our methods with other computational methods working on the complete energy landscape showing that our small roadmap ca