Poster abstracts

Poster number 2 submitted by Robert Forties

Computational Prediction of Local Melting in Cyclized Double-Stranded DNA

Robert Forties (The Ohio State University Department of Physics), Ralf Bundschuh (The Ohio State University Department of Physics)

Abstract:
Many biological processes, including gene regulation, binding of transcription factors, and DNA packaging, require the formation of DNA loops. We posit that melted segments of double-stranded DNA (dsDNA) are more flexible that closed dsDNA, and therefore that dsDNA constrained to a loop may melt locally to reduce the overall bending energy for the loop. We computationally predict sites where local melting may be observed in cyclized dsDNA molecules approximately 100 basepairs (bps) in length. The free energy cost of melting a segment of dsDNA is taken to be the sum of the stacking energies for the open bps and the loop entropy for the open segment. We use a generalized semiflexible polymer model, where melted sites may have elasticities that differ from that of closed dsDNA, and estimate the flexiblilty of these sites needed to explain results of cyclization experiments. The predictions presented here may be compared with experimental measurements of the frequency with which melting occurs made using Forster resonance energy transfer (FRET).

Keywords: DNA loops, DNA melting