Poster abstracts

Poster number 12 submitted by Robert Forties

A model for the flexibility of double-stranded DNA incorporating local melting

Robert A. Forties (Department of Physics, The Ohio State University), Ralf Bundschuh (Department of Physics, The RNA Group, Biophysics Graduate Program, The Ohio State University), Michael Poirier (Department of Physics, Biophysics Graduate Program, Ohio State Biochemistry Program, The Ohio State University)

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 than 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 J factors, which are proportional to the probability of cyclization, over a range of temperatures. Our model predicts that cyclization is more favorable at higher temperatures, as more local melting will occur. We also predict that DNA molecules containing segments with low melting temperatures will cyclize more readily than predicted by the standard worm-like chain model.

We measure J factors in cyclization experiments for a 200 basepair (bp) fragment of lambda DNA and two 116 bp sequences. One 116 bp sequence is designed to melt more easily, and therefore cyclize more readily than the other. We determine J factors by measuring the concentrations of fluorescently labeled ligation products visualized on polyacrylamide gels. The measured temperature and sequence dependence of J factors is found to be in agreement with our model predictions using reasonable values for the flexibility of melted segments of dsDNA.

Keywords: DNA cyclization, DNA bending, DNA melting