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Center for Nonlinear Studies |
Thermal fluctuations in double-stranded DNA induce localized, sequence-dependent openings of its base pairs. These openings have, in certain cases, been associated with the formation of the DNA transcription complex. We describe these fluctuational openings at the atomic level with a minimally frustrated Go potential. This potential simplifies the non-covalent energetics of DNA, while including geometric constraints and configurational entropies associated with helix melting. The simplified treatment of the energetics allows for the simulation of large-scale fluctuations in relatively large systems. With this atomistic model, we study the melting and bubble formation in DNA sequences containing at least 60 base pairs. Equilibrium averages from molecular dynamics simulations at different temperatures show a sharp transition in the number of open base pairs as a function of temperature, in agreement with experimental observations. Prior to the transition temperature, localized thermal openings appear. At higher temperatures, they nucleate to form large single-stranded bubbles that insert within the double-strand domains. We also simulate a known gene promoter sequence and show that bubbles form at locations associated with transcription initiation and regulatory sites.