Modeling thermal openings of double stranded DNA

George Kalosakas

Max Planck Institute for the Physics of Complex Systems, Nothnitzer Str. 38, D-01187, Dresden, Germany

The Peyrard-Bishop-Dauxois nonlinear model has been used to simulate thermal openings of viral and bacteriofage gene promoter DNA segments. The obtained statistics of the openings has been experimentally tested using S1 nuclease cleavage assays. Preferential large openings correlate with transcriptional start sites and major regulatory sites. These results link sequence-dependent intrinsic fluctuations with transcriptional activity.


[1] C.H. Choi et al., Nucleic Acids Res. 32, 1584 (2004).
[2] G. Kalosakas et al., Europhys. Lett. (2004), in press.