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Profiling the Thermodynamic Softness of Adenoviral Promoters

Chu H. Choi ^*, Zoi Rapti ^* , Vladimir Gelev ^*, Michele R. Hacker , Boian Alexandrov , Evelyn J. Park ^*, Jae Suk Park ^*, Nobuo Horikoshi ^¶, Augusto Smerzi , Kim Ø. Rasmussen , Alan R. Bishop  and Anny Usheva ^*

^* Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, Illinois; Department of Obstetrics and Gynecology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts; Center for Nonlinear Studies, Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico; and ^¶ Radiation Oncology Department, Washington University School of Medicine, St. Louis, Missouri

Correspondence: Address reprint requests to Chu H. Choi, Tel.: 617-667-1377; E-mail: cchoi{at}bidmc.harvard.edu.

We showed previously that anharmonic DNA dynamical features correlate with transcriptional activity in selected viral promoters, and hypothesized that areas of DNA softness may represent loci of functional significance. The nine known promoters from human adenovirus type 5 were analyzed for inherent DNA softness using the Peyrard-Bishop-Dauxois model and a statistical mechanics approach, using a transfer integral operator. We found a loosely defined pattern of softness peaks distributed both upstream and downstream of the transcriptional start sites, and that early transcriptional regions tended to be softer than late promoter regions. When reported transcription factor binding sites were superimposed on our calculated softness profiles, we observed a close correspondence in many cases, which suggests that DNA duplex breathing dynamics may play a role in protein recognition of specific nucleotide sequences and protein-DNA binding. These results suggest that genetic information is stored not only in explicit codon sequences, but also may be encoded into local dynamic and structural features, and that it may be possible to access this obscured information using DNA dynamics calculations.