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 Rasmussen, Alan R. Bishop, Anny Usheva

Research output: Contribution to journalArticle

20 Scopus citations

Abstract

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 humanadenovirus 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.

Original languageEnglish (US)
Pages (from-to)597-608
Number of pages12
JournalBiophysical Journal
Volume95
Issue number2
DOIs
StatePublished - Jul 15 2008

ASJC Scopus subject areas

  • Biophysics

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    Choi, C. H., Rapti, Z., Gelev, V., Hacker, M. R., Alexandrov, B., Park, E. J., Park, J. S., Horikoshi, N., Smerzi, A., Rasmussen, K., Bishop, A. R., & Usheva, A. (2008). Profiling the thermodynamic softness of adenoviral promoters. Biophysical Journal, 95(2), 597-608. https://doi.org/10.1529/biophysj.107.123471