title: Profiling the thermodynamic softness of adenoviral promoters.
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 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.
authors.affiliation: Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, USA. cchoi@bidmc.harvard.edu
authors.forename: Chu H
authors.initials: CH
authors.lastname: Choi
authors.forename: Zoi
authors.initials: Z
authors.lastname: Rapti
authors.forename: Vladimir
authors.initials: V
authors.lastname: Gelev
authors.forename: Michele R
authors.initials: MR
authors.lastname: Hacker
authors.forename: Boian
authors.initials: B
authors.lastname: Alexandrov
authors.forename: Evelyn J
authors.initials: EJ
authors.lastname: Park
authors.forename: Jae Suk
authors.initials: JS
authors.lastname: Park
authors.forename: Nobuo
authors.initials: N
authors.lastname: Horikoshi
authors.forename: Augusto
authors.initials: A
authors.lastname: Smerzi
authors.forename: Kim Ø
authors.initials: KØ
authors.lastname: Rasmussen
authors.forename: Alan R
authors.initials: AR
authors.lastname: Bishop
authors.forename: Anny
authors.initials: A
authors.lastname: Usheva
mesh_terms: D000256:Adenoviridae / Q000235:genetics*; D001665:Binding Sites; D003198:Computer Simulation; D004279:DNA, Viral / Q000737:chemistry* / Q000235:genetics*; D008956:Models, Chemical; D008957:Models, Genetic; D011401:Promoter Regions, Genetic / Q000235:genetics*; D013816:Thermodynamics; D015533:Transcriptional Activation / Q000235:genetics
chemical_list: D004279:DNA, Viral