2003/11/06 by Dimitri E. Kamashev, Kamashev, Dimitri E., Alexey K. Mazur +1
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biological Physics (physics.bio-ph) #Biomolecules (q-bio.BM) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #RNA Interference and Gene Delivery #RNA and protein synthesis mechanisms #Soft Condensed Matter (cond-mat.soft) #cond-mat.soft #physics.bio-ph #q-bio.BM
paper · pdf · doi:10.48550/arxiv.q-bio/0311003
13 two-column pages, 9 integrated eps plates, RevTeX4
arxiv created 2003/11/06 · openalex publication_date 2003/11/06 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
The recently proposed compressed backbone theory suggested that the intrinsic curvature in DNA can result from a geometric mismatch between the specific backbone length and optimal base stacking orientations. It predicted that the curvature in A-tract repeats can be relaxed by introducing single stranded breaks (nicks). This effect has not been tested earlier and it would not be accounted for by alternative models of DNA bending. Here the curvature in a specifically designed series of nicked DNA fragments is tested experimentally by gel mobility assays and, simultaneously, by free molecular dynamics simulations. Single stranded breaks produce virtually no effect upon the gel mobility of the random sequence DNA. In contrast, nicked A-tract fragments reveal a regular modulation of curvature depending upon the position of the strand break with respect to the overall bend. Maximal relaxation is observed when nicks occur inside A-tracts. The results are partially reproduced in simulations. Analysis of computed curved DNA conformations reveals a group of sugar atoms that exhibit reduced backbone length within A-tracts, which can correspond to the compression hypothesis.