|
| | | | |
| | | |
| Stat |
Members: 3645
Articles: 2'503'724
Articles rated: 2609
24 April 2024 |
|
| | | | |
|
Article overview
| |
|
|
Relaxation of DNA curvature by single stranded breaks: Simulations and experiments | | Dimitri E. Kamashev
; Alexey K. Mazur
; | | Date: |
6 Nov 2003 | | Subject: | Biomolecules; Biological Physics; Soft Condensed Matter | q-bio.BM cond-mat.soft physics.bio-ph | | Abstract: | 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. | | Source: | arXiv, q-bio.BM/0311003 | | Services: | Forum | Review | PDF | Favorites | |
|
|
No review found.
Did you like this article?
Note: answers to reviews or questions about the article must be posted in the forum section.
Authors are not allowed to review their own article. They can use the forum section.
browser Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com)
|
| |
|
|
|
|
News, job offers and information for researchers and scientists:
| |
REGISTER