RECORD
Relaxation of DNA curvature by single stranded breaks: Simulations and experiments
Biomolecules · Submitted 6 Nov 2003
abstract compiled · 2026-09-23 · no language-model review
The authors' main claim Maximal relaxation is observed when nicks occur inside A-tracts.
The compiled record
The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.
Open the compiled record
The abstract, sentence by sentence
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.
background contribution method result interpretation main claim
| # | sentence | role | the authors' own work | states the main conclusion | strength |
|---|---|---|---|---|---|
| s0 | 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. | background 1.00 | 0.04 | 0.03 | hedged possibility 0.84 |
| s1 | It predicted that the curvature in A-tract repeats can be relaxed by introducing single stranded breaks (nicks). | background 0.99 | 0.06 | 0.13 | asserted 0.83 |
| s2 | This effect has not been tested earlier and it would not be accounted for by alternative models of DNA bending. | gap 1.00 | 0.07 | 0.04 | asserted 0.93 |
| s3 | 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. | method 0.55 | 0.95 | 0.04 | asserted 0.98 |
| s4 | Single stranded breaks produce virtually no effect upon the gel mobility of the random sequence DNA. | result 1.00 | 0.93 | 0.06 | asserted 1.00 |
| s5 | 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. | result 1.00 | 0.95 | 0.34 | asserted 1.00 |
| s6 | Maximal relaxation is observed when nicks occur inside A-tracts. | result 1.00 | 0.94 | 0.42 | asserted 1.00 |
| s7 | The results are partially reproduced in simulations. | result 0.78 | 0.90 | 0.10 | asserted 0.86 |
| s8 | 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. | interpretation 0.70 | 0.92 | 0.14 | hedged possibility 0.93 |
What was examined, and what was not
- arXiv listing abstract v1
- full text
- figures and tables
- references and citing sentences
- relations to other papers
- P abstract
- S sections
- T body sentences
- C citations
- R cross-paper relations
The paper
Original 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.
Human review
Discussion
Know something about this paper? Leave a comment, or highlight any passage above to comment on it.