Abstract
Molecular modelling with Jumna is used to study extreme stretching of the DNA double helix. The results, which correlate well with recent nanomanipulation experiments, show how the double helix can be extended to twice its normal length before its base pairs break. Depending on the way the duplex is stretched two types of conformation can occur, either an unwound flat ribbon or a narrow fibre with negatively inclined base pairs. The energetics of both types of deformation are similar and existing structures show that at least the flat ribbon form can exist locally under biological conditions.
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Selected References
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- Bensimon A., Simon A., Chiffaudel A., Croquette V., Heslot F., Bensimon D. Alignment and sensitive detection of DNA by a moving interface. Science. 1994 Sep 30;265(5181):2096–2098. doi: 10.1126/science.7522347. [DOI] [PubMed] [Google Scholar]
- Bensimon D, Simon AJ, Croquette V, V, Bensimon A. Stretching DNA with a receding meniscus: Experiments and models. Phys Rev Lett. 1995 Jun 5;74(23):4754–4757. doi: 10.1103/PhysRevLett.74.4754. [DOI] [PubMed] [Google Scholar]
- Boutonnet N., Hui X., Zakrzewska K. Looking into the grooves of DNA. Biopolymers. 1993 Mar;33(3):479–490. doi: 10.1002/bip.360330314. [DOI] [PubMed] [Google Scholar]
- Cluzel P., Lebrun A., Heller C., Lavery R., Viovy J. L., Chatenay D., Caron F. DNA: an extensible molecule. Science. 1996 Feb 9;271(5250):792–794. doi: 10.1126/science.271.5250.792. [DOI] [PubMed] [Google Scholar]
- Guzikevich-Guerstein G., Shakked Z. A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein. Nat Struct Biol. 1996 Jan;3(1):32–37. doi: 10.1038/nsb0196-32. [DOI] [PubMed] [Google Scholar]
- Heinemann U., Lauble H., Frank R., Blöcker H. Crystal structure analysis of an A-DNA fragment at 1.8 A resolution: d(GCCCGGGC). Nucleic Acids Res. 1987 Nov 25;15(22):9531–9550. doi: 10.1093/nar/15.22.9531. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kim J. L., Burley S. K. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol. 1994 Sep;1(9):638–653. doi: 10.1038/nsb0994-638. [DOI] [PubMed] [Google Scholar]
- Kim Y., Geiger J. H., Hahn S., Sigler P. B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 1993 Oct 7;365(6446):512–520. doi: 10.1038/365512a0. [DOI] [PubMed] [Google Scholar]
- Lavery R., Hartmann B. Modelling DNA conformational mechanics. Biophys Chem. 1994 May;50(1-2):33–45. doi: 10.1016/0301-4622(94)85018-6. [DOI] [PubMed] [Google Scholar]
- Rao B. J., Chiu S. K., Bazemore L. R., Reddy G., Radding C. M. How specific is the first recognition step of homologous recombination? Trends Biochem Sci. 1995 Mar;20(3):109–113. doi: 10.1016/s0968-0004(00)88976-8. [DOI] [PubMed] [Google Scholar]
- Smith S. B., Cui Y., Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science. 1996 Feb 9;271(5250):795–799. doi: 10.1126/science.271.5250.795. [DOI] [PubMed] [Google Scholar]
- WILKINS M. H. F., GOSLING R. G., SEEDS W. E. Physical studies of nucleic acid. Nature. 1951 May 12;167(4254):759–760. doi: 10.1038/167759a0. [DOI] [PubMed] [Google Scholar]
- Werner M. H., Gronenborn A. M., Clore G. M. Intercalation, DNA kinking, and the control of transcription. Science. 1996 Feb 9;271(5250):778–784. doi: 10.1126/science.271.5250.778. [DOI] [PubMed] [Google Scholar]
- Werner M. H., Huth J. R., Gronenborn A. M., Clore G. M. Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell. 1995 Jun 2;81(5):705–714. doi: 10.1016/0092-8674(95)90532-4. [DOI] [PubMed] [Google Scholar]