Modelling the thermal evolution of enzyme-created bubbles in DNA

Journal of the Royal Society Interface

Volumn 2, Issue 2, 2005, Pages 89-95

  Hennig, D ^a   Archilla, J F R ^b   Romero, J M ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b UNIVERSITY OF SEVILLE   (Spain)

Author keywords

Breathers; Bubbles; DNA; Enzymes

Indexed keywords

DNA; ENZYME;

ARTICLE; BIOLOGICAL MODEL; BIOSYNTHESIS; CHEMICAL MODEL; CHEMISTRY; CONFORMATION; DNA REPLICATION; HYDROGEN BOND; METABOLISM; NONLINEAR SYSTEM; TEMPERATURE;

DNA; DNA REPLICATION; ENZYMES; HYDROGEN BONDING; MODELS, BIOLOGICAL; MODELS, CHEMICAL; NONLINEAR DYNAMICS; NUCLEIC ACID CONFORMATION; TEMPERATURE;

EID: 33746911992     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2004.0024     Document Type: Article

References (17)

1. Agarwal, J. & Hennig, D. 2003 Breather solutions of a nonlinear DNA model including a longitudinal degree of freedom. Physica A 323, 519-533. (doi:10.1016/S0378-4371(02)02028-9.)
2. Barbi, M. 1998 Localized solutions in a model of DNA helicoidal structure. Ph.D. thesis, Università degli Studi di Firenze.
3. Barbi, M., Cocco, S. & Peyrard, M. 1999a Helicoidal model for DNA opening. Phys. Lett. A 253, 358-369. (doi:10.1016/ S0375-9601(99)00059-6.)
4. Barbi, M., Cocco, S., Peyrard, M. & Ruffo, S. 1999b A twist opening model for DNA. J. Biol. Phys. 24, 97-114. (doi:10. 1023/A:1005139326775.)
5. Cocco, S. & Monasson, R. 1999 Statistical mechanics of torque induced denaturation of DNA. Phys. Rev. Lett. 83, 5178-5181. (doi:10.1103/PhysRevLett. 83.5178.)
6. Dauxois, T., Peyrard, M. & Bishop, A. R. 1993 Dynamics and thermodynamics of a nonlinear model for DNA denaturation. Phys. Rev. B 47, 684-695. (doi:10.1103/PhysRevE. 47.684.)
7. Delagoutte, E. & von Hippel, P. H. 2003 Helicase mechanisms and the coupling of helicases within macromolecular machines. Part II. Integration of helicases into cellular processes. Q. Rev. Biophys. 36, 1-69. (doi:10.1017/ S0033583502003864.)
8. Englander, S. W., Kallenbach, N. R., Heeger, A. J., Krumhansl, J. A. & Litwin, S. 1980 Nature of the open state in long polynucleotide double helices: possibility of soliton excitations. Proc. Natl Acad. Sci. USA 77, 7222-7226.
9. Hennig, D. & Archilla, J. F. R. 2004 Multi-site H-bridge breathers in a DNA-shaped double strand. Phys. Scr. 69, 150-160.
10. Hoover, W. G. 1985 Canonical dynamics: equilibrium phase space distributions. Phys. Rev. A 31, 1695-1697. (doi:10. 1103/PhysRevA.31.1695.)
11. Nosé, S. 1984a A molecular-dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255-268.
12. Nosé, S. 1984b A unified formulation of the constant temperature molecular dynamics methods. J. Chem. Phys. 81, 511-519. (doi:10.1063/1.447334.)
13. Peyrard, M. & Bishop, A. R. 1989 Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett. 62, 2755-2758. (doi:10.1103/PhysRevLett.62.2755.)
14. Stryer, L., Berg, J. & Tymoczko, J. L. 2002 Biochemistry. New York: Freeman.
15. Sponer, J., Leszczynski, J. & Hobza, P. 2001 Electronic properties, hydrogen bonding, stacking, and cation binding of DNA and RNA bases. Biopolymers 61, 3-31. (doi:10.1002/1097-0282(2001)61:K3::AID-BIP10048>3. 0.CO;2-4.)
16. von Hippel, P. H. & Delagoutte, E. 2001 A general model for nucleic acid helicases and their 'coupling' within macromolecular machines. Cell 104, 117-190. (doi:10. 1016/S0092-8674(01)00203-3.)
17. Wu, L. & Hickson, I. D. 2001 DNA ends recQ-uire attention. Science 292, 229-230. (doi:10.1126/science.1060832.)