Molecular simulations of ultra-low-energy nitrogen ion bombardment of A-DNA in vacuum

Journal of Molecular Graphics and Modelling

Volumn 28, Issue 6, 2010, Pages 533-539

  Ngaojampa, Chanisorn ^a   Nimmanpipug, Piyarat ^a   Yu, Liangdeng ^b,c   Anuntalabhochai, Somboon ^b   Lee, Vannajan Sanghiran ^a  

^a Center for Innovation in Chemistry ^*  (Thailand)

^b CHIANG MAI UNIVERSITY   (Thailand)

^c THAILAND CENTER OF EXCELLENCE IN PHYSICS   (Thailand)

Author keywords

A DNA; Ion bombardment; Molecular dynamics; Monte Carlo

Indexed keywords

A-DNA; BOMBARDMENT ENERGY; DNA STRANDS; FLUENCES; IN-VACUUM; INTERACTION ENERGIES; LINEAR VELOCITY; LOW ENERGIES; LOW ENERGY ION BEAM; MC SIMULATION; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; MONTE CARLO; NAKED DNA;

DNA; GENE TRANSFER; GENES; IONS; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; MONTE CARLO METHODS;

ION BOMBARDMENT;

DOUBLE STRANDED DNA; NAKED DNA; NITROGEN; NUCLEOTIDE DERIVATIVE;

ARTICLE; CHEMICAL BOND; ENERGY; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MONTE CARLO METHOD; PRIORITY JOURNAL; SIMULATION; VACUUM; VELOCITY;

DNA, A-FORM; IONS; MOLECULAR DYNAMICS SIMULATION; NITROGEN; NUCLEIC ACID CONFORMATION; THERMODYNAMICS; VACUUM;

EID: 75049085780     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2009.11.009     Document Type: Article

References (38)

1. Yu L.D., Vilaithong T., and Brown I. Introduction to Ion Beam Biotechnology. English edition, originally authored by Yu Zengliang in Chinese (2006), Springer Science & Business Media, New York
2. Wei Z., Xei H., and Han G. Nucl. Instrum. Methods B95 (1994) 371
3. Zhao Y., Tan Z., Qiu G.Y., and Du Y.H. Nucl. Instrum. Methods B211 (2003) 211
4. Hunniford C.A., Timson D.J., Davies R.J.H., and McCullough R.W. Phys. Med. Biol. 52 (2007) 3729
5. Chen Y., Jiang B., Ding X., Liu X., Chen C., Guo X., and Yin G. Radiat. Environ. Biophys. 37 (1998) 101
6. Lacomb S., Le S.C., and Esaulov V.A. Phys. Med. Biol. 49 (2004) N65
7. Deng Z.W., Bald I., Illenberger E., and Huels M.A. Phys. Rev. Lett. 95 (2005) 153201
8. F.A. Chacon, Ion induced radiation damage on the molecular level, Ph.D. Thesis, University of Groningen, 2007.
9. Norarat R., Semsang N., Anuntalabhochai S., and Yu L.D. Very low-energy and low-fluence ion beam bombardment of naked plasmid DNA. Nucl. Instrum. Methods B 267 (2009) 1650-1653
10. Ryssel H., and Ruge I. Ion Implantation (1996), Wiley Chichester
11. Nastasi M., Mayer J.W., and Hirvonen J. Ion-Solid Interactions: Fundamentals and Applications (1996), Cambridge University Press
12. Hall E. Radiobiology for Radiobiologists (1993), Lippincott Williams & Wilkins
13. Yu Z. Study on the interaction of low-energy ions with organisms. Surf. Coat. Technol. 201 (2007) 8006-8013
14. 18 DNA. Sci. China C. Life. Sci. 40 (1997) 107-112
15. Wang Q., Zhang G., Du Y.H., Zhao Y., and Qiu G.Y. Low-energy (30 keV) carbon ion induced mutation spectrum in the lacZ gene of M13mp18 double-stranded DNA. Mutat. Res. Fundam. Mol. Mech. Mutagen. 528 (2003) 55-60
16. 60CO-γ ray irradiation in Escherichia coli. Genet. Mol. Biol. 27 (2004) 284-290
17. Kummerle E.A., and Pomplun E. A computer-generated supercoiled model of the pUC19 plasmid. Eur. Biophys. J. 34 (2005) 13-18
18. Bouchiat C., and Mezard M. Elastic rod model of a supercoiled DNA molecule. Eur. Phys. J. E. 2 (2000) 377-402
19. Lankas F., Lavery R., and Maddocks J.H. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14 (2006) 1527-1534
20. Olson W.K., and Zhurkin V.B. Modeling DNA deformations. Curr. Opin. Struct. Biol. 10 (2000) 286-297
21. Maher L.J. Mechanisms of DNA bending. Curr. Opin. Struct. Biol. 2 (1998) 688-694
22. Nikjoo H., Bolton C.E., Watanabe R., et al. Modelling of DNA damage induced by energetic electrons (100 eV to 100 keV). Radiat. Prot. Dosimetry 99 (2002) 77-80
23. Nikjoo H., Emfietzoglou D., Watanabe R., and Uehara S. Can Monte Carlo track structure codes reveal reaction mechanism in DNA damage and improve radiation therapy?. Radiat. Phys. Chem. 77 (2008) 1270-1279
24. Watanabe R., and Nikjoo H. Modelling the effect of incorporated halogenated pyrimidine on radiation-induced DNA strand breaks. Int. J. Radiat. Biol. 78 (2002) 953-966
25. Nikjoo H., O'Neill P., Wilson W.E., and Goodhead D.T. Computational approach for determining the spectrum of DNA damage induced by ionizing radiation. Radiat. Res. 156 (2001) 577-583
26. Li X., Sevilla M.D., and Sanche L. Density functional theory studies of electron interaction with DNA: can zero eV electrons induce strand breaks?. J. Am. Chem. Soc. 125 (2003) 13668-13669
27. Falcone J.M., Becker D., Sevilla M.D., and Swarts S.G. Products of the reactions of the dry and aqueous electron with hydrated DNA: hydrogen and 5,6-dihydropyrimidines. Radiat. Phys. Chem. 72 (2005) 257-264
28. Chalfie M., Tu Y., Euskirchen G., Ward W.W., and Prasher D.C. Green fluorescent protein as a marker for gene expression. Science 263 (1994) 802-805
29. Discovery studio 1.7.1, Accelrys Software Inc., San Diego, CA, 2006.
30. Foloppe N., and MacKerell Jr. A.D. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2000) 86-104
31. Materials Studio Modeling 4.3, Accelrys Software Inc., San Diego, CA, 2008.
32. Sun H. Compass: an ab initio force-field optimized for condensed-phase applications; overview with details on alkane and benzene compounds. J. Phys. Chem. B 102 (1998) 7338-7364
33. Rigby D., Sun H., and Eichinger B.E. Computer simulations of poly-(ethylene oxide): force field, PVT diagram and cyclization behavior. Polym. Int. 44 (1997) 311-330
34. Metropolis N., Rosenbluth A.W., Rosenbluth M.N., Teller A.H., and Teller E. Equation of state calculations by fast computing machines. J. Chem. Phys. 21 (1953) 1087-1092
35. D.A. Case, T.A. Darden, T.E. Cheatham Iii, et al., AMBER 9 (2004).
36. Rueda M., Kalko S.G., Luque F.J., and Orozco M. The structure and dynamics of DNA in the gas phase. J. Am. Chem. Soc. 125 (2003) 8007-8014
37. Rueda M., Luque F.J., and Orozco M. Nature of minor-groove binders DNA complexes in the gas phase. J. Am. Chem. Soc. 127 (2005) 11690-11698
38. Lebrun A., and Lavery R. Modelling extreme stretching of DNA. Nucl. Acids Res. 24 12 (1996) 2260-2267