메뉴 건너뛰기




Volumn 34, Issue 1, 2005, Pages 13-18

A computer-generated supercoiled model of the pUC19 plasmid

Author keywords

DNA modelling; Monte Carlo simulation; Polyline smoothing; Supercoiled plasmid; Track structure calculations

Indexed keywords

PLASMID DNA;

EID: 13744259777     PISSN: 01757571     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00249-004-0431-2     Document Type: Article
Times cited : (16)

References (23)
  • 1
    • 0017795493 scopus 로고
    • Structure and reactions of closed duplex DNA
    • Bauer WR (1978) Structure and reactions of closed duplex DNA. Annu Rev Biophys Bioeng 7:287-313
    • (1978) Annu Rev Biophys Bioeng , vol.7 , pp. 287-313
    • Bauer, W.R.1
  • 6
    • 0012017901 scopus 로고    scopus 로고
    • Program for analyzing knots represented by polygonal paths
    • Harris BA, Harvey SC (1999) Program for analyzing knots represented by polygonal paths. J Comput Chem 20:813-818 (now that uracil.cmc.uab.edu has been shut down, the program is available at http://rumour.biology.gatech.edu/ Publications/1998-2000.shtml)
    • (1999) J Comput Chem , vol.20 , pp. 813-818
    • Harris, B.A.1    Harvey, S.C.2
  • 7
    • 0029878720 scopus 로고    scopus 로고
    • VMD - Visual molecular dynamics
    • Humphrey W, Dalke A, Schulten K (1996) VMD - visual molecular dynamics. J Mol Graphics 14:33-38 (http://www.ks.uiuc. edu/Research/vmd)
    • (1996) J Mol Graphics , vol.14 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 8
    • 0032573605 scopus 로고    scopus 로고
    • Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition
    • Jian H, Schlick T, Vologodskii A (1998) Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. J Mol Biol 284:287-296
    • (1998) J Mol Biol , vol.284 , pp. 287-296
    • Jian, H.1    Schlick, T.2    Vologodskii, A.3
  • 9
    • 0032948767 scopus 로고    scopus 로고
    • Comparison of strand breaks in plasmid DNA after positional changes of Auger electron-emitting Iodine-125
    • Kassis AI, Harapanhalli RS, Adelstein SJ (1999) Comparison of strand breaks in plasmid DNA after positional changes of Auger electron-emitting Iodine-125. Radiat Res 151:167-176
    • (1999) Radiat Res , vol.151 , pp. 167-176
    • Kassis, A.I.1    Harapanhalli, R.S.2    Adelstein, S.J.3
  • 10
    • 0033679367 scopus 로고    scopus 로고
    • Double-strand break yield following I-125 decay - Effects of DNA conformation
    • Kassis AI, Walicka MA, Adelstein SJ (2000) Double-strand break yield following I-125 decay - effects of DNA conformation. Acta Oncol 39:721-726
    • (2000) Acta Oncol , vol.39 , pp. 721-726
    • Kassis, A.I.1    Walicka, M.A.2    Adelstein, S.J.3
  • 11
    • 0034668195 scopus 로고    scopus 로고
    • Computation of writhe in modeling of supercoiled DNA
    • Klenin K, Langowski J (2000) Computation of writhe in modeling of supercoiled DNA. Biopolymers 54:307-317
    • (2000) Biopolymers , vol.54 , pp. 307-317
    • Klenin, K.1    Langowski, J.2
  • 12
    • 0028725149 scopus 로고
    • Comparison of various Monte Carlo track structure codes for energetic electrons in gaseous and liquid water
    • Varma MN, Chatterjee A (eds) Plenum, New York
    • Nikjoo H, Uehara S (1994) Comparison of various Monte Carlo track structure codes for energetic electrons in gaseous and liquid water. In: Varma MN, Chatterjee A (eds) Computational approaches in molecular radiation biology. Plenum, New York, pp 167-185
    • (1994) Computational Approaches in Molecular Radiation Biology , pp. 167-185
    • Nikjoo, H.1    Uehara, S.2
  • 13
    • 0002078793 scopus 로고
    • Radiation track structure theory
    • Freeman GR (ed) Wiley, New York
    • Paretzke HG (1987) Radiation track structure theory. In: Freeman GR (ed) Kinematics of nonhomogeneous processes. Wiley, New York, pp 89-170
    • (1987) Kinematics of Nonhomogeneous Processes , pp. 89-170
    • Paretzke, H.G.1
  • 15
    • 0026099231 scopus 로고
    • A new DNA target model for track structure calculations and its first applications to I-125 Auger electrons
    • Pomplun E (1991) A new DNA target model for track structure calculations and its first applications to I-125 Auger electrons. Int J Radiat Biol 59:625-642
    • (1991) Int J Radiat Biol , vol.59 , pp. 625-642
    • Pomplun, E.1
  • 16
    • 0028558806 scopus 로고
    • Low-energy electrons inside active DNA models: A tool to elucidate the radiation action mechanisms
    • Pomplun E, Terrissol M (1994) Low-energy electrons inside active DNA models: a tool to elucidate the radiation action mechanisms. Radiat Environ Biophys 33:279-292
    • (1994) Radiat Environ Biophys , vol.33 , pp. 279-292
    • Pomplun, E.1    Terrissol, M.2
  • 18
    • 0028693591 scopus 로고
    • A nucleosome model for the simulation of DNA strand break experiments
    • Varma MN, Chatterjee A (eds) Plenum, New York
    • Terrissol M, Pomplun E (1994) A nucleosome model for the simulation of DNA strand break experiments. In: Varma MN, Chatterjee A (eds) Computational approaches in molecular radiation biology. Plenum, New York, pp 243-250
    • (1994) Computational Approaches in Molecular Radiation Biology , pp. 243-250
    • Terrissol, M.1    Pomplun, E.2
  • 19
    • 33748322209 scopus 로고    scopus 로고
    • Analogue Monte Carlo to model radiation induced DNA damage
    • Kling A, Barao F, Nagakawa M, Távora LMN, Vaz P (eds) Springer, Berlin Heidelberg New York
    • Terrissol M, Vrigneaud JM (2001) Analogue Monte Carlo to model radiation induced DNA damage. In: Kling A, Barao F, Nagakawa M, Távora LMN, Vaz P (eds) Advanced Monte Carlo for radiation physics, particle transport simulation and applications. Springer, Berlin Heidelberg New York, pp 261-266
    • (2001) Advanced Monte Carlo for Radiation Physics, Particle Transport Simulation and Applications , pp. 261-266
    • Terrissol, M.1    Vrigneaud, J.M.2
  • 20
    • 0031981518 scopus 로고    scopus 로고
    • Monte Carlo simulation of DNA strand-break induction in supercoiled plasmid pBR322 DNA from indirect effects
    • Tomita H, Kai M, Kusama T, Ito A (1998) Monte Carlo simulation of DNA strand-break induction in supercoiled plasmid pBR322 DNA from indirect effects. Radiat Environ Biophys 36:235-241
    • (1998) Radiat Environ Biophys , vol.36 , pp. 235-241
    • Tomita, H.1    Kai, M.2    Kusama, T.3    Ito, A.4
  • 22
    • 0042230853 scopus 로고    scopus 로고
    • Monte Carlo simulation of strand-break induction on plasmid DNA in aqueous solution by monoenergetic electrons
    • Watanabe R, Saito K (2002) Monte Carlo simulation of strand-break induction on plasmid DNA in aqueous solution by monoenergetic electrons. Radiat Environ Biophys 41:207-215
    • (2002) Radiat Environ Biophys , vol.41 , pp. 207-215
    • Watanabe, R.1    Saito, K.2
  • 23
    • 0021943518 scopus 로고
    • Improved M13 phage cloning vectors and host strains: Nucleotide sequences of the M13mp18 and pUC19 vectors
    • Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119
    • (1985) Gene , vol.33 , pp. 103-119
    • Yanisch-Perron, C.1    Vieira, J.2    Messing, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.