메뉴 건너뛰기




Volumn 89, Issue 1, 2005, Pages 32-42

Solid phase DNA amplification: A Brownian dynamics study of crowding effects

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PRIMER DNA;

EID: 23244435744     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.051904     Document Type: Article
Times cited : (18)

References (52)
  • 3
    • 0141450270 scopus 로고    scopus 로고
    • Solid phase DNA amplification: A simple Monte Carlo lattice model
    • Mercier, J. F., G. W. Slater, and P. Mayer. 2003. Solid phase DNA amplification: a simple Monte Carlo lattice model. Biophys. J. 85:2075-2086.
    • (2003) Biophys. J. , vol.85 , pp. 2075-2086
    • Mercier, J.F.1    Slater, G.W.2    Mayer, P.3
  • 4
    • 0017524356 scopus 로고
    • Adsorption of chain molecules with a polar head: A scaling description
    • Alexander, S. 1977. Adsorption of chain molecules with a polar head: a scaling description. J. Phys. E. 38:983-987.
    • (1977) J. Phys. E , vol.38 , pp. 983-987
    • Alexander, S.1
  • 5
    • 0343510028 scopus 로고
    • Conformations of polymers attached to an interface
    • Degennes, P. G. 1980. Conformations of polymers attached to an interface. Macromolecules. 13:1069-1075.
    • (1980) Macromolecules , vol.13 , pp. 1069-1075
    • Degennes, P.G.1
  • 6
    • 0042421406 scopus 로고    scopus 로고
    • Semiflexible polymer brushes: A scaling theory
    • Kuznetsov, D. V., and Z. Y. Chen. 1998. Semiflexible polymer brushes: a scaling theory. J. Chem. Phys. 109:7017-7027.
    • (1998) J. Chem. Phys. , vol.109 , pp. 7017-7027
    • Kuznetsov, D.V.1    Chen, Z.Y.2
  • 7
    • 0036876850 scopus 로고    scopus 로고
    • Scaling concepts for polymer brushes and their test with computer simulation
    • Binder, K. 2002. Scaling concepts for polymer brushes and their test with computer simulation. Eur. Phys. J. E. 9:293-298.
    • (2002) Eur. Phys. J. E , vol.9 , pp. 293-298
    • Binder, K.1
  • 8
    • 0024057280 scopus 로고
    • Theory of the grafted polymer brush
    • Milner, S. T., T. A. Witten, and M. E. Gates. 1988. Theory of the grafted polymer brush. Macromolecules. 21:2610-2619.
    • (1988) Macromolecules , vol.21 , pp. 2610-2619
    • Milner, S.T.1    Witten, T.A.2    Gates, M.E.3
  • 9
    • 0025445287 scopus 로고
    • Theory of adsorbed block copolymers
    • Whitmore, M. D., and J. Noolandi. 1990. Theory of adsorbed block copolymers. Macromolecules. 23:3321-3339.
    • (1990) Macromolecules , vol.23 , pp. 3321-3339
    • Whitmore, M.D.1    Noolandi, J.2
  • 10
    • 0002863784 scopus 로고
    • Off-lattice Monte Carlo simulation of polymer brushes in good solvents
    • Laradji, M., H. Guo, and M. J. Zuckermann. 1994. Off-lattice Monte Carlo simulation of polymer brushes in good solvents. Phys. Rev. E. 49:3199-3206.
    • (1994) Phys. Rev. E , vol.49 , pp. 3199-3206
    • Laradji, M.1    Guo, H.2    Zuckermann, M.J.3
  • 11
    • 0001509468 scopus 로고
    • Theory of the structure of adsorbed block-copolymers-detailed comparison with experiment
    • Baranowski, R., and M. D. Whitmore. 1995. Theory of the structure of adsorbed block-copolymers-detailed comparison with experiment. J. Chem. Phys. 103:2343-2353.
    • (1995) J. Chem. Phys. , vol.103 , pp. 2343-2353
    • Baranowski, R.1    Whitmore, M.D.2
  • 12
    • 0000734576 scopus 로고    scopus 로고
    • Numerical self-consistent field study of tethered chains in theta solvent
    • Baranowski, R., and M. D. Whitmore. 1998. Numerical self-consistent field study of tethered chains in theta solvent. J. Chem. Phys. 108:9885-9892.
    • (1998) J. Chem. Phys. , vol.108 , pp. 9885-9892
    • Baranowski, R.1    Whitmore, M.D.2
  • 13
    • 0031115656 scopus 로고    scopus 로고
    • Classical theory of polymer brushes
    • Netz, R. R., and M. Schick. 1997. Classical theory of polymer brushes. Europhys. Lett. 38:37-42.
    • (1997) Europhys. Lett. , vol.38 , pp. 37-42
    • Netz, R.R.1    Schick, M.2
  • 14
    • 0032120937 scopus 로고    scopus 로고
    • Polymer brushes: From self-consistent field theory to classical theory
    • Netz, R. R., and M. Schick. 1998. Polymer brushes: from self-consistent field theory to classical theory. Macromolecules. 31:5105-5122.
    • (1998) Macromolecules , vol.31 , pp. 5105-5122
    • Netz, R.R.1    Schick, M.2
  • 15
    • 0346340955 scopus 로고    scopus 로고
    • Monte Carlo and numerical self-consistent field study of end-tethered polymers in good solvent
    • Pepin, M. P., and M. D. Whitmore. 1999. Monte Carlo and numerical self-consistent field study of end-tethered polymers in good solvent. J. Chem. Phys. 111:10381-10388.
    • (1999) J. Chem. Phys. , vol.111 , pp. 10381-10388
    • Pepin, M.P.1    Whitmore, M.D.2
  • 16
    • 0035826603 scopus 로고    scopus 로고
    • Monte Carlo and numerical self-consistent field study of systems with end-grafted and free polymers in good solvent
    • Pepin, M. P., and M. D. Whitmore. 2001. Monte Carlo and numerical self-consistent field study of systems with end-grafted and free polymers in good solvent. J. Chem. Phys. 114:8181-8195.
    • (2001) J. Chem. Phys. , vol.114 , pp. 8181-8195
    • Pepin, M.P.1    Whitmore, M.D.2
  • 17
    • 0347591147 scopus 로고    scopus 로고
    • Non-linear osmotic brush regime: Simulations and mean-field theory
    • Naji, A., R. R. Netz, and C. Seidel. 2003. Non-linear osmotic brush regime: simulations and mean-field theory. Eur. Phys. J. E. 12:223-237.
    • (2003) Eur. Phys. J. E , vol.12 , pp. 223-237
    • Naji, A.1    Netz, R.R.2    Seidel, C.3
  • 18
    • 0000179346 scopus 로고
    • Analysis of Monte Carlo results on kinetics of lattice polymer chains with excluded volume
    • Hilhorst, H. J., and J. M. Deutch. 1975. Analysis of Monte Carlo results on kinetics of lattice polymer chains with excluded volume. J. Chem. Phys. 63:5153-5161.
    • (1975) J. Chem. Phys. , vol.63 , pp. 5153-5161
    • Hilhorst, H.J.1    Deutch, J.M.2
  • 19
    • 0000482864 scopus 로고
    • Effect of bead movement rules on the relaxation of cubic lattice models of polymer chains
    • Gurler, M. T., C. C. Crabb, D. M. Dahlin, and J. Kovac. 1983. Effect of bead movement rules on the relaxation of cubic lattice models of polymer chains. Macromolecules. 16:398-403.
    • (1983) Macromolecules , vol.16 , pp. 398-403
    • Gurler, M.T.1    Crabb, C.C.2    Dahlin, D.M.3    Kovac, J.4
  • 20
    • 0024753841 scopus 로고
    • Structure of a grafted polymer brush - A molecular-dynamics simulation
    • Murat, M.,and G. S. Grest. 1989. Structure of a grafted polymer brush-a molecular-dynamics simulation. Macromolecules. 22:4054-4059.
    • (1989) Macromolecules , vol.22 , pp. 4054-4059
    • Murat, M.1    Grest, G.S.2
  • 21
    • 0025698270 scopus 로고
    • Density profile of terminally anchored polymer chains - A Monte Carlo study
    • Chakrabarti, A., and R. Toral. 1990. Density profile of terminally anchored polymer chains-a Monte Carlo study. Macromolecules. 23:2016-2021.
    • (1990) Macromolecules , vol.23 , pp. 2016-2021
    • Chakrabarti, A.1    Toral, R.2
  • 22
    • 0000153390 scopus 로고
    • Structure and dynamics of grafted polymer layers - A Monte Carlo simulation
    • Lai, P. Y., and K. Binder. 1991. Structure and dynamics of grafted polymer layers-a Monte Carlo simulation. J. Chem. Phys. 95:9288-9299.
    • (1991) J. Chem. Phys. , vol.95 , pp. 9288-9299
    • Lai, P.Y.1    Binder, K.2
  • 23
    • 0026869991 scopus 로고
    • Self-consistent field-theories for polymer brushes-lattice calculations and an asymptotic analytical description
    • Wijmans, C. M., J. M. H. M. Scheutjens, and E. B. Zhulina. 1992. Self-consistent field-theories for polymer brushes-lattice calculations and an asymptotic analytical description. Macromolecules. 25:2657-2665.
    • (1992) Macromolecules , vol.25 , pp. 2657-2665
    • Wijmans, C.M.1    Scheutjens, J.M.H.M.2    Zhulina, E.B.3
  • 24
    • 0027911305 scopus 로고
    • Structure of grafted polymeric brushes in solvents of varying quality - A molecular-dynamics study
    • Grest, G. S., and M. Murat. 1993. Structure of grafted polymeric brushes in solvents of varying quality-a molecular-dynamics study. Macromolecules. 26:3108-3117.
    • (1993) Macromolecules , vol.26 , pp. 3108-3117
    • Grest, G.S.1    Murat, M.2
  • 25
    • 0028196114 scopus 로고
    • Grafted polymer brushes - A constant surface pressure molecular-dynamics simulation
    • Grest, G. S. 1994. Grafted polymer brushes-a constant surface pressure molecular-dynamics simulation. Macromolecules. 27:418-426.
    • (1994) Macromolecules , vol.27 , pp. 418-426
    • Grest, G.S.1
  • 26
    • 0001032569 scopus 로고
    • Polyelectrolyte brush density profiles
    • Vongoeler, F., and M. Muthukumar. 1995. Polyelectrolyte brush density profiles. Macromolecules. 28:6608-6617.
    • (1995) Macromolecules , vol.28 , pp. 6608-6617
    • Vongoeler, F.1    Muthukumar, M.2
  • 27
    • 0033886390 scopus 로고    scopus 로고
    • Individual polymer paths and end-point stretching in polymer brushes
    • Seidel, C., and R. R. Netz. 2000. Individual polymer paths and end-point stretching in polymer brushes. Macromolecules. 33:634-640.
    • (2000) Macromolecules , vol.33 , pp. 634-640
    • Seidel, C.1    Netz, R.R.2
  • 28
    • 0033752605 scopus 로고    scopus 로고
    • Strongly charged polyelectrolyte brushes: A molecular dynamics study
    • Seidel, C., and F. S. Csajka. 2000. Strongly charged polyelectrolyte brushes: a molecular dynamics study. Macromolecules. 33:2728-2739.
    • (2000) Macromolecules , vol.33 , pp. 2728-2739
    • Seidel, C.1    Csajka, F.S.2
  • 29
    • 0037426463 scopus 로고    scopus 로고
    • Strongly stretched polyelectrolyte brushes
    • Seidel, C. 2003. Strongly stretched polyelectrolyte brushes. Macromolecules. 36:2536-2543.
    • (2003) Macromolecules , vol.36 , pp. 2536-2543
    • Seidel, C.1
  • 30
    • 0032047428 scopus 로고    scopus 로고
    • Tethered chains in θ-solvent conditions: An experimental study involving Langmuir diblock copolymer monolayers
    • Kent, M. S., J. Majewski, G. S. Smith, L. T. Lee, and S. Satija. 1998. Tethered chains in θ-solvent conditions: an experimental study involving Langmuir diblock copolymer monolayers. J. Chem. Phys. 108:5635-5645.
    • (1998) J. Chem. Phys. , vol.108 , pp. 5635-5645
    • Kent, M.S.1    Majewski, J.2    Smith, G.S.3    Lee, L.T.4    Satija, S.5
  • 31
    • 29444433368 scopus 로고
    • Tethered chains in good solvent conditions - An experimental study involving Langmuir diblock copolymer monolayers
    • Kent, M. S., L. T. Lee, B. J. Factor, F. Rondelez, and G. S. Smith. 1995. Tethered chains in good solvent conditions-an experimental study involving Langmuir diblock copolymer monolayers. J. Chem. Phys. 103:2320-2342.
    • (1995) J. Chem. Phys. , vol.103 , pp. 2320-2342
    • Kent, M.S.1    Lee, L.T.2    Factor, B.J.3    Rondelez, F.4    Smith, G.S.5
  • 32
    • 0027116072 scopus 로고
    • Characterization of diblock copolymer monolayers at the liquid air interface by neutron reflectivity and surface-tension measurements
    • Kent, M. S., L. T. Lee, B. Farnoux, and F. Rondelez. 1992. Characterization of diblock copolymer monolayers at the liquid air interface by neutron reflectivity and surface-tension measurements. Macromolecules. 25:6240-6247.
    • (1992) Macromolecules , vol.25 , pp. 6240-6247
    • Kent, M.S.1    Lee, L.T.2    Farnoux, B.3    Rondelez, F.4
  • 34
    • 0001579905 scopus 로고
    • Characterization of the brush regime for grafted polymer layers at the solid-liquid interface
    • Auroy, P., L. Auvray, and L. Leger. 1991. Characterization of the brush regime for grafted polymer layers at the solid-liquid interface. Phys. Rev. Lett. 66:719-722.
    • (1991) Phys. Rev. Lett. , vol.66 , pp. 719-722
    • Auroy, P.1    Auvray, L.2    Leger, L.3
  • 35
    • 0026418496 scopus 로고
    • Neutron reflectivity studies of polymers adsorbed on mica from solution
    • Cosgrove, T., T. G. Heath, J. S. Phipps, and R. M. Richardson. 1991. Neutron reflectivity studies of polymers adsorbed on mica from solution. Macromolecules. 24:94-98.
    • (1991) Macromolecules , vol.24 , pp. 94-98
    • Cosgrove, T.1    Heath, T.G.2    Phipps, J.S.3    Richardson, R.M.4
  • 36
    • 0033075693 scopus 로고    scopus 로고
    • Direct view of structural regimes of end-grafted polymer monolayers: A scanning force microscopy study
    • Koutsos, V., E. W. van der Vegte, and G. Hadziioannou. 1999. Direct view of structural regimes of end-grafted polymer monolayers: a scanning force microscopy study. Macromolecules. 32:1233-1236.
    • (1999) Macromolecules , vol.32 , pp. 1233-1236
    • Koutsos, V.1    Van Der Vegte, E.W.2    Hadziioannou, G.3
  • 38
    • 84986772884 scopus 로고
    • Aggregation of flexible-rigid-flexible triblock copolymers
    • Raphael, E., and P. G. Degennes. 1992. Aggregation of flexible-rigid-flexible triblock copolymers. Makromol. Chemie Macromol. Symp. 62:1-17.
    • (1992) Makromol. Chemie Macromol. Symp. , vol.62 , pp. 1-17
    • Raphael, E.1    Degennes, P.G.2
  • 39
    • 0030171780 scopus 로고    scopus 로고
    • Surface waves on polymer brushes
    • Xi, H. W., and S. T. Milner. 1996. Surface waves on polymer brushes. Macromolecules. 29:4772-4776.
    • (1996) Macromolecules , vol.29 , pp. 4772-4776
    • Xi, H.W.1    Milner, S.T.2
  • 41
    • 0034228237 scopus 로고    scopus 로고
    • Compression and escape of a star polymer
    • Sevick, E. M. 2000. Compression and escape of a star polymer. Macromolecules. 33:5743-5746.
    • (2000) Macromolecules , vol.33 , pp. 5743-5746
    • Sevick, E.M.1
  • 42
    • 0033546839 scopus 로고    scopus 로고
    • Escape transition of a compressed polymer mushroom under good solvent conditions
    • Milchev, A., V. Yamakov, and K. Binder. 1999. Escape transition of a compressed polymer mushroom under good solvent conditions. Europhys. Lett. 47:675-680.
    • (1999) Europhys. Lett. , vol.47 , pp. 675-680
    • Milchev, A.1    Yamakov, V.2    Binder, K.3
  • 43
    • 0001557676 scopus 로고    scopus 로고
    • Compression of a polymer chain by a small obstacle: The effect of fluctuations on the escape transition
    • Ennis, J., E. M. Sevick, and D. R. M. Williams. 1999. Compression of a polymer chain by a small obstacle: the effect of fluctuations on the escape transition. Phys. Rev. E. 60:6906-6918.
    • (1999) Phys. Rev. E , vol.60 , pp. 6906-6918
    • Ennis, J.1    Sevick, E.M.2    Williams, D.R.M.3
  • 44
    • 0033573165 scopus 로고    scopus 로고
    • In situ localized amplification and contact replication of many individual DNA molecules
    • Mitra, R. D., and G. M. Church. 1999. In situ localized amplification and contact replication of many individual DNA molecules. Nucleic Acids Res. 27:e34.
    • (1999) Nucleic Acids Res. , vol.27
    • Mitra, R.D.1    Church, G.M.2
  • 46
    • 0042528668 scopus 로고    scopus 로고
    • Single molecule profiling of alternative pre-mRNA splicing
    • Zhu, J., J. Shendure, R. D. Mitra, and G. M. Church. 2003. Single molecule profiling of alternative pre-mRNA splicing. Science. 301:836-838.
    • (2003) Science , vol.301 , pp. 836-838
    • Zhu, J.1    Shendure, J.2    Mitra, R.D.3    Church, G.M.4
  • 48
    • 33750652614 scopus 로고
    • Brownian dynamics with hydrodynamic interactions
    • Ermak, D. L., and J. A. McCammon. 1978. Brownian dynamics with hydrodynamic interactions. J. Chem. Phys. 69:1352-1360.
    • (1978) J. Chem. Phys. , vol.69 , pp. 1352-1360
    • Ermak, D.L.1    McCammon, J.A.2
  • 49
    • 5544254964 scopus 로고
    • Molecular dynamics simulation for polymers in the presence of a heat bath
    • Grest, G. S., and K. Kremer. 1986. Molecular dynamics simulation for polymers in the presence of a heat bath. Phys. Rev. A. 33:3628-3631.
    • (1986) Phys. Rev. A , vol.33 , pp. 3628-3631
    • Grest, G.S.1    Kremer, K.2
  • 51
    • 19644400697 scopus 로고    scopus 로고
    • Thickness and density profiles of polyelectrolyte brushes: Dependence on grafting density and salt concentration
    • Romet-Lemoinne, G., J. Daillant, P. Guenou, and J. Y. J. W. Mays. 2004. Thickness and density profiles of polyelectrolyte brushes: dependence on grafting density and salt concentration. Phys. Rev. Lett. 93:148301.
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 148301
    • Romet-Lemoinne, G.1    Daillant, J.2    Guenou, P.3    Mays, J.Y.J.W.4
  • 52
    • 0029935969 scopus 로고    scopus 로고
    • Theoretical uncertainty of measurements using quantitative polymerase chain reaction
    • Peccoud, J., and C. Jacob. 1996. Theoretical uncertainty of measurements using quantitative polymerase chain reaction. Biophys. J. 71:101-118.
    • (1996) Biophys. J. , vol.71 , pp. 101-118
    • Peccoud, J.1    Jacob, C.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.