메뉴 건너뛰기




Volumn 88, Issue 3, 2005, Pages 1684-1691

Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; DNA;

EID: 21244498669     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.046912     Document Type: Article
Times cited : (90)

References (38)
  • 1
    • 0030872242 scopus 로고    scopus 로고
    • Reconstructing potential energy functions from simulated force-induced unbinding processes
    • Baisera, M., S. Stepaniants, S. Izraliev, Y. Oono, and K. Schulten. 1997. Reconstructing potential energy functions from simulated force-induced unbinding processes. Biophys. J. 73:1281-1287.
    • (1997) Biophys. J. , vol.73 , pp. 1281-1287
    • Baisera, M.1    Stepaniants, S.2    Izraliev, S.3    Oono, Y.4    Schulten, K.5
  • 4
    • 0034979287 scopus 로고    scopus 로고
    • Probing the relation between force-lifetime and chemistry in single molecular bonds
    • Evans, E. 2001. Probing the relation between force-lifetime and chemistry in single molecular bonds. Annu. Rev. Biophys. Biomol. Struct. 30:105-128.
    • (2001) Annu. Rev. Biophys. Biomol. Struct. , vol.30 , pp. 105-128
    • Evans, E.1
  • 5
    • 0042852135 scopus 로고    scopus 로고
    • Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations
    • Gullingsrud, J. R., R. Braun, and K. Schulten. 1999. Reconstructing potentials of mean force through time series analysis of steered molecular dynamics simulations. J. Comput. Phys. 151:190-211.
    • (1999) J. Comput. Phys. , vol.151 , pp. 190-211
    • Gullingsrud, J.R.1    Braun, R.2    Schulten, K.3
  • 7
    • 4243754128 scopus 로고    scopus 로고
    • Nonequilibrium equality for free energy differences
    • Jarzynski, C. 1997. Nonequilibrium equality for free energy differences. Phys. Rev. Lett. 78:2690-2693.
    • (1997) Phys. Rev. Lett. , vol.78 , pp. 2690-2693
    • Jarzynski, C.1
  • 8
    • 0034691149 scopus 로고    scopus 로고
    • Native topology determines force-induced unfolding pathways in globular proteins
    • Klimov, D. K., and D. Thirumalai. 2000. Native topology determines force-induced unfolding pathways in globular proteins. Proc. Natl. Acad. Sci. USA. 97:7254-7259.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 7254-7259
    • Klimov, D.K.1    Thirumalai, D.2
  • 9
    • 0029909230 scopus 로고    scopus 로고
    • Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure
    • Konrad, M. W., and J. I. Bolonick. 1996. Molecular dynamics simulation of DNA stretching is consistent with the tension observed for extension and strand separation and predicts a novel ladder structure. J. Am. Chem. Soc. 118:10989-10994.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 10989-10994
    • Konrad, M.W.1    Bolonick, J.I.2
  • 10
    • 0033603393 scopus 로고    scopus 로고
    • DNA stretching and compression: Large-scale simulations of double helical structures
    • Kosikov, K. M., A. A. Gorin, V. B. Zhurkin, and W. K. Olson. 1999. DNA stretching and compression: large-scale simulations of double helical structures. J. Mol. Biol. 289:1301-1326.
    • (1999) J. Mol. Biol. , vol.289 , pp. 1301-1326
    • Kosikov, K.M.1    Gorin, A.A.2    Zhurkin, V.B.3    Olson, W.K.4
  • 11
    • 0033393463 scopus 로고    scopus 로고
    • Modelling DNA stretching for physics and biology
    • Lavery, R., and A. Lebrun. 1999. Modelling DNA stretching for physics and biology. Genetica. 106:75-84.
    • (1999) Genetica , vol.106 , pp. 75-84
    • Lavery, R.1    Lebrun, A.2
  • 13
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids-conventions and principles
    • Lavery, R., and H. Sklenar. 1989. Defining the structure of irregular nucleic acids-conventions and principles. J. Biomol. Strut. Dyn. 6:655-667.
    • (1989) J. Biomol. Strut. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 14
    • 0029899989 scopus 로고    scopus 로고
    • Modelling extreme stretching of DNA
    • Lebrun, A., and R. Lavery. 1996. Modelling extreme stretching of DNA. Nucleic Acids Res. 24:2260-2267.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 2260-2267
    • Lebrun, A.1    Lavery, R.2
  • 15
    • 0037036070 scopus 로고    scopus 로고
    • Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality
    • Liphardt, J., S. Dumont, S. B. Smith, I. Tinoco Jr., and C. Bustamante. 2002. Equilibrium information from nonequilibrium measurements in an experimental test of Jarzynski's equality. Science. 296:1832-1835.
    • (2002) Science , vol.296 , pp. 1832-1835
    • Liphardt, J.1    Dumont, S.2    Smith, S.B.3    Tinoco Jr., I.4    Bustamante, C.5
  • 16
    • 0344327079 scopus 로고    scopus 로고
    • Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
    • MacKerell, A. D., and G. U. Lee. 1999. Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads. Eur. Biophys. J. 28:415-426.
    • (1999) Eur. Biophys. J. , vol.28 , pp. 415-426
    • MacKerell, A.D.1    Lee, G.U.2
  • 17
    • 0023513912 scopus 로고
    • The structure of an oligo(dA).oligo(dT) tract and its biological implications
    • Nelson, H. C. M., J. T. Finch, B. F. Luisi, and A. Klug. 1987. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 330:221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 19
    • 0032919143 scopus 로고    scopus 로고
    • Sequence-dependent mechanics of single DNA molecules
    • Rief, M., H. Clausen-Schaumann, and H. E. Gaub. 1999. Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6:346-349.
    • (1999) Nat. Struct. Biol. , vol.6 , pp. 346-349
    • Rief, M.1    Clausen-Schaumann, H.2    Gaub, H.E.3
  • 20
    • 0037109040 scopus 로고    scopus 로고
    • A two-state kinetic model for the unfolding of single molecules by mechanical force
    • Ritort, F., C. Bustamante, and I. Tinoco Jr. 2002. A two-state kinetic model for the unfolding of single molecules by mechanical force. Proc. Natl. Acad. Sci. USA. 99:13544-13548.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 13544-13548
    • Ritort, F.1    Bustamante, C.2    Tinoco Jr., I.3
  • 21
    • 0035146646 scopus 로고    scopus 로고
    • Force-induced melting of the DNA double helix. 1. Thermodynamics analysis
    • Rouzina, I., and V. A. Bloomfield. 2001a. Force-induced melting of the DNA double helix. 1. Thermodynamics analysis. Biophys. J. 80:882-893.
    • (2001) Biophys. J. , vol.80 , pp. 882-893
    • Rouzina, I.1    Bloomfield, V.A.2
  • 22
    • 0035144566 scopus 로고    scopus 로고
    • Force-induced melting of the DNA double helix. 2. Effect of solution conditions
    • Rouzina, I., and V. A. Bloomfield. 2001b. Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophys. J. 80:894-900.
    • (2001) Biophys. J. , vol.80 , pp. 894-900
    • Rouzina, I.1    Bloomfield, V.A.2
  • 23
    • 0035314075 scopus 로고    scopus 로고
    • Entropy calculations on the molten globule state of a protein: Side-chain entropies of alpha-lactabumin
    • Schafer, H., X. Daura, A. E. Mark, and W. F. van Gunsteren. 2001. Entropy calculations on the molten globule state of a protein: side-chain entropies of alpha-lactabumin. Proteins. 43:45-56.
    • (2001) Proteins , vol.43 , pp. 45-56
    • Schafer, H.1    Daura, X.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 24
    • 0034323089 scopus 로고    scopus 로고
    • Absolute entropies from molecular dynamics simulation trajectories
    • Schafer, H., A. E. Mark, and W. F. van Gunsteren. 2000. Absolute entropies from molecular dynamics simulation trajectories. J. Chem. Phys. 113:7809-7817.
    • (2000) J. Chem. Phys. , vol.113 , pp. 7809-7817
    • Schafer, H.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 25
    • 0001351515 scopus 로고
    • Estimations of absolute and relative entropies of macromolecules using the covariance matrix
    • Schlitter, J. 1993. Estimations of absolute and relative entropies of macromolecules using the covariance matrix. J. Chem. Phys. Lett. 215: 617-621.
    • (1993) J. Chem. Phys. Lett. , vol.215 , pp. 617-621
    • Schlitter, J.1
  • 28
    • 0030873459 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the d(T·A·T) triple helix
    • Shields, G., C. A. Laughton, and M. Orozco. 1997. Molecular dynamics simulations of the d(T·A·T) triple helix. J. Am. Chem. Soc. 119:7463-7469.
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 7463-7469
    • Shields, G.1    Laughton, C.A.2    Orozco, M.3
  • 29
    • 0034725383 scopus 로고    scopus 로고
    • Molecular dynamics simulations of PNA·DNA and PNA·RNA duplexes in aqueous solution
    • Soliva, R., E. Sherer, F. J. Luque, C. A. Laughton, and M. Orozco. 2000. Molecular dynamics simulations of PNA·DNA and PNA·RNA duplexes in aqueous solution. J. Am. Chem. Soc. 122:5997-6008.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 5997-6008
    • Soliva, R.1    Sherer, E.2    Luque, F.J.3    Laughton, C.A.4    Orozco, M.5
  • 30
    • 0032560959 scopus 로고    scopus 로고
    • Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
    • Srinivasan, J., T. E. Cheatham III, P. Kollman, and D. A. Case. 1998. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120:9401-9409.
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham III, T.E.2    Kollman, P.3    Case, D.A.4
  • 31
    • 37649028695 scopus 로고    scopus 로고
    • Theory of high-force stretching and overstretching
    • Storm, C., and P. C. Nelson. 2003. Theory of high-force stretching and overstretching. Phys. Rev. E. 67:051906.
    • (2003) Phys. Rev. E , vol.67 , pp. 051906
    • Storm, C.1    Nelson, P.C.2
  • 33
    • 0033861876 scopus 로고    scopus 로고
    • Model energy landscapes and the force-induced dissociation of ligand-receptor bonds
    • Strunz, T., K. Oroszlan, H. J. Güntherodt, and M. Henger. 2000. Model energy landscapes and the force-induced dissociation of ligand-receptor bonds. Biophys. J. 79:1206-1212.
    • (2000) Biophys. J. , vol.79 , pp. 1206-1212
    • Strunz, T.1    Oroszlan, K.2    Güntherodt, H.J.3    Henger, M.4
  • 35
    • 0037058902 scopus 로고    scopus 로고
    • The effect of force on thermodynamics and kinetics of single molecule reactions
    • Tinoco, I. Jr., and C. Bustamante. 2002. The effect of force on thermodynamics and kinetics of single molecule reactions. Biophys. Chem. 101-102:513-533.
    • (2002) Biophys. Chem. , vol.101-102 , pp. 513-533
    • Tinoco Jr., I.1    Bustamante, C.2
  • 36
    • 0034701222 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acids with a generalised Born solvation model
    • Tsui, V., and D. A. Case. 2000. Molecular dynamics simulations of nucleic acids with a generalised Born solvation model. J. Am. Chem. Soc. 122:2489-2498.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2489-2498
    • Tsui, V.1    Case, D.A.2
  • 37
    • 0036009140 scopus 로고    scopus 로고
    • Thermodynamics of DNA interactions from single molecule stretching experiments
    • Williams, M. C., I. Rouzina, and V. A. Bloomfield. 2002. Thermodynamics of DNA interactions from single molecule stretching experiments. Acc. Chem. Res. 35:159-166.
    • (2002) Acc. Chem. Res. , vol.35 , pp. 159-166
    • Williams, M.C.1    Rouzina, I.2    Bloomfield, V.A.3
  • 38
    • 0035072057 scopus 로고    scopus 로고
    • Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching
    • Williams, M. C., J. R. Wenner, I. Rouzina, and V. Bloomfield. 2001. Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching. Biophys. J. 80:1932-1939.
    • (2001) Biophys. J. , vol.80 , pp. 1932-1939
    • Williams, M.C.1    Wenner, J.R.2    Rouzina, I.3    Bloomfield, V.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.