메뉴 건너뛰기




Volumn 40, Issue 9, 2012, Pages 3812-3821

End-to-end attraction of duplex DNA

Author keywords

[No Author keywords available]

Indexed keywords

DNA FRAGMENT; DOUBLE STRANDED DNA; ELECTROLYTE;

EID: 84861375893     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1220     Document Type: Article
Times cited : (84)

References (61)
  • 1
    • 34249983213 scopus 로고    scopus 로고
    • DNA nanomachines
    • DOI 10.1038/nnano.2007.104, PII NNANO2007104
    • Bath, J. and Turberfield, A.J. (2007) DNA nanomachines. Nat. Nanotech., 2, 275-284. (Pubitemid 46882966)
    • (2007) Nature Nanotechnology , vol.2 , Issue.5 , pp. 275-284
    • Bath, J.1    Turberfield, A.J.2
  • 3
    • 33645028600 scopus 로고    scopus 로고
    • Folding DNA to create nanoscale shapes and patterns
    • Rothemund, P. (2006) Folding DNA to create nanoscale shapes and patterns. Nature, 440, 297-302.
    • (2006) Nature , vol.440 , pp. 297-302
    • Rothemund, P.1
  • 5
    • 4444298687 scopus 로고    scopus 로고
    • A synthetic DNA walker for molecular transport
    • DOI 10.1021/ja047543j
    • Shin, J.-S. and Pierce, N.A. (2004) A synthetic DNA walker for molecular transport. J. Am. Chem. Soc., 126, 10834-10835. (Pubitemid 39180556)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.35 , pp. 10834-10835
    • Shin, J.-S.1    Pierce, N.A.2
  • 6
    • 0035936116 scopus 로고    scopus 로고
    • Programmable and autonomous computing machine made of biomolecules
    • DOI 10.1038/35106533
    • Benenson, Y., Paz-Elizur, T., Adar, R., Keinan, E., Livneh, Z. and Shapiro, E. (2001) Programmable and autonomous computing machine made of biomolecules. Nature, 414, 430-434. (Pubitemid 34173721)
    • (2001) Nature , vol.414 , Issue.6862 , pp. 430-434
    • Benenson, Y.1    Paz-Elizur, T.2    Adar, R.3    Keinan, E.4    Llvneh, Z.5    Shapiro, E.6
  • 7
    • 38749133726 scopus 로고    scopus 로고
    • DNA-guided crystallization of colloidal nanoparticles
    • DOI 10.1038/nature06560, PII NATURE06560
    • Nykypanchuk, D., Maye, M.M., van der Lelie, D. and Gang, O. (2008) DNA-guided crystallization of colloidal nanoparticles. Nature, 451, 549-552. (Pubitemid 351186275)
    • (2008) Nature , vol.451 , Issue.7178 , pp. 549-552
    • Nykypanchuk, D.1    Maye, M.M.2    Van Der Lelie, D.3    Gang, O.4
  • 8
    • 38749110388 scopus 로고    scopus 로고
    • DNA-programmable nanoparticle crystallization
    • DOI 10.1038/nature06508, PII NATURE06508
    • Park, S.Y., Lytton-Jean, A.K.R., Lee, B., Weigand, S., Schatz, G.C. and Mirkin, C.A. (2008) DNA-programmable nanoparticle crystallization. Nature, 451, 553-556. (Pubitemid 351186267)
    • (2008) Nature , vol.451 , Issue.7178 , pp. 553-556
    • Park, S.Y.1    Lytton-Jean, A.K.R.2    Lee, B.3    Weigand, S.4    Schatz, G.C.5    Mirkin, C.A.6
  • 9
    • 78049347710 scopus 로고    scopus 로고
    • Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach
    • Gan, H.H. and Schlick, T. (2010) Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach. Biophys. J., 99, 2587-2596.
    • (2010) Biophys. J. , vol.99 , pp. 2587-2596
    • Gan, H.H.1    Schlick, T.2
  • 13
    • 44849088283 scopus 로고    scopus 로고
    • Closing the lid on DNA end-to-end stacking interactions
    • Li, L., Pabit, S.A., Lamb, J.S., Park, H.Y. and Pollack, L. (2008) Closing the lid on DNA end-to-end stacking interactions. Appl. Phys. Lett., 92, 223901-1-223901-3.
    • (2008) Appl. Phys. Lett. , vol.92 , pp. 2239011-2239013
    • Li, L.1    Pabit, S.A.2    Lamb, J.S.3    Park, H.Y.4    Pollack, L.5
  • 14
    • 0001533502 scopus 로고
    • Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: Hydration forces between parallel DNA double helices
    • Rau, D.C., Lee, B. and Parsegian, V.A. (1984) Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices. Proc. Natl Acad. Sci. USA, 81, 2621-2625. (Pubitemid 14109311)
    • (1984) Proceedings of the National Academy of Sciences of the United States of America , vol.81 , Issue.9 , pp. 2621-2625
    • Rau, D.C.1    Lee, B.2    Parsegian, V.A.3
  • 16
    • 77951687980 scopus 로고    scopus 로고
    • Electrostatics of strongly charged biological polymers: Ion-mediated interactions and self-organization in nucleic acids and proteins
    • Wong, G.C.L. and Pollack, L. (2010) Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins. Ann. Rev. Phys. Chem., 61, 171-189.
    • (2010) Ann. Rev. Phys. Chem. , vol.61 , pp. 171-189
    • Wong, G.C.L.1    Pollack, L.2
  • 17
    • 0036055199 scopus 로고    scopus 로고
    • Colloquium: The physics of charge inversion in chemical and biological systems
    • Grosberg, A.Y., Nguyen, T.T. and Shklovskii, B.I. (2002) Colloquium: the physics of charge inversion in chemical and biological systems. Rev. Mod. Phys., 74, 329-345.
    • (2002) Rev. Mod. Phys. , vol.74 , pp. 329-345
    • Grosberg, A.Y.1    Nguyen, T.T.2    Shklovskii, B.I.3
  • 18
    • 77957903315 scopus 로고    scopus 로고
    • Physics of DNA: Unravelling hidden abilities encoded in the structure of 'the most important molecule'
    • Kornyshev, A.A. (2010) Physics of DNA: unravelling hidden abilities encoded in the structure of 'the most important molecule' . Phys. Chem. Chem. Phys., 12, 12352-12378.
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 12352-12378
    • Kornyshev, A.A.1
  • 20
    • 41949124146 scopus 로고    scopus 로고
    • Molecular dynamics simulations of nucleic acid-protein complexes
    • MacKerell, A. Jr and Nilsson, L. (2008) Molecular dynamics simulations of nucleic acid-protein complexes. Curr. Op. Struct. Biol., 18, 194-199.
    • (2008) Curr. Op. Struct. Biol. , vol.18 , pp. 194-199
    • MacKerell Jr., A.1    Nilsson, L.2
  • 22
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • DOI 10.1529/biophysj.106.097782
    • Perez, A., Marchan, I., Svozil, D., Sponer, J., Cheatham, T.E., Laughton, C.A. and Orozco, M. (2007) Refinement of the AMBER force field for nucleic acids: improving the description of a/g conformers. Biophys. J., 92, 3817-3829. (Pubitemid 46910569)
    • (2007) Biophysical Journal , vol.92 , Issue.11 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham III, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 23
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phase and helical repeat
    • Cheatham, T.E.I., Cieplak, P. and Kollman, P.A. (1999) A modified version of the Cornell et al. force field with improved sugar pucker phase and helical repeat. J. Biomol. Struct. Dyn., 16, 845.
    • (1999) J. Biomol. Struct. Dyn. , vol.16 , pp. 845
    • Cheatham, T.E.I.1    Cieplak, P.2    Kollman, P.A.3
  • 25
    • 0001655657 scopus 로고
    • Finite representation of an infinite bulk system: Solvent boundary potential for computer simulations
    • Beglov, D. and Roux, B. (1994) Finite representation of an infinite bulk system: solvent boundary potential for computer simulations. J. Chem. Phys., 100, 9050-9063.
    • (1994) J. Chem. Phys. , vol.100 , pp. 9050-9063
    • Beglov, D.1    Roux, B.2
  • 26
    • 36449003554 scopus 로고
    • Constant pressure molecular dynamics algorithms
    • Martyna, G.J., Tobias, D.J. and Klein, M.L. (1994) Constant pressure molecular dynamics algorithms. J. Chem. Phys., 101, 4177-4189.
    • (1994) J. Chem. Phys. , vol.101 , pp. 4177-4189
    • Martyna, G.J.1    Tobias, D.J.2    Klein, M.L.3
  • 27
    • 11944256577 scopus 로고
    • Iterative minimization techniques for ab initio total-energy calculations: Molecular dynamics and conjugate gradients
    • Payne, M.C., Teter, M.P., Allan, D.C., Arias, T.A. and Joannopoulos, J.D. (1992) Iterative minimization techniques for ab initio total-energy calculations: molecular dynamics and conjugate gradients. Rev. Mod. Phys., 64, 1045-1097.
    • (1992) Rev. Mod. Phys. , vol.64 , pp. 1045-1097
    • Payne, M.C.1    Teter, M.P.2    Allan, D.C.3    Arias, T.A.4    Joannopoulos, J.D.5
  • 28
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic rates and activation free energies from single-molecule pulling experiments
    • Dudko, O., Hummer, G. and Szabo, A. (2006) Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys. Rev. Lett., 96, 108101.
    • (2006) Phys. Rev. Lett. , vol.96 , pp. 108101
    • Dudko, O.1    Hummer, G.2    Szabo, A.3
  • 31
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. and Valleau, J. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys., 23, 187-199.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.1    Valleau, J.2
  • 32
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. (1995) The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun., 91, 275-282.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 36
    • 77955692216 scopus 로고    scopus 로고
    • Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition
    • Wereszczynski, J. and Andricioaei, I. (2010) Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition. Biophys. J., 99, 869-878.
    • (2010) Biophys. J. , vol.99 , pp. 869-878
    • Wereszczynski, J.1    Andricioaei, I.2
  • 37
    • 0025693458 scopus 로고
    • Analytical solution of reversible step growth polymerization in semibatch reactors
    • Kumar, A. and Khanna, A. (1990) Analytical solution of reversible step growth polymerization in semibatch reactors. J. Appl. Polymer Sci., 41, 2077-2094.
    • (1990) J. Appl. Polymer Sci. , vol.41 , pp. 2077-2094
    • Kumar, A.1    Khanna, A.2
  • 39
    • 0034194135 scopus 로고    scopus 로고
    • Thermodynamic parameters for DNA sequences with dangling ends
    • Bommarito, S., Peyret, N. and SantaLucia, J. Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucl. Acids Res., 28, 1929-1934. (Pubitemid 30229658)
    • (2000) Nucleic Acids Research , vol.28 , Issue.9 , pp. 1929-1934
    • Bommarito, S.1    Peyret, N.2    SantaLucia Jr., J.3
  • 40
    • 0035369056 scopus 로고    scopus 로고
    • Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips
    • Vasiliskov, V.A., Prokopenko, D.V. and Mirzabekov, A.D. (2001) Parallel multiplex thermodynamic analysis of coaxial base stacking in DNA duplexes by oligodeoxyribonucleotide microchips. Nucl. Acids Res., 29, 2303-2313. (Pubitemid 32514933)
    • (2001) Nucleic Acids Research , vol.29 , Issue.11 , pp. 2303-2313
    • Vasiliskov, V.A.1    Prokopenko, D.V.2    Mirzabekov, A.D.3
  • 41
    • 0348010259 scopus 로고    scopus 로고
    • Efficiency of coaxial stacking depends on the DNA duplex structure
    • Pyshnyi, D.V., Goldberg, E.L. and Ivanova, E.M. (2003) Efficiency of coaxial stacking depends on the DNA duplex structure. J. Biomol. Struct. Dyn., 21, 459-468.
    • (2003) J. Biomol. Struct. Dyn. , vol.21 , pp. 459-468
    • Pyshnyi, D.V.1    Goldberg, E.L.2    Ivanova, E.M.3
  • 42
    • 4444260310 scopus 로고    scopus 로고
    • Stacked-unstacked equilibrium at the nick site of DNA
    • DOI 10.1016/j.jmb.2004.07.075, PII S0022283604009167
    • Protozanova, E., Yakovchuk, P. and Frank-Kamenetskii, M.D. (2004) Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol., 342, 775-785. (Pubitemid 39165649)
    • (2004) Journal of Molecular Biology , vol.342 , Issue.3 , pp. 775-785
    • Protozanova, E.1    Yakovchuk, P.2    Frank-Kamenetskii, M.D.3
  • 43
    • 32644434270 scopus 로고    scopus 로고
    • Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
    • DOI 10.1093/nar/gkj454
    • Yakovchuk, P., Protozanova, E. and Frank-Kamenetskii, M.D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucl. Acids Res., 34, 564-574. (Pubitemid 43240244)
    • (2006) Nucleic Acids Research , vol.34 , Issue.2 , pp. 564-574
    • Yakovchuk, P.1    Protozanova, E.2    Frank-Kamenetskii, M.D.3
  • 44
    • 61649101956 scopus 로고    scopus 로고
    • Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy
    • Manohar, S., Mantz, A.R., Bancroft, K.E., Hui, C.-Y., Jagota, A. and Vezenov, D.V. (2008) Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy. Nano Lett., 8, 4365-4372.
    • (2008) Nano Lett. , vol.8 , pp. 4365-4372
    • Manohar, S.1    Mantz, A.R.2    Bancroft, K.E.3    Hui, C.-Y.4    Jagota, A.5    Vezenov, D.V.6
  • 45
    • 14944373219 scopus 로고    scopus 로고
    • On the mechanism of hydrophobic association of nanoscopic solutes
    • DOI 10.1021/ja0441817
    • Choudhury, N. and Pettitt, B.M. (2005) On the mechanism of hydrophobic association of nanoscopic solutes. J. Am. Chem. Soc., 127, 3556-3567. (Pubitemid 40365294)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.10 , pp. 3556-3567
    • Choudhury, N.1    Pettitt, B.M.2
  • 46
    • 53549119413 scopus 로고    scopus 로고
    • Interaction of C60 derivatives and ssDNA from simulations
    • Zhao, X. (2008) Interaction of C60 derivatives and ssDNA from simulations. J. Phys. Chem. C, 112, 8898-8906.
    • (2008) J. Phys. Chem. , vol.112 C , pp. 8898-8906
    • Zhao, X.1
  • 47
    • 38749118972 scopus 로고    scopus 로고
    • Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics
    • DOI 10.1021/nl071909j
    • Johnson, R.R., Johnson, A.T.C. and Klein, M.L. (2008) Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics. Nano Lett., 8, 69-75. (Pubitemid 351177777)
    • (2008) Nano Letters , vol.8 , Issue.1 , pp. 69-75
    • Johnson, R.R.1    Johnson, A.T.C.2    Klein, M.L.3
  • 49
    • 0042839614 scopus 로고    scopus 로고
    • Mechanism and regulation of human non-homologous DNA end-joining
    • DOI 10.1038/nrm1202
    • Lieber, M.R., Ma, Y., Pannicke, U. and Schwarz, K. (2003) Mechanism and regulation of human non-homologous DNA end-joining. Nat. Rev. Mol. Cell Biol., 4, 712-720. (Pubitemid 37082186)
    • (2003) Nature Reviews Molecular Cell Biology , vol.4 , Issue.9 , pp. 712-720
    • Lieber, M.R.1    Ma, Y.2    Pannicke, U.3    Schwarz, K.4
  • 50
    • 4544362838 scopus 로고    scopus 로고
    • The mechanism of non-homologous end-joining: A synopsis of synapsis
    • DOI 10.1016/j.dnarep.2004.06.003, PII S156878640400179X
    • Weterings, E. and van Gent, D.C. (2004) The mechanism of nonhomologous end-joining: a synopsis of synapsis. DNA Repair, 3, 1425-1435. (Pubitemid 39221740)
    • (2004) DNA Repair , vol.3 , Issue.11 , pp. 1425-1435
    • Weterings, E.1    Van Gent, D.C.2
  • 51
    • 0026796061 scopus 로고
    • DNA bending flexibility, and helical repeat by cyclization kinetics
    • Crothers, D.M., Drak, J., Kahn, J.D. and Levene, S.D. (1992) DNA bending, flexibility, and helical repeat by cyclization kinetics. Meth. Enzym., 212, 3-29.
    • (1992) Meth. Enzym. , vol.212 , pp. 3-29
    • Crothers, D.M.1    Drak, J.2    Kahn, J.D.3    Levene, S.D.4
  • 52
    • 0030834853 scopus 로고    scopus 로고
    • Binding pathway of retinal to bacterio-opsin: A prediction by molecular dynamics simulations
    • Isralewitz, B., Izrailev, S. and Schulten, K. (1997) Binding pathway of retinal to bacterio-opsin: a prediction by molecular dynamics simulations. Biophys. J., 73, 2972-2979. (Pubitemid 27525764)
    • (1997) Biophysical Journal , vol.73 , Issue.6 , pp. 2972-2979
    • Isralewitz, B.1    Izrailev, S.2    Schulten, K.3
  • 53
    • 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. (Pubitemid 127655287)
    • (1997) Physical Review Letters , vol.78 , Issue.14 , pp. 2690-2693
    • Jarzynski, C.1
  • 54
    • 0032753202 scopus 로고    scopus 로고
    • Free energy calculations of watson-crick base pairing in aqueous solution
    • Stofer, E., Chipot, C. and Lavery, R. (1999) Free energy calculations of watson-crick base pairing in aqueous solution. J. Am. Chem. Soc., 121, 9503-9508.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9503-9508
    • Stofer, E.1    Chipot, C.2    Lavery, R.3
  • 55
    • 0342929614 scopus 로고
    • Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling
    • Torrie, G. and Valleau, J. (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J. Comput. Phys., 23, 187-199.
    • (1977) J. Comput. Phys. , vol.23 , pp. 187-199
    • Torrie, G.1    Valleau, J.2
  • 56
    • 0029633155 scopus 로고
    • The calculation of the potential of mean force using computer simulations
    • Roux, B. (1995) The calculation of the potential of mean force using computer simulations. Comput. Phys. Commun., 91, 275-282.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 275-282
    • Roux, B.1
  • 59
    • 0038311893 scopus 로고    scopus 로고
    • Osmotic shock and the strength of viral capsids
    • Cordova, A., Deserno, M., Gelbart, W.M., Gelbart, W.M. and Ben-Shaul, A. (2003) Osmotic shock and the strength of viral capsids. Biophys. J., 85, 70-74. (Pubitemid 36753617)
    • (2003) Biophysical Journal , vol.85 , Issue.1 , pp. 70-74
    • Cordova, A.1    Deserno, M.2    Gelbart, W.M.3    Ben-Shaul, A.4
  • 60
    • 0035418738 scopus 로고    scopus 로고
    • Osmotic properties of DNA: Critical evaluation of counterion condensation theory
    • Hansen, P., Podgornik, R. and Parsegian, V. (2001) Osmotic properties of DNA: critical evaluation of counterion condensation theory. Phys. Rev. E, 64, 1-4.
    • (2001) Phys. Rev. e , vol.64 , pp. 1-4
    • Hansen, P.1    Podgornik, R.2    Parsegian, V.3
  • 61
    • 0025693458 scopus 로고
    • Analytical solution of reversible step growth polymerization in semibatch reactors
    • Kumar, A. and Khanna, A. (1990) Analytical solution of reversible step growth polymerization in semibatch reactors. J. Appl. Polymer Sci., 41, 2077-2094.
    • (1990) J. Appl. Polymer Sci. , vol.41 , pp. 2077-2094
    • Kumar, A.1    Khanna, A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.