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Volumn 12, Issue 11, 2011, Pages 3870-3879

Understanding the effect of polylysine architecture on DNA binding using molecular dynamics simulations

Author keywords

[No Author keywords available]

Indexed keywords

ATOMISTIC MOLECULAR DYNAMICS SIMULATIONS; BINDING FREE ENERGY; DNA TRANSFECTION; DNA-BINDING; ENTROPIC CONTRIBUTIONS; MOLECULAR DYNAMICS SIMULATIONS; POLY-L-LYSINE; POLYCATIONS; POLYLYSINE; THERMODYNAMIC EFFECT; TRANSFECTION EFFICIENCY;

EID: 81255184847     PISSN: 15257797     EISSN: 15264602     Source Type: Journal    
DOI: 10.1021/bm201113y     Document Type: Article
Times cited : (78)

References (39)
  • 1
    • 15944400651 scopus 로고    scopus 로고
    • Towards safe, non-viral therapeutic gene expression in humans
    • Glover, D. J.; Lipps, H. J.; Jans, D. A. Towards safe, non-viral therapeutic gene expression in humans Nat. Rev. Genet. 2005, 6 (4) 299-U29
    • (2005) Nat. Rev. Genet. , vol.6 , Issue.4
    • Glover, D.J.1    Lipps, H.J.2    Jans, D.A.3
  • 4
    • 78751704429 scopus 로고    scopus 로고
    • Reconfiguring polylysine architectures for controlling polyplex binding and non-viral transfection
    • Parelkar, S. S.; Chan-Seng, D.; Emrick, T. Reconfiguring polylysine architectures for controlling polyplex binding and non-viral transfection Biomaterials 2011, 32 (9) 2432-2444
    • (2011) Biomaterials , vol.32 , Issue.9 , pp. 2432-2444
    • Parelkar, S.S.1    Chan-Seng, D.2    Emrick, T.3
  • 5
    • 52649155092 scopus 로고    scopus 로고
    • Pentalysine-grafted ROMP polymers for DNA complexation and delivery
    • Breitenkamp, R. B.; Emrick, T. Pentalysine-grafted ROMP polymers for DNA complexation and delivery Biomacromolecules 2008, 9 (9) 2495-500
    • (2008) Biomacromolecules , vol.9 , Issue.9 , pp. 2495-500
    • Breitenkamp, R.B.1    Emrick, T.2
  • 6
    • 0030775528 scopus 로고    scopus 로고
    • The influence of polymer structure on the interactions of cationic polymers with DNA and morphology of the resulting complexes
    • Tang, M. X.; Szoka, F. C. The influence of polymer structure on the interactions of cationic polymers with DNA and morphology of the resulting complexes Gene Ther. 1997, 4 (8) 823-32 (Pubitemid 27380165)
    • (1997) Gene Therapy , vol.4 , Issue.8 , pp. 823-832
    • Tang, M.X.1    Szoka, F.C.2
  • 7
    • 14744297069 scopus 로고    scopus 로고
    • Intracellular routing of plasmid DNA during non-viral gene transfer
    • DOI 10.1016/j.addr.2004.12.008, PII S0169409X05000098, Pharmacokinetics in Gene Delivery
    • Lechardeur, D.; Verkman, A. S.; Lukacs, G. L. Intracellular routing of plasmid DNA during non-viral gene transfer Adv. Drug Delivery Rev. 2005, 57 (5) 755-67 (Pubitemid 40332601)
    • (2005) Advanced Drug Delivery Reviews , vol.57 , Issue.5 , pp. 755-767
    • Lechardeur, D.1    Verkman, A.S.2    Lukacs, G.L.3
  • 8
    • 22144447455 scopus 로고    scopus 로고
    • Design and development of polymers for gene delivery
    • DOI 10.1038/nrd1775
    • Pack, D. W.; Hoffman, A. S.; Pun, S.; Stayton, P. S. Design and development of polymers for gene delivery Nat. Rev. Drug Discovery 2005, 4 (7) 581-93 (Pubitemid 40975711)
    • (2005) Nature Reviews Drug Discovery , vol.4 , Issue.7 , pp. 581-593
    • Pack, D.W.1    Hoffman, A.S.2    Pun, S.3    Stayton, P.S.4
  • 9
    • 79953840392 scopus 로고    scopus 로고
    • Branched polyethylenimine derivatives with reductively cleavable periphery for safe and efficient in vitro gene transfer
    • Wang, Y.; Zheng, M.; Meng, F.; Zhang, J.; Peng, R.; Zhong, Z. Branched polyethylenimine derivatives with reductively cleavable periphery for safe and efficient in vitro gene transfer Biomacromolecules 2011, 12 (4) 1032-40
    • (2011) Biomacromolecules , vol.12 , Issue.4 , pp. 1032-40
    • Wang, Y.1    Zheng, M.2    Meng, F.3    Zhang, J.4    Peng, R.5    Zhong, Z.6
  • 10
    • 0027655718 scopus 로고
    • Polyamidoamine cascade polymers mediate efficient transfection of cells in culture
    • Haensler, J.; Szoka, F. C., Jr. Polyamidoamine cascade polymers mediate efficient transfection of cells in culture Bioconjugate Chem. 1993, 4 (5) 372-379
    • (1993) Bioconjugate Chem. , vol.4 , Issue.5 , pp. 372-379
    • Haensler, J.1    Szoka Jr., F.C.2
  • 11
    • 34547139187 scopus 로고    scopus 로고
    • Langevin dynamics of semiflexible polyelectrolytes: Rod-toroid-globule- coil structures and counterion distribution
    • Ou, Z.; Muthukumar, M. Langevin dynamics of semiflexible polyelectrolytes: rod-toroid-globule-coil structures and counterion distribution J. Chem. Phys. 2005, 123 (7) 074905-074905
    • (2005) J. Chem. Phys. , vol.123 , Issue.7 , pp. 074905-074905
    • Ou, Z.1    Muthukumar, M.2
  • 12
    • 77954814144 scopus 로고    scopus 로고
    • Effect of chain stiffness on the morphology of polyelectrolyte complexes. A Monte Carlo simulation study
    • Narambuena, C. F.; Leiva, E. P. M.; Chávez-Páez, M.; Pérez, E. Effect of chain stiffness on the morphology of polyelectrolyte complexes. A Monte Carlo simulation study Polymer 2010, 51 (14) 3293-3302
    • (2010) Polymer , vol.51 , Issue.14 , pp. 3293-3302
    • Narambuena, C.F.1    Leiva, E.P.M.2    Chávez-Páez, M.3    Pérez, E.4
  • 13
    • 70350026253 scopus 로고    scopus 로고
    • Molecular Dynamics Simulations of DNA-Polycation Complex Formation
    • Ziebarth, J.; Wang, Y. M. Molecular Dynamics Simulations of DNA-Polycation Complex Formation Biophys. J. 2009, 97 (7) 1971-1983
    • (2009) Biophys. J. , vol.97 , Issue.7 , pp. 1971-1983
    • Ziebarth, J.1    Wang, Y.M.2
  • 14
    • 77954713630 scopus 로고    scopus 로고
    • Structure and Dynamics of Multiple Cationic Vectors- siRNA Complexation by All-Atomic Molecular Dynamics Simulations
    • Ouyang, D.; Zhang, H.; Parekh, H. S.; Smith, S. C. Structure and Dynamics of Multiple Cationic Vectors- siRNA Complexation by All-Atomic Molecular Dynamics Simulations J. Phys. Chem. B 2010, 114 (28) 9231-9237
    • (2010) J. Phys. Chem. B , vol.114 , Issue.28 , pp. 9231-9237
    • Ouyang, D.1    Zhang, H.2    Parekh, H.S.3    Smith, S.C.4
  • 15
    • 67650504216 scopus 로고    scopus 로고
    • Modeling the multivalent recognition between dendritic molecules and DNA: Understanding how ligand "sacrifice" and screening can enhance binding
    • Pavan, G. M.; Danani, A.; Pricl, S.; Smith, D. K. Modeling the multivalent recognition between dendritic molecules and DNA: understanding how ligand "sacrifice" and screening can enhance binding J. Am. Chem. Soc. 2009, 131 (28) 9686-94
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.28 , pp. 9686-94
    • Pavan, G.M.1    Danani, A.2    Pricl, S.3    Smith, D.K.4
  • 16
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • Cheatham, T. E.; Cieplak, P.; Kollman, P. A. A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 1999, 16 (4) 845-862 (Pubitemid 29157655)
    • (1999) Journal of Biomolecular Structure and Dynamics , vol.16 , Issue.4 , pp. 845-862
    • Cheatham III, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 17
    • 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.; Orozco, M. Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers Biophys. J. 2007, 92 (11) 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
  • 22
    • 0036890178 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
    • DOI 10.1002/jcc.10128
    • Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation J. Comput. Chem. 2002, 23 (16) 1623-41 (Pubitemid 35330860)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.16 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 23
    • 0347602124 scopus 로고    scopus 로고
    • Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf
    • Gohlke, H.; Case, D. A. Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf J. Comput. Chem. 2004, 25 (2) 238-50
    • (2004) J. Comput. Chem. , vol.25 , Issue.2 , pp. 238-50
    • Gohlke, H.1    Case, D.A.2
  • 24
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models Acc. Chem. Res. 2000, 33 (12) 889-897 (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 26
    • 35748981535 scopus 로고    scopus 로고
    • Implicit nonpolar solvent models
    • DOI 10.1021/jp073399n
    • Tan, C.; Tan, Y.-H.; Luo, R. Implicit nonpolar solvent models J. Phys. Chem. B 2007, 111 (42) 12263-74 (Pubitemid 350046101)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.42 , pp. 12263-12274
    • Tan, C.1    Tan, Y.-H.2    Luo, R.3
  • 27
    • 0025264701 scopus 로고
    • Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids
    • Mascotti, D. P.; Lohman, T. M. Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids Proc. Natl. Acad. Sci. U. S. A. 1990, 87 (8) 3142-6
    • (1990) Proc. Natl. Acad. Sci. U. S. A. , vol.87 , Issue.8 , pp. 3142-6
    • Mascotti, D.P.1    Lohman, T.M.2
  • 28
    • 0033640317 scopus 로고    scopus 로고
    • Direct evidence for counterion release upon cationic lipid-DNA condensation
    • DOI 10.1021/la991268a
    • Wagner, K.; Harries, D.; May, S.; Kahl, V.; Rädler, J. O.; Ben-Shaul, A. Direct Evidence for Counterion Release upon Cationic Lipid-DNA Condensation Langmuir 2000, 16 (2) 303-306 (Pubitemid 32211215)
    • (2000) Langmuir , vol.16 , Issue.2 , pp. 303-306
    • Wagner, K.1    Harries, D.2    May, S.3    Kahl, V.4    Radler, J.O.5    Ben-Shaul, A.6
  • 29
    • 34447503697 scopus 로고    scopus 로고
    • Conformational entropy in molecular recognition by proteins
    • DOI 10.1038/nature05959, PII NATURE05959
    • Frederick, K. K.; Marlow, M. S.; Valentine, K. G.; Wand, A. J. Conformational entropy in molecular recognition by proteins Nature 2007, 448 (7151) 325-9 (Pubitemid 47080342)
    • (2007) Nature , vol.448 , Issue.7151 , pp. 325-329
    • Frederick, K.K.1    Marlow, M.S.2    Valentine, K.G.3    Wand, A.J.4
  • 30
    • 77951281285 scopus 로고    scopus 로고
    • The role of conformational entropy in molecular recognition by calmodulin
    • Marlow, M. S.; Dogan, J.; Frederick, K. K.; Valentine, K. G.; Wand, A. J. The role of conformational entropy in molecular recognition by calmodulin Nat. Chem. Biol. 2010, 6 (5) 352-8
    • (2010) Nat. Chem. Biol. , vol.6 , Issue.5 , pp. 352-8
    • Marlow, M.S.1    Dogan, J.2    Frederick, K.K.3    Valentine, K.G.4    Wand, A.J.5
  • 31
    • 34547854001 scopus 로고    scopus 로고
    • Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics simulations
    • Ou, Z.; Muthukumar, M. Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics simulations J. Chem. Phys. 2006, 124 (15) 154902-154902
    • (2006) J. Chem. Phys. , vol.124 , Issue.15 , pp. 154902-154902
    • Ou, Z.1    Muthukumar, M.2
  • 32
    • 63749108613 scopus 로고    scopus 로고
    • In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides
    • Li, D. W.; Bruschweiler, R. In silico Relationship between Configurational Entropy and Soft Degrees of Freedom in Proteins and Peptides Phys. Rev. Lett. 2009, 102 (11) 4
    • (2009) Phys. Rev. Lett. , vol.102 , Issue.11 , pp. 4
    • Li, D.W.1    Bruschweiler, R.2
  • 33
    • 67650529401 scopus 로고    scopus 로고
    • A Dictionary for Protein Side-Chain Entropies from NMR Order Parameters
    • Li, D. W.; Bruschweiler, R. A Dictionary for Protein Side-Chain Entropies from NMR Order Parameters J. Am. Chem. Soc. 2009, 131 (21) 7226-7227
    • (2009) J. Am. Chem. Soc. , vol.131 , Issue.21 , pp. 7226-7227
    • Li, D.W.1    Bruschweiler, R.2
  • 34
    • 63649131960 scopus 로고    scopus 로고
    • A Mesoscale Model of DNA and Its Renaturation
    • Sambriski, E. J.; Schwartz, D. C.; de Pablo, J. J. A Mesoscale Model of DNA and Its Renaturation Biophys. J. 2009, 96 (5) 1675-1690
    • (2009) Biophys. J. , vol.96 , Issue.5 , pp. 1675-1690
    • Sambriski, E.J.1    Schwartz, D.C.2    De Pablo, J.J.3
  • 35
    • 77951212412 scopus 로고    scopus 로고
    • PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
    • Gopal, S. M.; Mukherjee, S.; Cheng, Y.-M.; Feig, M. PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy Proteins 2010, 78 (5) 1266-81
    • (2010) Proteins , vol.78 , Issue.5 , pp. 1266-81
    • Gopal, S.M.1    Mukherjee, S.2    Cheng, Y.-M.3    Feig, M.4
  • 36
    • 39749103470 scopus 로고    scopus 로고
    • Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations
    • DOI 10.1002/prot.21674
    • Stumpff-Kane, A. W.; Maksimiak, K.; Lee, M. S.; Feig, M. Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations Proteins 2008, 70 (4) 1345-1356 (Pubitemid 351304094)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.4 , pp. 1345-1356
    • Stumpff-Kane, A.W.1    Maksimiak, K.2    Lee, M.S.3    Feig, M.4
  • 37
    • 46149109506 scopus 로고    scopus 로고
    • The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
    • Noid, W. G.; Chu, J. W.; Ayton, G. S.; Krishna, V.; Izvekov, S.; Voth, G. A.; Das, A.; Andersen, H. C. The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J. Chem. Phys. 2008, 128 (24).
    • (2008) J. Chem. Phys. , vol.128 , Issue.24
    • Noid, W.G.1    Chu, J.W.2    Ayton, G.S.3    Krishna, V.4    Izvekov, S.5    Voth, G.A.6    Das, A.7    Andersen, H.C.8
  • 38
    • 34247852583 scopus 로고    scopus 로고
    • Coarse-grained peptide modeling using a systematic multiscale approach
    • DOI 10.1529/biophysj.106.094425
    • Zhou, J.; Thorpe, I. F.; Izvekov, S.; Voth, G. A. Coarse-grained peptide modeling using a systematic multiscale approach Biophys. J. 2007, 92 (12) 4289-4303 (Pubitemid 46910544)
    • (2007) Biophysical Journal , vol.92 , Issue.12 , pp. 4289-4303
    • Zhou, J.1    Thorpe, I.F.2    Izvekov, S.3    Voth, G.A.4
  • 39
    • 24144475073 scopus 로고    scopus 로고
    • Adsorption of comb copolymers on weakly attractive solid surfaces
    • Striolo, A.; Jayaraman, A.; Genzer, J.; Hall, C. K. Adsorption of comb copolymers on weakly attractive solid surfaces. J. Chem. Phys. 2005, 123 (6).
    • (2005) J. Chem. Phys. , vol.123 , Issue.6
    • Striolo, A.1    Jayaraman, A.2    Genzer, J.3    Hall, C.K.4


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