메뉴 건너뛰기




Volumn 98, Issue 5, 2010, Pages 834-842

Microscopic basis for the mesoscopic extensibility of dendrimer-compacted DNA

Author keywords

[No Author keywords available]

Indexed keywords


EID: 77749317228     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2009.11.020     Document Type: Article
Times cited : (19)

References (49)
  • 1
    • 0021586266 scopus 로고
    • A new class of polymers-starburst-dendritic macromolecules
    • Tomalia, D. A., H. Baker, ..., P. Smith. 1985. A new class of polymers-starburst-dendritic macromolecules. Polym. J. 17:117-132.
    • (1985) Polym. J , vol.17 , pp. 117-132
    • Tomalia, D.A.1    Baker, H.2    Smith, P.3
  • 3
    • 0037959570 scopus 로고    scopus 로고
    • Structure control within poly(amidoamine) dendrimers: Size, shape and regio-chemical mimicry of globular proteins
    • Tomalia, D. A., B. Huang, ., J. W. Klimash. 2003. Structure control within poly(amidoamine) dendrimers: size, shape and regio-chemical mimicry of globular proteins. Tetrahedron. 59:3799-3813.
    • (2003) Tetrahedron , vol.59 , pp. 3799-3813
    • Tomalia, D.A.1    Huang, B.2    Klimash, J.W.3
  • 6
    • 28144454996 scopus 로고    scopus 로고
    • Mesomorphic complexes of poly(amidoamine) dendrimer with DNA
    • Liu, Y. C., H. L. Chen, ..., U. S. Jeng. 2005. Mesomorphic complexes of poly(amidoamine) dendrimer with DNA. Macromolecules. 38:9434-9440.
    • (2005) Macromolecules , vol.38 , pp. 9434-9440
    • Liu, Y.C.1    Chen, H.L.2    Jeng, U.S.3
  • 7
    • 50149085060 scopus 로고    scopus 로고
    • Atomic force microscopy investigations of the effect of DNase I on DNA-PAMAM dendrimer complexes
    • Abdelhady, H. G., S. Allen, ..., P. M. Williams. 2003. Atomic force microscopy investigations of the effect of DNase I on DNA-PAMAM dendrimer complexes. Biophys. J. 84:471A.
    • (2003) Biophys. J , vol.84
    • Abdelhady, H.G.1    Allen, S.2    Williams, P.M.3
  • 8
    • 0033528624 scopus 로고    scopus 로고
    • An EPR study of the interactions between starburst dendrimers and polynucleotides
    • Ottaviani, M. F., and B. Sacchi. 1999. An EPR study of the interactions between starburst dendrimers and polynucleotides. Macromolecules. 32:2275-2282.
    • (1999) Macromolecules , vol.32 , pp. 2275-2282
    • Ottaviani, M.F.1    Sacchi, B.2
  • 9
    • 33846164122 scopus 로고    scopus 로고
    • Structure and dynamics of DNA-dendrimer complexation: Role of counterions, water, and base pair sequence
    • Maiti, P. K., and B. Bagchi. 2006. Structure and dynamics of DNA-dendrimer complexation: role of counterions, water, and base pair sequence. Nano Lett. 6:2478-2485.
    • (2006) Nano Lett , vol.6 , pp. 2478-2485
    • Maiti, P.K.1    Bagchi, B.2
  • 10
    • 27644443819 scopus 로고    scopus 로고
    • DNA-dendrimer nanocluster electrostatics prediction with the nonlinear Poisson-Boltzmann equation
    • Nikakhtar, A., A. Nasehzadeh, ., G. A. Mansoori. 2005. DNA-dendrimer nanocluster electrostatics prediction with the nonlinear Poisson-Boltzmann equation. J. Comput. Theor. Nanosci. 2:378-384.
    • (2005) J. Comput. Theor. Nanosci , vol.2 , pp. 378-384
    • Nikakhtar, A.1    Nasehzadeh, A.2    Mansoori, G.A.3
  • 11
    • 34547112276 scopus 로고    scopus 로고
    • Formation and stability conditions of DNA-dendrimer nano-clusters
    • Nikakhtar, A., A. Nasehzadeh, and G. A. Mansoori. 2007. Formation and stability conditions of DNA-dendrimer nano-clusters. J. Comput. Theor. Nanosci. 4:521-528.
    • (2007) J. Comput. Theor. Nanosci , vol.4 , pp. 521-528
    • Nikakhtar, A.1    Nasehzadeh, A.2    Mansoori, G.A.3
  • 12
    • 34249881599 scopus 로고    scopus 로고
    • Dynamic light scattering and fluorescence study of the interaction between double-stranded DNA and poly(amidoamine) dendrimers
    • Orberg, M. L., K. Schillén, and T. Nylander. 2007. Dynamic light scattering and fluorescence study of the interaction between double-stranded DNA and poly(amidoamine) dendrimers. Biomacromolecules. 8:1557-1563.
    • (2007) Biomacromolecules , vol.8 , pp. 1557-1563
    • Orberg, M.L.1    Schillén, K.2    Nylander, T.3
  • 13
    • 33646563152 scopus 로고    scopus 로고
    • Amine terminated G-6 PAMAM dendrimer and its interaction with DNA probed by Hoechst 33258
    • Choi, Y. S., T. S. Cho, ..., S. K. Kim. 2006. Amine terminated G-6 PAMAM dendrimer and its interaction with DNA probed by Hoechst 33258. Biophys. Chem. 121:142-149.
    • (2006) Biophys. Chem , vol.121 , pp. 142-149
    • Choi, Y.S.1    Cho, T.S.2    Kim, S.K.3
  • 14
    • 33645150517 scopus 로고    scopus 로고
    • Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers
    • Ritort, F., S. Mihardja, ..., C. Bustamante. 2006. Condensation transition in DNA-polyaminoamide dendrimer fibers studied using optical tweezers. Phys. Rev. Lett. 96:118301.
    • (2006) Phys. Rev. Lett , vol.96 , pp. 118301
    • Ritort, F.1    Mihardja, S.2    Bustamante, C.3
  • 15
    • 0342929614 scopus 로고
    • Non-physical sampling distributions in Monte Carlo free-energy estimation-umbrella sampling
    • Torrie, G. M. , and J. P. Valleau. 1977. Non-physical 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.M.1    Valleau, J.P.2
  • 16
    • 0019558179 scopus 로고
    • Structure of a B-DNA dodecamer: Conformation and dynamics
    • Drew, H. R., R. M. Wing, ..., R. E. Dickerson. 1981. Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl. Acad. Sci. USA. 78:2179-2183.
    • (1981) Proc. Natl. Acad. Sci. USA , vol.78 , pp. 2179-2183
    • Drew, H.R.1    Wing, R.M.2    Dickerson, R.E.3
  • 17
    • 0004016501 scopus 로고
    • Comparison of simple potential functions for simulating liquid water
    • Jorgensen, W. L., J. Chandrasekhar, ..., M. L. Klein. 1983. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79:926-935.
    • (1983) J. Chem. Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Klein, M.L.3
  • 18
    • 0242593434 scopus 로고    scopus 로고
    • Development and current status of the CHARMM force field for nucleic acids
    • MacKerell, Jr., A. D., N. Banavali, and N. Foloppe. 2000-2001. Development and current status of the CHARMM force field for nucleic acids. Biopolymers. 56:257-265.
    • (2000) Biopolymers , vol.56 , pp. 257-265
    • MacKerell Jr., A.D.1    Banavali, N.2    Foloppe, N.3
  • 19
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P., G. Ciccotti, and H. J. C. Berendsen. 1977. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23:327-341.
    • (1977) J. Comput. Phys , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 20
    • 33645961739 scopus 로고
    • A smooth particle mesh Ewald method
    • Essmann, U., L. Perera, ..., L. G. Pedersen. 1995. A smooth particle mesh Ewald method. J. Chem. Phys. 103:8577-8593.
    • (1995) J. Chem. Phys , vol.103 , pp. 8577-8593
    • Essmann, U.1    Perera, L.2    Pedersen, L.G.3
  • 21
    • 34547809547 scopus 로고
    • A unified formulation of the constant temperature molecular-dynamics methods
    • Nosé, E. 1984. A unified formulation of the constant temperature molecular-dynamics methods. J. Chem. Phys. 81:511-519.
    • (1984) J. Chem. Phys , vol.81 , pp. 511-519
    • Nosé, E.1
  • 22
    • 0001538909 scopus 로고
    • Canonical dynamics: Equilibrium phase-space distributions
    • Hoover, W. G. 1985. Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A. 31:1695-1697.
    • (1985) Phys. Rev. A , vol.31 , pp. 1695-1697
    • Hoover, W.G.1
  • 23
    • 84986519238 scopus 로고
    • The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
    • Kumar, S., D. Bouzida, ..., J. M. Rosenberg. 1992. The weighted histogram analysis method for free-energy calculations on biomolecules. I. The method. J. Comput. Chem. 13:1011-1021.
    • (1992) J. Comput. Chem , vol.13 , pp. 1011-1021
    • Kumar, S.1    Bouzida, D.2    Rosenberg, J.M.3
  • 24
    • 0002372072 scopus 로고    scopus 로고
    • Using ethidium bromide to probe the interactions between DNA and dendrimers
    • Chen, W., N. Turro, and D. Tomalia. 2000. Using ethidium bromide to probe the interactions between DNA and dendrimers. Langmuir. 16:15-19.
    • (2000) Langmuir , vol.16 , pp. 15-19
    • Chen, W.1    Turro, N.2    Tomalia, D.3
  • 25
    • 0034284109 scopus 로고    scopus 로고
    • Structural basis of polyamine-DNA recognition: Spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy
    • Deng, H., V. A. Bloomfield, ..., G. J. Thomas, Jr. 2000. Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res. 28:3379-3385.
    • (2000) Nucleic Acids Res , vol.28 , pp. 3379-3385
    • Deng, H.1    Bloomfield, V.A.2    Thomas Jr., G.J.3
  • 26
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond, T. J., and C. A. Davey. 2003. The structure of DNA in the nucleosome core. Nature. 423:145-150.
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 28
    • 0027349270 scopus 로고
    • Bending of DNA by transcription factors
    • van der Vliet, P. C., and C. P. Verrijzer. 1993. Bending of DNA by transcription factors. Bioessays. 15:25-32.
    • (1993) Bioessays , vol.15 , pp. 25-32
    • van der Vliet, P.C.1    Verrijzer, C.P.2
  • 29
    • 0038574350 scopus 로고    scopus 로고
    • Non-viral gene therapy: Polycation-mediated DNA delivery
    • Thomas, M., and A. M. Klibanov. 2003. Non-viral gene therapy: polycation-mediated DNA delivery. Appl. Microbiol. Biotechnol. 62: 27-34.
    • (2003) Appl. Microbiol. Biotechnol , vol.62 , pp. 27-34
    • Thomas, M.1    Klibanov, A.M.2
  • 30
    • 1542375269 scopus 로고    scopus 로고
    • Mechanism of DNA compaction by yeast mitochondrial protein Abf2p
    • Friddle, R. W., J. E. Klare, ..., A. Noy. 2004. Mechanism of DNA compaction by yeast mitochondrial protein Abf2p. Biophys. J. 86: 1632-1639.
    • (2004) Biophys. J , vol.86 , pp. 1632-1639
    • Friddle, R.W.1    Klare, J.E.2    Noy, A.3
  • 31
    • 34249041190 scopus 로고    scopus 로고
    • Inter-DNA electrostatics from explicit solvent molecular dynamics simulations
    • Savelyev, A., and G. A. Papoian. 2007. Inter-DNA electrostatics from explicit solvent molecular dynamics simulations. J. Am. Chem. Soc. 129:6060-6061.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 6060-6061
    • Savelyev, A.1    Papoian, G.A.2
  • 32
    • 41149115685 scopus 로고    scopus 로고
    • Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules
    • Dai, L., Y. G. Mu, ..., J. R. van der Maarel. 2008. Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules. Phys. Rev. Lett. 100:118301.
    • (2008) Phys. Rev. Lett , vol.100 , pp. 118301
    • Dai, L.1    Mu, Y.G.2    van der Maarel, J.R.3
  • 33
    • 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
  • 34
    • 34548414064 scopus 로고    scopus 로고
    • Role of tension and twist in single-molecule DNA condensation
    • Besteman, K., S. Hage, ..., S. G. Lemay. 2007. Role of tension and twist in single-molecule DNA condensation. Nat. Phys. 3:641-644.
    • (2007) Nat. Phys , vol.3 , pp. 641-644
    • Besteman, K.1    Hage, S.2    Lemay, S.G.3
  • 35
    • 0034071761 scopus 로고    scopus 로고
    • Stretching of single collapsed DNA molecules
    • Baumann, C. G., V. A. Bloomfield, ..., S. M. Block. 2000. Stretching of single collapsed DNA molecules. Biophys. J. 78:1965-1978.
    • (2000) Biophys. J , vol.78 , pp. 1965-1978
    • Baumann, C.G.1    Bloomfield, V.A.2    Block, S.M.3
  • 36
    • 0037428451 scopus 로고    scopus 로고
    • Elastic response of single DNA molecules exhibits a reentrant collapsing transition
    • Murayama, Y., Y. Sakamaki, and M. Sano. 2003. Elastic response of single DNA molecules exhibits a reentrant collapsing transition. Phys. Rev. Lett. 90:018102.
    • (2003) Phys. Rev. Lett , vol.90 , pp. 018102
    • Murayama, Y.1    Sakamaki, Y.2    Sano, M.3
  • 37
    • 0000959868 scopus 로고    scopus 로고
    • Reentrant condensation of DNA induced by multivalent counterions
    • Nguyen, T. T., I. Rouzina, and B. I. Shklovskii. 2000. Reentrant condensation of DNA induced by multivalent counterions. J. Chem. Phys. 112:2562-2568.
    • (2000) J. Chem. Phys , vol.112 , pp. 2562-2568
    • Nguyen, T.T.1    Rouzina, I.2    Shklovskii, B.I.3
  • 38
    • 13444283512 scopus 로고    scopus 로고
    • The pulling force of a single DNA molecule condensed by spermidine
    • Zhang, R., and B. I. Shklovskii. 2005. The pulling force of a single DNA molecule condensed by spermidine. Physica A. 349:563-570.
    • (2005) Physica A , vol.349 , pp. 563-570
    • Zhang, R.1    Shklovskii, B.I.2
  • 39
    • 33646471468 scopus 로고
    • Statistical mechanics of fluid mixtures
    • Kirkwood, J. G. 1935. Statistical mechanics of fluid mixtures. J. Chem. Phys. 3:300-313.
    • (1935) J. Chem. Phys , vol.3 , pp. 300-313
    • Kirkwood, J.G.1
  • 40
    • 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
  • 41
    • 11544281834 scopus 로고    scopus 로고
    • Elastically coupled two-level systems as a model for biopolymer extensibility
    • Reif, J. M., M. Fernandez, and H. E. Gaub. 1998. Elastically coupled two-level systems as a model for biopolymer extensibility. Phys. Rev. Lett. 81:4764-4767.
    • (1998) Phys. Rev. Lett , vol.81 , pp. 4764-4767
    • Reif, J.M.1    Fernandez, M.2    Gaub, H.E.3
  • 42
    • 33751233867 scopus 로고    scopus 로고
    • The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force
    • Manning, G. S. 2006. The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys. J. 91:3607-3616.
    • (2006) Biophys. J , vol.91 , pp. 3607-3616
    • Manning, G.S.1
  • 43
    • 0022838901 scopus 로고
    • Intramolecular collapse of DNA structure and dynamics
    • Porschke, D. 1986. Intramolecular collapse of DNA structure and dynamics. J. Biomol. Struct. Dyn. 4:373-389.
    • (1986) J. Biomol. Struct. Dyn , vol.4 , pp. 373-389
    • Porschke, D.1
  • 45
    • 0018101150 scopus 로고
    • Models for the specific adhesion of cells to cells
    • Bell, G. I. 1978. Models for the specific adhesion of cells to cells. Science. 200:618-627.
    • (1978) Science , vol.200 , pp. 618-627
    • Bell, G.I.1
  • 46
    • 0000162429 scopus 로고    scopus 로고
    • Salt dependence of the free energy, enthalpy, and entropy of nonsequence specific DNA binding
    • Lundback, T., and T. Hard. 1996. Salt dependence of the free energy, enthalpy, and entropy of nonsequence specific DNA binding. J. Phys. Chem. 100:17690-17695.
    • (1996) J. Phys. Chem , vol.100 , pp. 17690-17695
    • Lundback, T.1    Hard, T.2
  • 47
    • 32644449056 scopus 로고    scopus 로고
    • A general method for manipulating DNA sequences from any organism with optical tweezers
    • Fuller, D. N., G. J. Gemmen, ..., D. E. Smith. 2006. A general method for manipulating DNA sequences from any organism with optical tweezers. Nucleic Acids Res. 34:e15.
    • (2006) Nucleic Acids Res , vol.34
    • Fuller, D.N.1    Gemmen, G.J.2    Smith, D.E.3
  • 48
    • 33845353937 scopus 로고    scopus 로고
    • Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA
    • Gemmen, G. J., R. Millin, and D. E. Smith. 2006. Dynamics of single DNA looping and cleavage by Sau3AI and effect of tension applied to the DNA. Biophys. J. 91:4154-4165.
    • (2006) Biophys. J , vol.91 , pp. 4154-4165
    • Gemmen, G.J.1    Millin, R.2    Smith, D.E.3
  • 49
    • 33645004171 scopus 로고    scopus 로고
    • Intrinsic rates and activation free energies from single-molecule pulling experiments
    • Dudko, O. K., G. Hummer, and A. Szabo. 2006. Intrinsic rates and activation free energies from single-molecule pulling experiments. Phys. Rev. Lett. 96:108101-108104.
    • (2006) Phys. Rev. Lett , vol.96 , pp. 108101-108104
    • Dudko, O.K.1    Hummer, G.2    Szabo, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.