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Volumn 8, Issue 6, 2012, Pages 2145-2156

DNA bending through large angles is aided by ionic screening

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EID: 84862168795     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300177r     Document Type: Article
Times cited : (34)

References (92)
  • 1
    • 20544460658 scopus 로고    scopus 로고
    • Protein-DNA recognition patterns and predictions
    • Sarai, A.; Kono, H. Protein-DNA recognition patterns and predictions Annu. Rev. Biophys. Biomol. Struct. 2005, 34, 379-398
    • (2005) Annu. Rev. Biophys. Biomol. Struct. , vol.34 , pp. 379-398
    • Sarai, A.1    Kono, H.2
  • 2
    • 0031238604 scopus 로고    scopus 로고
    • DNA recognition and bending
    • Allemann, R. K.; Egli, M. DNA recognition and bending Chem. Biol. 1997, 4, 643-650
    • (1997) Chem. Biol. , vol.4 , pp. 643-650
    • Allemann, R.K.1    Egli, M.2
  • 3
    • 0034435652 scopus 로고    scopus 로고
    • Structural and thermodynamic strategies for site-specific DNA binding proteins
    • Jen-Jacobson, L.; Engler, L. E.; Jacobson, L. A. Structural and thermodynamic strategies for site-specific DNA binding proteins Structure 2000, 8, 1015-1023
    • (2000) Structure , vol.8 , pp. 1015-1023
    • Jen-Jacobson, L.1    Engler, L.E.2    Jacobson, L.A.3
  • 4
    • 0036307707 scopus 로고    scopus 로고
    • Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 angstrom resolution
    • Davey, C. A.; Sargent, D. F.; Luger, K.; Maeder, A. W.; Richmond, T. J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 angstrom resolution J. Mol. Biol. 2002, 319, 1097-1113
    • (2002) J. Mol. Biol. , vol.319 , pp. 1097-1113
    • Davey, C.A.1    Sargent, D.F.2    Luger, K.3    Maeder, A.W.4    Richmond, T.J.5
  • 5
    • 0037992395 scopus 로고    scopus 로고
    • The structure of DNA in the nucleosome core
    • Richmond, T. J.; Davey, C. A. The structure of DNA in the nucleosome core Nature 2003, 423, 145-150
    • (2003) Nature , vol.423 , pp. 145-150
    • Richmond, T.J.1    Davey, C.A.2
  • 6
    • 0034610814 scopus 로고    scopus 로고
    • The language of covalent histone modifications
    • Strahl, B. D.; Allis, C. D. The language of covalent histone modifications Nature 2000, 403, 41-45
    • (2000) Nature , vol.403 , pp. 41-45
    • Strahl, B.D.1    Allis, C.D.2
  • 7
    • 84982060514 scopus 로고
    • Röntgenuntersuchung gelöster Fadenmoleküle
    • Kratky, O.; Porod, G. Röntgenuntersuchung gelöster Fadenmoleküle Recl. Trav. Chim. Pays-Bas 1949, 68, 1106-1123
    • (1949) Recl. Trav. Chim. Pays-Bas , vol.68 , pp. 1106-1123
    • Kratky, O.1    Porod, G.2
  • 8
    • 0025355712 scopus 로고
    • Application of the method of phage-T4 DNA ligase-catalyzed ring closure to the study of DNA structure. 2. NaCl dependence of DNA flexibility and helical repeat
    • Taylor, W. H.; Hagerman, P. J. Application of the method of phage-T4 DNA ligase-catalyzed ring closure to the study of DNA structure. 2. NaCl dependence of DNA flexibility and helical repeat J. Mol. Biol. 1990, 212, 363-376
    • (1990) J. Mol. Biol. , vol.212 , pp. 363-376
    • Taylor, W.H.1    Hagerman, P.J.2
  • 10
    • 85015087906 scopus 로고    scopus 로고
    • Ten years of tension: Single-molecule DNA mechanics
    • Bustamante, C.; Bryant, Z.; Smith, S. Ten years of tension: single-molecule DNA mechanics Nature 2003, 421, 423-427
    • (2003) Nature , vol.421 , pp. 423-427
    • Bustamante, C.1    Bryant, Z.2    Smith, S.3
  • 11
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier, T. E.; Widom, J. Spontaneous sharp bending of double-stranded DNA Mol. Cell 2004, 14, 355-352
    • (2004) Mol. Cell , vol.14 , pp. 355-352
    • Cloutier, T.E.1    Widom, J.2
  • 16
    • 0036293430 scopus 로고    scopus 로고
    • Contribution of the intrinsic curvature to measured DNA persistence length
    • Vologodskaia, M.; Vologodskii, A. Contribution of the intrinsic curvature to measured DNA persistence length J. Mol. Biol. 2002, 317, 205-213
    • (2002) J. Mol. Biol. , vol.317 , pp. 205-213
    • Vologodskaia, M.1    Vologodskii, A.2
  • 17
    • 70349602563 scopus 로고    scopus 로고
    • Probing the conformational distributions of subpersistence length DNA
    • Mastroianni, A. J.; Sivak, D. A.; Geisser, P. L.; Alivisatos, A. P. Probing the conformational distributions of subpersistence length DNA Biophys. J. 2009, 97, 1408-1417
    • (2009) Biophys. J. , vol.97 , pp. 1408-1417
    • Mastroianni, A.J.1    Sivak, D.A.2    Geisser, P.L.3    Alivisatos, A.P.4
  • 19
    • 0016850069 scopus 로고
    • Kinky helix
    • Crick, F. H. C.; Klug, A. Kinky helix Nature 1975, 255, 530-533
    • (1975) Nature , vol.255 , pp. 530-533
    • Crick, F.H.C.1    Klug, A.2
  • 21
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • Yan, J.; Marko, J. F. Localized single-stranded bubble mechanism for cyclization of short double helix DNA Phys. Rev. Lett. 2004, 93, 108108
    • (2004) Phys. Rev. Lett. , vol.93 , pp. 108108
    • Yan, J.1    Marko, J.F.2
  • 22
    • 20144362111 scopus 로고    scopus 로고
    • DNA dynamics: Bubble n flip for DNA cyclisation?
    • Travers, A. DNA dynamics: Bubble n flip for DNA cyclisation? Curr. Biol. 2005, 15, R377-R379
    • (2005) Curr. Biol. , vol.15
    • Travers, A.1
  • 23
    • 33749986806 scopus 로고    scopus 로고
    • Spontaneous sharp bending of DNA: Role of melting bubbles
    • Yuan, C.; Rhoades, E.; Lou, X. W.; Archer, L. A. Spontaneous sharp bending of DNA: role of melting bubbles Nucleic Acids Res. 2006, 34, 4554-4560
    • (2006) Nucleic Acids Res. , vol.34 , pp. 4554-4560
    • Yuan, C.1    Rhoades, E.2    Lou, X.W.3    Archer, L.A.4
  • 26
    • 77957240284 scopus 로고    scopus 로고
    • DNA curvature and flexibility in vitro and in vivo
    • Peters, J. P.; Maher, L. J. DNA curvature and flexibility in vitro and in vivo Q. Rev. Biophys. 2010, 44, 23-63
    • (2010) Q. Rev. Biophys. , vol.44 , pp. 23-63
    • Peters, J.P.1    Maher, L.J.2
  • 27
    • 0017895903 scopus 로고
    • The molecular theory of polyelectrolyte solutions with applications to the electrostatic solutions of polynucleotides
    • Manning, G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic solutions of polynucleotides Q. Rev. Biophys. 1978, 11, 179-246
    • (1978) Q. Rev. Biophys. , vol.11 , pp. 179-246
    • Manning, G.S.1
  • 30
    • 0036569686 scopus 로고    scopus 로고
    • Bending of DNA by asymmetric charge neutralization: All-atom energy simulations
    • Kosikov, K. M.; Gorin, A. A.; Lu, X. J.; Olson, W. K.; Manning, G. S. Bending of DNA by asymmetric charge neutralization: All-atom energy simulations J. Am. Chem. Soc. 2002, 124, 4838-4847
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 4838-4847
    • Kosikov, K.M.1    Gorin, A.A.2    Lu, X.J.3    Olson, W.K.4    Manning, G.S.5
  • 33
    • 3242882127 scopus 로고    scopus 로고
    • Origin of the intrinsic rigidity of DNA
    • Mills, J. B.; Hagerman, P. J. Origin of the intrinsic rigidity of DNA Nucleic Acids Res. 2004, 32, 4055-4059
    • (2004) Nucleic Acids Res. , vol.32 , pp. 4055-4059
    • Mills, J.B.1    Hagerman, P.J.2
  • 35
    • 28444490422 scopus 로고    scopus 로고
    • Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps
    • Dixit, S. B.; Beveridge, D. L.; Case, D. A.; Cheatham, T. E., 3rd; Giudice, E.; Lankas, F.; Lavery, R.; Maddocks, J. H.; Osman, R.; Sklenar, H.; Thayer, K. M.; Varnai, P. Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: Sequence context effects on the dynamical structures of the 10 unique dinucleotide steps Biophys. J. 2005, 89, 3721-3740
    • (2005) Biophys. J. , vol.89 , pp. 3721-3740
    • Dixit, S.B.1    Beveridge, D.L.2    Case, D.A.3    Giudice Iii, E.4    Giudice, E.5    Lankas, F.6    Lavery, R.7    Maddocks, J.H.8    Osman, R.9    Sklenar, H.10    Thayer, K.M.11    Varnai, P.12
  • 37
  • 38
    • 33749259954 scopus 로고    scopus 로고
    • Kinking occurs during molecular dynamics simulation of small DNA minicircles
    • Lankas, F.; Lavery, R.; Maddocks, J. H. Kinking occurs during molecular dynamics simulation of small DNA minicircles Structure 2006, 14, 1527-1534
    • (2006) Structure , vol.14 , pp. 1527-1534
    • Lankas, F.1    Lavery, R.2    Maddocks, J.H.3
  • 39
    • 42449117606 scopus 로고    scopus 로고
    • Magnitude and direction of DNA bending induced by screw-axis orientation: Influence of sequence mismatches and abasic sites
    • Curuksu, J.; Zakrzewska, K.; Zacharias, M. Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence mismatches and abasic sites Nucleic Acids Res. 2008, 36, 2268-2283
    • (2008) Nucleic Acids Res. , vol.36 , pp. 2268-2283
    • Curuksu, J.1    Zakrzewska, K.2    Zacharias, M.3
  • 40
    • 34250318638 scopus 로고    scopus 로고
    • Refinement of the AMBER force field for nucleic acids: Improving the description of α/γ conformers
    • Perez, A.; Marchan, I.; Svozil, D.; Sponer, J.; Cheatham, T. E.; Laughton, C. A.; Orozco, M. Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 2007, 92, 3817-3829
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 41
    • 67649883207 scopus 로고    scopus 로고
    • Local and global effects of strong DNA bending induced during molecular dynamics simulations
    • Curuksu, J.; Zacharias, M.; Lavery, R.; Zakrzewska, K. Local and global effects of strong DNA bending induced during molecular dynamics simulations Nucleic Acids Res. 2009, 37, 3766-3773
    • (2009) Nucleic Acids Res. , vol.37 , pp. 3766-3773
    • Curuksu, J.1    Zacharias, M.2    Lavery, R.3    Zakrzewska, K.4
  • 42
    • 82555175927 scopus 로고    scopus 로고
    • Is DNAs Rigidity Dominated by Electrostatic or Nonelectrostatic Interactions?
    • Savalyev, A.; Materese, C. K.; Papoian, G. A. Is DNAs Rigidity Dominated by Electrostatic or Nonelectrostatic Interactions? J. Am. Chem. Soc. 2011, 133, 19290-19293
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 19290-19293
    • Savalyev, A.1    Materese, C.K.2    Papoian, G.A.3
  • 43
    • 0032522139 scopus 로고    scopus 로고
    • DNA bending: The prevalence of kinkiness and the virtues of normality
    • Dickerson, R. E. DNA bending: the prevalence of kinkiness and the virtues of normality Nucleic Acids Res. 1998, 26, 1906-1926
    • (1998) Nucleic Acids Res. , vol.26 , pp. 1906-1926
    • Dickerson, R.E.1
  • 44
    • 0000087970 scopus 로고
    • An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol
    • Hooft, R. W. W.; van Eijck, B. P.; Kroon, J. An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol J. Chem. Phys. 1992, 97, 6690-6694
    • (1992) J. Chem. Phys. , vol.97 , pp. 6690-6694
    • Hooft, R.W.W.1    Van Eijck, B.P.2    Kroon, J.3
  • 45
    • 4344606960 scopus 로고    scopus 로고
    • Multidimensional Adaptive Umbrella Sampling: Applications to Main Chain and Side Chain Peptide Conformations
    • Bartels, C.; Karplus, M. Multidimensional Adaptive Umbrella Sampling: Applications to Main Chain and Side Chain Peptide Conformations J. Comput. Chem. 1997, 18, 1450-1462
    • (1997) J. Comput. Chem. , vol.18 , pp. 1450-1462
    • Bartels, C.1    Karplus, M.2
  • 46
    • 0348244547 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
    • Foloppe, N.; MacKerell, A. D., Jr. All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 2000, 21, 86-104
    • (2000) J. Comput. Chem. , vol.21 , pp. 86-104
    • Foloppe, N.1    Mackerell Jr., A.D.2
  • 47
    • 0000214231 scopus 로고    scopus 로고
    • All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
    • MacKerell, A. D., Jr.; Banavali, N. K. All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution J. Comput. Chem. 2000, 21, 105-120
    • (2000) J. Comput. Chem. , vol.21 , pp. 105-120
    • Mackerell Jr., A.D.1    Banavali, N.K.2
  • 48
    • 0029126044 scopus 로고
    • The assessment of the geometry of dinucleotide steps in double-helical DNA; A new local calculation scheme
    • El Hassan, M. A.; Calladine, C. R. The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme J. Mol. Biol. 1995, 251, 648-664
    • (1995) J. Mol. Biol. , vol.251 , pp. 648-664
    • El Hassan, M.A.1    Calladine, C.R.2
  • 49
    • 0024539180 scopus 로고
    • Defining the structure of irregular nucleic acids: Conventions and principles
    • Lavery, R.; Sklenar, H. Defining the structure of irregular nucleic acids: conventions and principles J. Biomol. Struct. Dyn. 1989, 6, 655-667
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 655-667
    • Lavery, R.1    Sklenar, H.2
  • 51
    • 0024543897 scopus 로고
    • A self-consistent formulation for analysis and generation of non-uniform DNA structures
    • Bhattacharya, D.; Bansal, M. A self-consistent formulation for analysis and generation of non-uniform DNA structures J. Biomol. Struct. Dyn. 1989, 6, 635-653
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 635-653
    • Bhattacharya, D.1    Bansal, M.2
  • 52
    • 0028230287 scopus 로고
    • Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures
    • Babcock, M. S.; Pendault, E. P. D.; Olson, W. K. Nucleic acid structure analysis: Mathematics for local cartesian and helical structure parameters that are truly comparable between structures J. Mol. Biol. 1994, 237, 125-156
    • (1994) J. Mol. Biol. , vol.237 , pp. 125-156
    • Babcock, M.S.1    Pendault, E.P.D.2    Olson, W.K.3
  • 53
    • 0028931709 scopus 로고
    • B-DNA twisting correlates with base pair morphology
    • Gorin, A. A.; Zhurkin, V. B.; Olson, W. K. B-DNA twisting correlates with base pair morphology J. Mol. Biol. 1995, 247, 34-48
    • (1995) J. Mol. Biol. , vol.247 , pp. 34-48
    • Gorin, A.A.1    Zhurkin, V.B.2    Olson, W.K.3
  • 54
    • 0242396923 scopus 로고    scopus 로고
    • 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
    • Lu, X.-J.; Olson, W. K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 2003, 31, 5108-5121
    • (2003) Nucleic Acids Res. , vol.31 , pp. 5108-5121
    • Lu, X.-J.1    Olson, W.K.2
  • 55
    • 0033614014 scopus 로고    scopus 로고
    • Resolving the discrepancies among nucleic acid conformational analyses
    • Lu, X.-J.; Olson, W. K. Resolving the discrepancies among nucleic acid conformational analyses J. Mol. Biol. 1999, 285, 1563-1575
    • (1999) J. Mol. Biol. , vol.285 , pp. 1563-1575
    • Lu, X.-J.1    Olson, W.K.2
  • 56
    • 77953897406 scopus 로고    scopus 로고
    • Mechanism of the Calcium-Induced trans-cis Isomerization of a Non-Prolyl Peptide Bond in Clostridium histolyticum Collagenase
    • Spiriti, J.; van der Vaart, A. Mechanism of the Calcium-Induced trans-cis Isomerization of a Non-Prolyl Peptide Bond in Clostridium histolyticum Collagenase Biochem. 2010, 49, 5314-5320
    • (2010) Biochem. , vol.49 , pp. 5314-5320
    • Spiriti, J.1    Van Der Vaart, A.2
  • 57
    • 41449104758 scopus 로고    scopus 로고
    • Modulation of protein stability by O-glycosylation in a designed Gc-MAF analog
    • Spiriti, J.; Bogani, F.; Ghirlanda, G.; van der Vaart, A. Modulation of protein stability by O-glycosylation in a designed Gc-MAF analog Biophys. Chem. 2008, 134, 157-167
    • (2008) Biophys. Chem. , vol.134 , pp. 157-167
    • Spiriti, J.1    Bogani, F.2    Ghirlanda, G.3    Van Der Vaart, A.4
  • 59
    • 0001276779 scopus 로고
    • Dynamics of Ligand Escape from the Heme Pocket of Myoglobin
    • Kottalam, J.; Case, D. A. Dynamics of Ligand Escape from the Heme Pocket of Myoglobin J. Am. Chem. Soc. 1988, 110, 7690-7697
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 7690-7697
    • Kottalam, J.1    Case, D.A.2
  • 61
    • 0030059225 scopus 로고    scopus 로고
    • Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force
    • Grubmüller, H.; Heymann, B.; Tavan, P. Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force Science 1996, 271, 997-999
    • (1996) Science , vol.271 , pp. 997-999
    • Grubmüller, H.1    Heymann, B.2    Tavan, P.3
  • 63
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes J. Comput. Phys. 1977, 23, 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 64
    • 33646987405 scopus 로고
    • Optimized Monte-Carlo data-analysis
    • Ferrenberg, A. M.; Swendsen, R. H. Optimized Monte-Carlo data-analysis Phys. Rev. Lett. 1989, 63, 1195-1198
    • (1989) Phys. Rev. Lett. , vol.63 , pp. 1195-1198
    • Ferrenberg, A.M.1    Swendsen, R.H.2
  • 65
    • 27744578574 scopus 로고    scopus 로고
    • A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
    • Coman, D.; Russu, I. M. A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA Biophys. J. 2005, 89, 3285-3292
    • (2005) Biophys. J. , vol.89 , pp. 3285-3292
    • Coman, D.1    Russu, I.M.2
  • 67
    • 33845381916 scopus 로고    scopus 로고
    • Evaluation of Elastic Properties of Atomistic DNA Models
    • Mazur, A. K. Evaluation of Elastic Properties of Atomistic DNA Models Biophys. J. 2006, 91, 4507-4518
    • (2006) Biophys. J. , vol.91 , pp. 4507-4518
    • Mazur, A.K.1
  • 68
    • 0031592942 scopus 로고    scopus 로고
    • Structure and conformation of helical nucleic acids: Analysis program (SCHNAaP)
    • Lu, X.-J.; El Hassan, M. A.; Hunter, C. A. Structure and conformation of helical nucleic acids: analysis program (SCHNAaP) J. Mol. Biol. 1997, 273, 668-680
    • (1997) J. Mol. Biol. , vol.273 , pp. 668-680
    • Lu, X.-J.1    El Hassan, M.A.2    Hunter, C.A.3
  • 69
    • 85014002810 scopus 로고    scopus 로고
    • Modeling DNA structure, elasticity, and deformations at the base-pair level
    • Mergell, B.; Ejtehadi, M.; Everaers, R. Modeling DNA structure, elasticity, and deformations at the base-pair level Phys. Rev. E 2003, 68, 021911
    • (2003) Phys. Rev. e , vol.68 , pp. 021911
    • Mergell, B.1    Ejtehadi, M.2    Everaers, R.3
  • 70
    • 77952355398 scopus 로고    scopus 로고
    • Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics
    • Dans, P. D.; Zeida, A.; Pantano, S.; Coarse Grained, A Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics J. Chem. Theory Comput. 2010, 6, 1711-1725
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1711-1725
    • Dans, P.D.1    Zeida, A.2    Pantano, S.3    Coarse Grained, A.4
  • 71
    • 78650553525 scopus 로고    scopus 로고
    • Chemically accurate coarse graining of double-stranded DNA
    • Savelyev, A.; Papoian, G. A. Chemically accurate coarse graining of double-stranded DNA Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 20340-20345
    • (2010) Proc. Natl. Acad. Sci. U.S.A. , vol.107 , pp. 20340-20345
    • Savelyev, A.1    Papoian, G.A.2
  • 72
    • 77951569390 scopus 로고    scopus 로고
    • DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
    • Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. DNA Nanotweezers Studied with a Coarse-Grained Model of DNA Phys. Rev. Lett. 2010, 104, 178101
    • (2010) Phys. Rev. Lett. , vol.104 , pp. 178101
    • Ouldridge, T.E.1    Louis, A.A.2    Doye, J.P.K.3
  • 73
    • 50249107536 scopus 로고    scopus 로고
    • Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling
    • Voth, G. A. CRC Press: Boca Raton, FL
    • Olson, W. K.; Colasanti, A. V.; Czapla, L.; Zheng, G., Insights into the Sequence-Dependent Macromolecular Properties of DNA from Base-Pair Level Modeling. In Coarse-Graining of Condensed Phase and Biomolecular Systems, Voth, G. A., Ed.; CRC Press: Boca Raton, FL, 2009; pp 205-224.
    • (2009) Coarse-Graining of Condensed Phase and Biomolecular Systems , pp. 205-224
    • Olson, W.K.1    Colasanti, A.V.2    Czapla, L.3    Zheng, G.4
  • 76
    • 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, 1266-1281
    • (2010) Proteins , vol.78 , pp. 1266-1281
    • Gopal, S.M.1    Mukherjee, S.2    Cheng, Y.-M.3    Feig, M.4
  • 77
    • 77949889822 scopus 로고    scopus 로고
    • A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
    • Morriss-Andrews, A.; Rottler, J.; Plotkin, S. S. A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality J. Chem. Phys. 2010, 132, 035105
    • (2010) J. Chem. Phys. , vol.132 , pp. 035105
    • Morriss-Andrews, A.1    Rottler, J.2    Plotkin, S.S.3
  • 79
    • 34147191973 scopus 로고    scopus 로고
    • DNA stretching and extreme kinking in the nucleosome core
    • Ong, M. S.; Richmond, T. J.; Davey, C. A. DNA stretching and extreme kinking in the nucleosome core J. Mol. Biol. 2007, 368, 1067-1074
    • (2007) J. Mol. Biol. , vol.368 , pp. 1067-1074
    • Ong, M.S.1    Richmond, T.J.2    Davey, C.A.3
  • 81
    • 33644791019 scopus 로고    scopus 로고
    • Generalized theory of semiflexible polymers
    • Wiggins, P. A.; Nelson, P. C. Generalized theory of semiflexible polymers Phys. Rev. E 2006, 73, 31906
    • (2006) Phys. Rev. e , vol.73 , pp. 31906
    • Wiggins, P.A.1    Nelson, P.C.2
  • 82
    • 33748621478 scopus 로고    scopus 로고
    • Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
    • Sponer, J.; Leszczynski, J.; Hobza, P. Nature of nucleic acid-base stacking: Nonempirical ab initio and empirical potential characterization of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs J. Phys. Chem. 1996, 100, 5590-5596
    • (1996) J. Phys. Chem. , vol.100 , pp. 5590-5596
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 83
    • 0001225025 scopus 로고    scopus 로고
    • Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations
    • Sponer, J.; Leszczynski, J.; Hobza, P. Base stacking in cytosine dimer. A comparison of correlated ab initio calculations with three empirical potential models and density functional theory calculations J. Comput. Chem. 1996, 17, 841-850
    • (1996) J. Comput. Chem. , vol.17 , pp. 841-850
    • Sponer, J.1    Leszczynski, J.2    Hobza, P.3
  • 84
    • 33645326510 scopus 로고    scopus 로고
    • Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
    • Sponer, J.; Jurecka, P.; Marchan, I.; Luque, J.; Orozco, M.; Hobza, P. Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps Chem. - Eur. J. 2006, 12, 2854-2865
    • (2006) Chem. - Eur. J. , vol.12 , pp. 2854-2865
    • Sponer, J.1    Jurecka, P.2    Marchan, I.3    Luque, J.4    Orozco, M.5    Hobza, P.6
  • 85
    • 77954996425 scopus 로고    scopus 로고
    • On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes
    • Kolář, M.; Berka, K.; Jurečka, P.; Hobza, P. On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes ChemPhysChem 2010, 11, 2399-2408
    • (2010) ChemPhysChem , vol.11 , pp. 2399-2408
    • Kolář, M.1    Berka, K.2    Jurečka, P.3    Hobza, P.4
  • 86
    • 79951819347 scopus 로고    scopus 로고
    • Cy3-DNA stacking interactions strongly depend on the identity of the terminal base pair
    • Spiriti, J.; Binder, J. K.; Levitus, M.; van der Vaart, A. Cy3-DNA stacking interactions strongly depend on the identity of the terminal base pair Biophys. J. 2011, 100, 1049-1057
    • (2011) Biophys. J. , vol.100 , pp. 1049-1057
    • Spiriti, J.1    Binder, J.K.2    Levitus, M.3    Van Der Vaart, A.4
  • 87
    • 79251594507 scopus 로고    scopus 로고
    • The Energetic Contribution of Induced Electrostatic Asymmetry to DNA Bending by a Site-Specific Protein
    • Hancock, S. P.; Hiller, D. A.; Perona, J. J.; Jen-Jacobson, L. The Energetic Contribution of Induced Electrostatic Asymmetry to DNA Bending by a Site-Specific Protein J. Mol. Biol. 2011, 406, 285-312
    • (2011) J. Mol. Biol. , vol.406 , pp. 285-312
    • Hancock, S.P.1    Hiller, D.A.2    Perona, J.J.3    Jen-Jacobson, L.4
  • 88
    • 36749098380 scopus 로고    scopus 로고
    • Dynamics of B-DNA on the Microsecond Time Scale
    • Perez, A.; Luque, F. J.; Orozco, M. Dynamics of B-DNA on the Microsecond Time Scale J. Am. Chem. Soc. 2007, 129, 14739-14745
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 14739-14745
    • Perez, A.1    Luque, F.J.2    Orozco, M.3
  • 89
    • 78751654619 scopus 로고    scopus 로고
    • Ion and Solvent Density Distributions around Canonical DNA from Integral Equations
    • Howard, J. J.; Lynch, G. C.; Pettitt, B. M. Ion and Solvent Density Distributions around Canonical DNA from Integral Equations J. Phys. Chem. B 2011, 115, 547-556
    • (2011) J. Phys. Chem. B , vol.115 , pp. 547-556
    • Howard, J.J.1    Lynch, G.C.2    Pettitt, B.M.3
  • 90
    • 84856748887 scopus 로고    scopus 로고
    • Do monovalent mobile ions affect DNAs flexibility at high salt content?
    • Savelyev, A. Do monovalent mobile ions affect DNAs flexibility at high salt content? Phys. Chem. Chem. Phys. 2012, 14, 2250-2254
    • (2012) Phys. Chem. Chem. Phys. , vol.14 , pp. 2250-2254
    • Savelyev, A.1
  • 91
    • 0030593510 scopus 로고    scopus 로고
    • Structure of the CAP-DNA complex at 2.5 angstrom resolution: A complete picture of the protein-DNA interface
    • Parkinson, G.; Wilson, C.; Gunasekera, A.; Ebright, Y. W.; Ebright, R. E.; Berman, H. M. Structure of the CAP-DNA complex at 2.5 angstrom resolution: A complete picture of the protein-DNA interface J. Mol. Biol. 1996, 260, 395-408
    • (1996) J. Mol. Biol. , vol.260 , pp. 395-408
    • Parkinson, G.1    Wilson, C.2    Gunasekera, A.3    Ebright, Y.W.4    Ebright, R.E.5    Berman, H.M.6
  • 92
    • 0034708226 scopus 로고    scopus 로고
    • Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
    • Bruner, S. D.; Norman, D. P. G.; Verdine, G. L. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA Nature 2000, 403, 859-866.
    • (2000) Nature , vol.403 , pp. 859-866
    • Bruner, S.D.1    Norman, D.P.G.2    Verdine, G.L.3


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