-
1
-
-
33845810345
-
High flexibility of DNA on short length scales probed by atomic force microscopy
-
Wiggins P A, van der Heijden T, Moreno-Herrero F, Spakowitz A, Phillips R, Widom J, Dekker C and Nelson P C 2006 High flexibility of DNA on short length scales probed by atomic force microscopy Nature Nanotechnol. 1 137-41
-
(2006)
Nature Nanotechnol.
, vol.1
, pp. 137-141
-
-
Wiggins, P.A.1
Van Der Heijden, T.2
Moreno-Herrero, F.3
Spakowitz, A.4
Phillips, R.5
Widom, J.6
Dekker, C.7
Nelson, P.C.8
-
2
-
-
62649085538
-
The DNA-encoded nucleosome organization of a eukaryotic genome
-
Kaplan N, Moore I K, Fondufe-Mittendorf Y, Gossett A J, Tillo D, Field Y, LeProust E M, Hughes T R, Lieb J D, Widom J and Segal E 2009 The DNA-encoded nucleosome organization of a eukaryotic genome Nature 458 362-6
-
(2009)
Nature
, vol.458
, pp. 362-366
-
-
Kaplan, N.1
Moore, I.K.2
Fondufe-Mittendorf, Y.3
Gossett, A.J.4
Tillo, D.5
Field, Y.6
Leproust, E.M.7
Hughes, T.R.8
Lieb, J.D.9
Widom, J.10
Segal, E.11
-
3
-
-
84865546608
-
Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
-
Vafabakhsh R and Ha T 2012 Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization Science 337 1097-101
-
(2012)
Science
, vol.337
, pp. 1097-1101
-
-
Vafabakhsh, R.1
Ha, T.2
-
4
-
-
80052461558
-
Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine
-
Ito S, Shen L, Dai Q, Wu S C, Collins L B, Swenberg J A, He C and Zhang Y 2011 Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine Science 333 1300-3
-
(2011)
Science
, vol.333
, pp. 1300-1303
-
-
Ito, S.1
Shen, L.2
Dai, Q.3
Wu, S.C.4
Collins, L.B.5
Swenberg, J.A.6
He, C.7
Zhang, Y.8
-
5
-
-
0002610948
-
Independent functions of viral protein and nucleic acid in growth of bacteriophage
-
Hershey A D and Chase M 1952 Independent functions of viral protein and nucleic acid in growth of bacteriophage J. Gen. Physiol. 36 39-56
-
(1952)
J. Gen. Physiol.
, vol.36
, pp. 39-56
-
-
Hershey, A.D.1
Chase, M.2
-
6
-
-
0038497542
-
A structure for deoxyribose nucleic acids
-
Watson J D and Crick F H C 1953 A structure for deoxyribose nucleic acids Nature 171 737-8
-
(1953)
Nature
, vol.171
, pp. 737-738
-
-
Watson, J.D.1
Crick, F.H.C.2
-
7
-
-
34347111095
-
Beziehungen zwischen Molekülgröße, statistischer Molekülgestalt und elastischen Eigenschaften hochpolymerer Stoffe
-
Kuhn W 1936 Beziehungen zwischen Molekülgröße, statistischer Molekülgestalt und elastischen Eigenschaften hochpolymerer Stoffe Colloid Polym. Sci. 76 258-71
-
(1936)
Colloid Polym. Sci.
, vol.76
, pp. 258-271
-
-
Kuhn, W.1
-
8
-
-
36849116660
-
The behavior of macromolecules in inhomogeneous flow
-
Kramers H A 1946 The behavior of macromolecules in inhomogeneous flow J. Chem. Phys. 14 415
-
(1946)
J. Chem. Phys.
, vol.14
, pp. 415
-
-
Kramers, H.A.1
-
9
-
-
84982060514
-
Röntgenuntersuchung gelöster Fadenmoleküle
-
Kratky O and Porod G 1949 Röntgenuntersuchung gelöster Fadenmoleküle Recl. Trav. Chim. Pay. B 68 1106-22
-
(1949)
Recl. Trav. Chim. Pay.
, vol.68
, pp. 1106-1122
-
-
Kratky, O.1
Porod, G.2
-
10
-
-
0012450870
-
Lichtzerstreuung an ziemlich gestreckten Fadenmolekülen
-
Peterlin V A 1953 Lichtzerstreuung an ziemlich gestreckten Fadenmolekülen Makromol. Chem. 9 244-68
-
(1953)
Makromol. Chem.
, vol.9
, pp. 244-268
-
-
Peterlin, V.A.1
-
11
-
-
70449163337
-
The physical chemistry of deoxyribonucleic acids
-
Doty P 1957 The physical chemistry of deoxyribonucleic acids J. Cell. Comparat. Physiol. 49 27-57
-
(1957)
J. Cell. Comparat. Physiol.
, vol.49
, pp. 27-57
-
-
Doty, P.1
-
12
-
-
36849138710
-
Generalization of the one-dimensional Ising model applicable to helix transitions in nucleic acids and proteins
-
Hill T L 1959 Generalization of the one-dimensional Ising model applicable to helix transitions in nucleic acids and proteins J. Chem. Phys. 30 383-7
-
(1959)
J. Chem. Phys.
, vol.30
, pp. 383-387
-
-
Hill, T.L.1
-
13
-
-
0000448226
-
Statistical mechanics of helix-coil transitions in biological macromolecules
-
Gibbs J H and DiMarzio E A 1959 Statistical mechanics of helix-coil transitions in biological macromolecules J. Chem. Phys. 30 271
-
(1959)
J. Chem. Phys.
, vol.30
, pp. 271
-
-
Gibbs, J.H.1
Dimarzio, E.A.2
-
14
-
-
0000754002
-
Theory of 'melting' of the helical form in double chains of the DNA type
-
Zimm B H 1960 Theory of 'melting' of the helical form in double chains of the DNA type J. Chem. Phys. 33 1349-56
-
(1960)
J. Chem. Phys.
, vol.33
, pp. 1349-1356
-
-
Zimm, B.H.1
-
15
-
-
0005060615
-
Some conformation problems for long macromolecules
-
de Gennes P G 1969 Some conformation problems for long macromolecules Rep. Prog. Phys. 32 187-205
-
(1969)
Rep. Prog. Phys.
, vol.32
, Issue.1
, pp. 187-205
-
-
De Gennes, P.G.1
-
17
-
-
0017642366
-
Visualization of drug-nucleic acid interactions at atomic resolution: III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions
-
Sobell H M, Tsai C C, Jain S C and Gilbert S G 1977 Visualization of drug-nucleic acid interactions at atomic resolution: III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions J. Mol. Biol. 114 333-65
-
(1977)
J. Mol. Biol.
, vol.114
, pp. 333-365
-
-
Sobell, H.M.1
Tsai, C.C.2
Jain, S.C.3
Gilbert, S.G.4
-
18
-
-
0000652458
-
Possibility of nonkinked packing of DNA in chromatin
-
Sussman J L and Trifonov E N 1978 Possibility of nonkinked packing of DNA in chromatin Proc. Natl Acad. Sci. USA 75 103-7
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, pp. 103-107
-
-
Sussman, J.L.1
Trifonov, E.N.2
-
19
-
-
0001766554
-
How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations
-
Levitt M 1978 How many base-pairs per turn does DNA have in solution and in chromatin? Some theoretical calculations Proc. Natl Acad. Sci. USA 75 640-4
-
(1978)
Proc. Natl Acad. Sci. USA
, vol.75
, pp. 640-644
-
-
Levitt, M.1
-
20
-
-
84987058889
-
Interaction of water with DNA single and double helix in the B conformation
-
Clementi E and Corongiu G 1979 Interaction of water with DNA single and double helix in the B conformation Int. J. Quantum Chem. 16 897-915
-
(1979)
Int. J. Quantum Chem.
, vol.16
, pp. 897-915
-
-
Clementi, E.1
Corongiu, G.2
-
21
-
-
0001545373
-
A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T = 300 K
-
Clementi E and Corongiu G 1980 A theoretical study on the water structure for nucleic acids bases and base pairs in solution at T = 300 K J. Chem. Phys. 72 3979-92
-
(1980)
J. Chem. Phys.
, vol.72
, pp. 3979-3992
-
-
Clementi, E.1
Corongiu, G.2
-
22
-
-
0020262664
-
Computer simulation of DNA double-helix dynamics
-
Levitt M 1983 Computer simulation of DNA double-helix dynamics Symp. on Quantitative Biology (Cold Spring Harbor, NY,) vol 47 pp 251-62
-
(1983)
Symp. on Quantitative Biology
, vol.47
, pp. 251-262
-
-
Levitt, M.1
-
24
-
-
0001555216
-
A molecular dynamics simulation of double-helical B-DNA including counterions and water
-
Seibel G L, Singh U C and Kollman P A 1985 A molecular dynamics simulation of double-helical B-DNA including counterions and water Proc. Natl Acad. Sci. USA 82 6537-40
-
(1985)
Proc. Natl Acad. Sci. USA
, vol.82
, pp. 6537-6540
-
-
Seibel, G.L.1
Singh, U.C.2
Kollman, P.A.3
-
25
-
-
0002593973
-
Molecular dynamics simulation on hydration, structure and motions of DNA oligomers
-
ed E Westhof (Boca Raton, FL: CRC Press) chapter 6
-
Beveridge D L, Swaminathan S, Ravishanker G, Withka J M, Srinivasan J, Prevost C, Louise-May S, Langley D R, DiCapua F M and Bolton P H 1993 Molecular dynamics simulation on hydration, structure and motions of DNA oligomers Water and Biological Macromolecules ed E Westhof (Boca Raton, FL: CRC Press) chapter 6 p 165
-
(1993)
Water and Biological Macromolecules
, pp. 165
-
-
Beveridge, D.L.1
Swaminathan, S.2
Ravishanker, G.3
Withka, J.M.4
Srinivasan, J.5
Prevost, C.6
Louise-May, S.7
Langley, D.R.8
Dicapua, F.M.9
Bolton, P.H.10
-
26
-
-
0030007604
-
Modelling DNA in aqueous solutions - Theoretical and computer simulation studies on the ion atmosphere of DNA
-
Jayaram B and Beveridge D 1996 Modelling DNA in aqueous solutions - theoretical and computer simulation studies on the ion atmosphere of DNA Annu. Rev. Biophys. Biomol. Struct. 25 367-94
-
(1996)
Annu. Rev. Biophys. Biomol. Struct.
, vol.25
, pp. 367-394
-
-
Jayaram, B.1
Beveridge, D.2
-
29
-
-
0029170114
-
Molecular dynamics simulations on solvated biomolecular systems: The particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins
-
Cheatham T E III, Miller J L, Fox T, Darden T A and Kollman P A 1995 Molecular dynamics simulations on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins J. Am. Chem. Soc. 117 4193-4
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
30
-
-
0033654654
-
Molecular dynamics simulation of nucleic acids
-
Cheatham T E and Kollman P A 2000 Molecular dynamics simulation of nucleic acids Annu. Rev. Phys. Chem. 51 435-71
-
(2000)
Annu. Rev. Phys. Chem.
, vol.51
, pp. 435-471
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
32
-
-
0029941154
-
Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution
-
Cheatham T E and Kollman P A 1996 Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution J. Mol. Biol. 259 434-44
-
(1996)
J. Mol. Biol.
, vol.259
, pp. 434-444
-
-
Cheatham, T.E.1
Kollman, P.A.2
-
33
-
-
0030862276
-
A 5-nanosecond molecular dynamics trajectory for B-DNA: Analysis of structure, motion and solvation
-
Young M A, Ravishanker G and Beveridge D L 1997 A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motion and solvation Biophys. J. 73 2313-36
-
(1997)
Biophys. J.
, vol.73
, pp. 2313-2336
-
-
Young, M.A.1
Ravishanker, G.2
Beveridge, D.L.3
-
34
-
-
14244271476
-
Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
-
Cheatham T E and Young M A 2000 Molecular dynamics simulation of nucleic acids: successes, limitations, and promise Biopolymers 56 232-56
-
(2000)
Biopolymers
, vol.56
, pp. 232-256
-
-
Cheatham, T.E.1
Young, M.A.2
-
35
-
-
0023029727
-
DNA conformation is determined by economics in the hydration of phosphate groups
-
Saenger W, Hunter W N and Kennard O 1986 DNA conformation is determined by economics in the hydration of phosphate groups Nature 324 385-8
-
(1986)
Nature
, vol.324
, pp. 385-388
-
-
Saenger, W.1
Hunter, W.N.2
Kennard, O.3
-
36
-
-
0006627150
-
A molecular simulation picture of DNA hydration around A- and B-DNA
-
Feig M and Pettitt B M 1998 A molecular simulation picture of DNA hydration around A- and B-DNA Biopolymers 48 199-209
-
(1998)
Biopolymers
, vol.48
, pp. 199-209
-
-
Feig, M.1
Pettitt, B.M.2
-
37
-
-
11644276439
-
Limiting laws and counterion condensation in polyelectrolyte solutions: I. Colligative properties
-
Manning G S 1969 Limiting laws and counterion condensation in polyelectrolyte solutions: I. Colligative properties J. Chem. Phys. 51 924
-
(1969)
J. Chem. Phys.
, vol.51
, pp. 924
-
-
Manning, G.S.1
-
38
-
-
0031047279
-
Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
-
Young M A, Jayaram B and Beveridge D L 1997 Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: fractional occupancy of electronegative pockets J. Am. Chem. Soc. 119 59-69
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 59-69
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
39
-
-
33645091351
-
Monte Carlo simulation study of ion distribution and osmotic pressure in hexagonally oriented DNA
-
Lyubartsev A P and Nordenskiöld L 1995 Monte Carlo simulation study of ion distribution and osmotic pressure in hexagonally oriented DNA J. Phys. Chem. 99 10373-82
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 10373-10382
-
-
Lyubartsev, A.P.1
Nordenskiöld, L.2
-
40
-
-
0032851951
-
Sodium and chlorine ions as part of the DNA solvation shell
-
Feig M and Pettitt B M 1999 Sodium and chlorine ions as part of the DNA solvation shell Biophys. J. 77 1769-81
-
(1999)
Biophys. J.
, vol.77
, pp. 1769-1781
-
-
Feig, M.1
Pettitt, B.M.2
-
41
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still W C, Tempczyk A, Hawley R C and Hendrickson T 1990 Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 112 6127-9
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrickson, T.4
-
42
-
-
0000043930
-
Solvation free energy of biomacromolecules: Parameters for a modified generalized Born model consistent with the AMBER force field
-
Jayaram B, Sprous D and Beveridge D L 1998 Solvation free energy of biomacromolecules: parameters for a modified generalized Born model consistent with the AMBER force field J. Phys. Chem. B 102 9571-6
-
(1998)
J. Phys. Chem.
, vol.102
, pp. 9571-9576
-
-
Jayaram, B.1
Sprous, D.2
Beveridge, D.L.3
-
43
-
-
84961985307
-
Development of a generalized Born model parametrization for proteins and nucleic acids
-
Dominy B N and Brooks C L III 1999 Development of a generalized Born model parametrization for proteins and nucleic acids J. Phys. Chem. B 103 3765-73
-
(1999)
J. Phys. Chem.
, vol.103
, pp. 3765-3773
-
-
Dominy, B.N.1
Brooks, C.L.2
-
44
-
-
0344327079
-
Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads
-
MacKerell A D and Lee G U 1999 Structure, force, and energy of a double-stranded DNA oligonucleotide under tensile loads Eur. Biophys. J. 28 415-26
-
(1999)
Eur. Biophys. J.
, vol.28
, pp. 415-426
-
-
MacKerell, A.D.1
Lee, G.U.2
-
45
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith S B, Cui Y and Bustamante C 1996 Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 795-9
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
46
-
-
84884944777
-
Nature and magnitude of aromatic base stacking in DNA and RNA: Quantum chemistry, molecular mechanics, and experiment
-
Šponer J, Šponer J E, Mládek A, Jurečka P, Banáš P and Otyepka M 2013 Nature and magnitude of aromatic base stacking in DNA and RNA: quantum chemistry, molecular mechanics, and experiment Biopolymers 99 978-88
-
(2013)
Biopolymers
, vol.99
, pp. 978-988
-
-
Šponer, J.1
Šponer, J.E.2
Mládek, A.3
Jurečka, P.4
Banáš, P.5
Otyepka, M.6
-
47
-
-
77957562056
-
DNA-DNA interactions in tight supercoils are described by a small effective charge density
-
Maffeo C, Schöpflin R, Brutzer H, Stehr R, Aksimentiev A, Wedemann G and Seidel R 2010 DNA-DNA interactions in tight supercoils are described by a small effective charge density Phys. Rev. Lett. 105 158101
-
(2010)
Phys. Rev. Lett.
, vol.105
-
-
Maffeo, C.1
Schöpflin, R.2
Brutzer, H.3
Stehr, R.4
Aksimentiev, A.5
Wedemann, G.6
Seidel, R.7
-
49
-
-
84890307278
-
In situ structure and dynamics of DNA origami determined through molecular dynamics simulations
-
Yoo J and Aksimentiev A 2013 In situ structure and dynamics of DNA origami determined through molecular dynamics simulations Proc. Natl Acad. Sci. USA 110 20099-104
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 20099-20104
-
-
Yoo, J.1
Aksimentiev, A.2
-
50
-
-
84887947465
-
Coarse-graining DNA for simulations of DNA nanotechnology
-
Doye J P K et al 2013 Coarse-graining DNA for simulations of DNA nanotechnology Phys. Chem. Chem. Phys. 15 20395-414
-
(2013)
Phys. Chem. Chem. Phys.
, vol.15
, pp. 20395-20414
-
-
Doye, J.P.K.1
-
51
-
-
41449113042
-
The role of DNA twist in the packaging of viral genomes
-
Rollins G C, Petrov A S and Harvey S C 2008 The role of DNA twist in the packaging of viral genomes Biophys. J. 94 L38-40
-
(2008)
Biophys. J.
, vol.94
, pp. 38-L40
-
-
Rollins, G.C.1
Petrov, A.S.2
Harvey, S.C.3
-
52
-
-
79952807125
-
Chromatin folding-from biology to polymer models and back
-
Tark-Dame M, van Driel R and Heermann D W 2011 Chromatin folding-from biology to polymer models and back J. Cell Sci. 124 839-45
-
(2011)
J. Cell Sci.
, vol.124
, pp. 839-845
-
-
Tark-Dame, M.1
Van Driel, R.2
Heermann, D.W.3
-
53
-
-
0036280718
-
Molecular dynamics applied to nucleic acids
-
Norberg J and Nilsson L 2002 Molecular dynamics applied to nucleic acids Acc. Chem. Res. 35 465-72
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 465-472
-
-
Norberg, J.1
Nilsson, L.2
-
54
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
Cheatham T E 2004 Simulation and modeling of nucleic acid structure, dynamics and interactions Curr. Opin. Struct. Biol. 14 360-7
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 360-367
-
-
Cheatham, T.E.1
-
55
-
-
84860477162
-
Frontiers in molecular dynamics simulations of DNA
-
Pérez A, Luque F J and Orozco M 2012 Frontiers in molecular dynamics simulations of DNA Acc. Chem. Res. 45 196-205
-
(2012)
Acc. Chem. Res.
, vol.45
, pp. 196-205
-
-
Pérez, A.1
Luque, F.J.2
Orozco, M.3
-
56
-
-
84867973569
-
The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies
-
Šponer J, Mládek A, Šponer J E, Svozil D, Zgarbová M, Banáš P, Jurečka P and Otyepka M 2012 The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies Phys. Chem. Chem. Phys. 14 15257-77
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 15257-15277
-
-
Šponer, J.1
Mládek, A.2
Šponer, J.E.3
Svozil, D.4
Zgarbová, M.5
Banáš, P.6
Jurečka, P.7
Otyepka, M.8
-
57
-
-
0036009329
-
DNA-cation interactions: Quo vadis?
-
Egli M 2002 DNA-cation interactions: quo vadis? Chem. Biol. 9 277-86
-
(2002)
Chem. Biol.
, vol.9
, pp. 277-286
-
-
Egli, M.1
-
58
-
-
84865511740
-
Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is 'worth its salt'
-
Mocci F and Laaksonen F 2012 Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is 'worth its salt' Soft Matter 8 9268
-
(2012)
Soft Matter
, vol.8
, pp. 9268
-
-
Mocci, F.1
Laaksonen, F.2
-
59
-
-
84855431691
-
Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems
-
Yoo J and Aksimentiev A 2012 Improved parametrization of Li+, Na+, K+, and Mg2+ ions for all-atom molecular dynamics simulations of nucleic acid systems J. Phys. Chem. Lett. 3 45-50
-
(2012)
J. Phys. Chem. Lett.
, vol.3
, pp. 45-50
-
-
Yoo, J.1
Aksimentiev, A.2
-
60
-
-
1242269406
-
Molecular dynamics simulations of DNA curvature and flexibility: Helix phasing and premelting
-
Beveridge D L, Dixit S B, Barreiro G and Thayer K M 2004 Molecular dynamics simulations of DNA curvature and flexibility: helix phasing and premelting Biopolymers 73 380-403
-
(2004)
Biopolymers
, vol.73
, pp. 380-403
-
-
Beveridge, D.L.1
Dixit, S.B.2
Barreiro, G.3
Thayer, K.M.4
-
62
-
-
77957240284
-
DNA curvature and flexibility in vitro and in vivo
-
Peters J P and Maher L J 2010 DNA curvature and flexibility in vitro and in vivo Quart. Rev. Biophys. 43 23-63
-
(2010)
Quart. Rev. Biophys.
, vol.43
, Issue.1
, pp. 23-63
-
-
Peters, J.P.1
Maher, L.J.2
-
64
-
-
0036286321
-
Simulations of nucleic acids and their complexes
-
Giudice E and Lavery R 2002 Simulations of nucleic acids and their complexes Acc. Chem. Res. 35 350-7
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 350-357
-
-
Giudice, E.1
Lavery, R.2
-
65
-
-
33745478907
-
Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations
-
Spiegel K and Magistrato A 2006 Modeling anticancer drug-DNA interactions via mixed QM/MM molecular dynamics simulations Org. Biomol. Chem. 4 2507-17
-
(2006)
Org. Biomol. Chem.
, vol.4
, pp. 2507-2517
-
-
Spiegel, K.1
Magistrato, A.2
-
66
-
-
34247517743
-
Molecular modelling methods for prediction of sequence-selectivity in DNA recognition
-
Wang H and Laughton C A 2007 Molecular modelling methods for prediction of sequence-selectivity in DNA recognition Methods 42 196-203
-
(2007)
Methods
, vol.42
, pp. 196-203
-
-
Wang, H.1
Laughton, C.A.2
-
67
-
-
33847770470
-
Multiscale modeling of nucleosome dynamics
-
Sharma S, Ding F and Dokholyan N V 2007 Multiscale modeling of nucleosome dynamics Biophys. J. 92 1457-70
-
(2007)
Biophys. J.
, vol.92
, pp. 1457-1470
-
-
Sharma, S.1
Ding, F.2
Dokholyan, N.V.3
-
68
-
-
4344671232
-
Simulations of DNA-nanotube interactions
-
Gao H and Kong Y 2004 Simulations of DNA-nanotube interactions Annu. Rev. Mater. Res. 34 129-52
-
(2004)
Annu. Rev. Mater. Res.
, vol.34
, Issue.1
, pp. 123-152
-
-
Gao, H.1
Kong, Y.2
-
69
-
-
4444234147
-
Microscopic kinetics of DNA translocation through synthetic nanopores
-
Aksimentiev A, Heng J B, Timp G and Schulten K 2004 Microscopic kinetics of DNA translocation through synthetic nanopores Biophys. J. 87 2086-97
-
(2004)
Biophys. J.
, vol.87
, pp. 2086-2097
-
-
Aksimentiev, A.1
Heng, J.B.2
Timp, G.3
Schulten, K.4
-
70
-
-
36749098380
-
Dynamics of B-DNA on the microsecond time scale
-
Pérez A, Luque F J and Orozco M 2007 Dynamics of B-DNA on the microsecond time scale J. Am. Chem. Soc. 129 14739-45
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14739-14745
-
-
Pérez, A.1
Luque, F.J.2
Orozco, M.3
-
71
-
-
33644848399
-
Molecular dynamics simulations of the complete satellite tobacco mosaic virus
-
Freddolino P L, Arkhipov A S, Larson S B, McPherson A and Schulten K 2006 Molecular dynamics simulations of the complete satellite tobacco mosaic virus Structure 14 437-49
-
(2006)
Structure
, vol.14
, pp. 437-449
-
-
Freddolino, P.L.1
Arkhipov, A.S.2
Larson, S.B.3
McPherson, A.4
Schulten, K.5
-
72
-
-
84861765128
-
Computational studies of molecular machines: The ribosome
-
Sanbonmatsu K Y 2012 Computational studies of molecular machines: the ribosome Curr. Opin. Struct. Biol. 22 168-74
-
(2012)
Curr. Opin. Struct. Biol.
, vol.22
, pp. 168-174
-
-
Sanbonmatsu, K.Y.1
-
73
-
-
0001533502
-
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 2621-5
-
(1984)
Proc. Natl Acad. Sci. USA
, vol.81
, pp. 2621-2625
-
-
Rau, D.C.1
Lee, B.2
Parsegian, V.A.3
-
75
-
-
33645028600
-
Folding DNA to create nanoscale shapes and patterns
-
Rothemund P W K 2006 Folding DNA to create nanoscale shapes and patterns Nature 440 297-302
-
(2006)
Nature
, vol.440
, pp. 297-302
-
-
Rothemund, P.W.K.1
-
76
-
-
68449088261
-
Folding DNA into twisted and curved nanoscale shapes
-
Dietz H, Douglas S M and Shih W M 2009 Folding DNA into twisted and curved nanoscale shapes Science 325 725-30
-
(2009)
Science
, vol.325
, pp. 725-730
-
-
Dietz, H.1
Douglas, S.M.2
Shih, W.M.3
-
77
-
-
70350639414
-
Multilayer DNA origami packed on a square lattice
-
Ke Y, Douglas S M, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih W M and Yan H 2009 Multilayer DNA origami packed on a square lattice J. Am. Chem. Soc. 131 15903-8
-
(2009)
J. Am. Chem. Soc.
, vol.131
, pp. 15903-15908
-
-
Ke, Y.1
Douglas, S.M.2
Liu, M.3
Sharma, J.4
Cheng, A.5
Leung, A.6
Liu, Y.7
Shih, W.M.8
Yan, H.9
-
78
-
-
84877743189
-
Coarse-graining methods for computational biology
-
Saunders M G and Voth G A 2013 Coarse-graining methods for computational biology Annu. Rev. Biophys. 42 73-93
-
(2013)
Annu. Rev. Biophys.
, vol.42
, pp. 73-93
-
-
Saunders, M.G.1
Voth, G.A.2
-
80
-
-
84886920979
-
An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
-
Hinckley D M, Freeman G S, Whitmer J K and de Pablo J J 2013 An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization J. Chem. Phys. 139 144903
-
(2013)
J. Chem. Phys.
, vol.139
-
-
Hinckley, D.M.1
Freeman, G.S.2
Whitmer, J.K.3
De Pablo, J.J.4
-
81
-
-
84867508975
-
Sequence-dependent thermodynamics of a coarse-grained DNA model
-
Šulc P, Romano F, Ouldridge T E, Rovigatti L, Doye J P K and Louis A A 2012 Sequence-dependent thermodynamics of a coarse-grained DNA model J. Chem. Phys. 137 135101
-
(2012)
J. Chem. Phys.
, vol.137
-
-
Šulc, P.1
Romano, F.2
Ouldridge, T.E.3
Rovigatti, L.4
Doye, J.P.K.5
Louis, A.A.6
-
82
-
-
84863650456
-
BROMOC-D: Brownian dynamics/Monte-Carlo program suite to study ion and DNA permeation in nanopores
-
De Biase P M, Solano C J F, Markosyan S, Czapla L and Noskov S Yu 2012 BROMOC-D: Brownian dynamics/Monte-Carlo program suite to study ion and DNA permeation in nanopores J. Chem. Theory Comput. 8 2540-51
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 2540-2551
-
-
De Biase, P.M.1
Solano, C.J.F.2
Markosyan, S.3
Czapla, L.4
Yu, N.S.5
-
83
-
-
78650553525
-
Chemically accurate coarse graining of double-stranded DNA
-
Savelyev A and Papoian G A 2010 Chemically accurate coarse graining of double-stranded DNA Proc. Natl Acad. Sci. USA 107 20340-5
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 20340-20345
-
-
Savelyev, A.1
Papoian, G.A.2
-
84
-
-
84874539246
-
Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix
-
He Y, Maciejczyk M, Ołdziej S, Scheraga H A and Liwo A 2013 Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix Phys. Rev. Lett. 110 098101
-
(2013)
Phys. Rev. Lett.
, vol.110
-
-
He, Y.1
MacIejczyk, M.2
Ołdziej, S.3
Scheraga, H.A.4
Liwo, A.5
-
86
-
-
77949889822
-
A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality
-
Morriss-Andrews A, Rottler J and Plotkin S S 2010 A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality J. Chem. Phys. 132 035105
-
(2010)
J. Chem. Phys.
, vol.132
-
-
Morriss-Andrews, A.1
Rottler, J.2
Plotkin, S.S.3
-
87
-
-
77952355398
-
A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics
-
Dans P D, Zeida A, Machado M R and Pantano S 2010 A coarse grained model for atomic-detailed DNA simulations with explicit electrostatics J. Chem. Theory Comput. 6 1711-25
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1711-1725
-
-
Dans, P.D.1
Zeida, A.2
MacHado, M.R.3
Pantano, S.4
-
89
-
-
77951212412
-
PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
-
Gopal S M, Mukherjee S, Cheng Y-M and Feig M 2010 PRIMO/PRIMONA: a coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy Proteins: Struct., Funct., Bioinf. 78 1266-81
-
(2010)
Proteins: Struct., Funct., Bioinf.
, vol.78
, pp. 1266-1281
-
-
Gopal, S.M.1
Mukherjee, S.2
Cheng, Y.-M.3
Feig, M.4
-
90
-
-
78651240463
-
A coarse-grained model of DNA with explicit solvation by water and ions
-
DeMille R C, Cheatham T E and Molinero V 2011 A coarse-grained model of DNA with explicit solvation by water and ions J. Phys. Chem. B 115 132-42
-
(2011)
J. Phys. Chem.
, vol.115
, pp. 132-142
-
-
Demille, R.C.1
Cheatham, T.E.2
Molinero, V.3
-
91
-
-
0032539693
-
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
-
SantaLucia J Jr 1998 A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl Acad. Sci. USA 95 1460-5
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 1460-1465
-
-
Santalucia, J.1
-
92
-
-
84906237862
-
A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment
-
Maffeo C, Ngo T T M, Ha T and Aksimentiev A 2014 A coarse-grained model of unstructured single-stranded DNA derived from atomistic simulation and single-molecule experiment J. Chem. Theory Comput. 10 2891-6
-
(2014)
J. Chem. Theory Comput.
, vol.10
, Issue.8
, pp. 2891-2896
-
-
Maffeo, C.1
Ngo, T.T.M.2
Ha, T.3
Aksimentiev, A.4
-
93
-
-
0018579565
-
Electrostatic potentials of deoxydinucleoside monophosphates: I. Deoxydinucleoside monophosphates and actinomycin chromophore interactions
-
Nuss M E and Kollman P A 1979 Electrostatic potentials of deoxydinucleoside monophosphates: I. Deoxydinucleoside monophosphates and actinomycin chromophore interactions J. Med. Chem. 22 1517-24
-
(1979)
J. Med. Chem.
, vol.22
, pp. 1517-1524
-
-
Nuss, M.E.1
Kollman, P.A.2
-
94
-
-
0019763828
-
Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers
-
Kollman P A, Weiner P K and Dearing A 1981 Studies of nucleotide conformations and interactions. The relative stabilities of double-helical B-DNA sequence isomers Biopolymers 20 2583-621
-
(1981)
Biopolymers
, vol.20
, pp. 2583-2621
-
-
Kollman, P.A.1
Weiner, P.K.2
Dearing, A.3
-
95
-
-
0000871204
-
Multiconfiguration thermodynamic integration
-
Straatsma T P and McCammon J A 1991 Multiconfiguration thermodynamic integration J. Chem. Phys. 95 1175
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 1175
-
-
Straatsma, T.P.1
McCammon, J.A.2
-
97
-
-
77951142226
-
Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field
-
Baker C M, Lopes P E M, Zhu X, Roux B and MacKerell A D 2010 Accurate calculation of hydration free energies using pair-specific Lennard-Jones parameters in the CHARMM Drude polarizable force field J. Chem. Theory Comput. 6 1181-98
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 1181-1198
-
-
Baker, C.M.1
Lopes, P.E.M.2
Zhu, X.3
Roux, B.4
MacKerell, A.D.5
-
98
-
-
77749298172
-
Current status of the AMOEBA polarizable force field
-
Ponder J W et al 2010 Current status of the AMOEBA polarizable force field J. Phys. Chem. B 114 2549-64
-
(2010)
J. Phys. Chem.
, vol.114
, pp. 2549-2564
-
-
Ponder, J.W.1
-
99
-
-
84900474707
-
All-atom polarizable force field for DNA based on the classical Drude oscillator model
-
Savelyev A and MacKerell A D 2014 All-atom polarizable force field for DNA based on the classical Drude oscillator model J. Comput. Chem. 35 1219-39
-
(2014)
J. Comput. Chem.
, vol.35
, pp. 1219-1239
-
-
Savelyev, A.1
MacKerell, A.D.2
-
100
-
-
84902951608
-
Balancing the interactions of ions, water, and DNA in the Drude polarizable force field
-
Savelyev A and MacKerell A D 2014 Balancing the interactions of ions, water, and DNA in the Drude polarizable force field J. Phys. Chem. B 118 6742-57
-
(2014)
J. Phys. Chem.
, vol.118
, pp. 6742-6757
-
-
Savelyev, A.1
MacKerell, A.D.2
-
101
-
-
4544342928
-
Potassium channels and the atomic basis of selective ion conduction (nobel lecture)
-
Mackinnon R 2004 Potassium channels and the atomic basis of selective ion conduction (nobel lecture) Angew. Chem. Int. Edn 43 4265-77
-
(2004)
Angew. Chem. Int. Edn
, vol.43
, pp. 4265-4277
-
-
MacKinnon, R.1
-
102
-
-
2142813682
-
Computer simulation of molecular dynamics: Methodology, applications, and perspectives in chemistry
-
van Gunsteren W F and Berendsen H J C 1990 Computer simulation of molecular dynamics: methodology, applications, and perspectives in chemistry Angew. Chem. Int. Edn Engl. 29 992-1023
-
(1990)
Angew. Chem. Int. Edn Engl.
, vol.29
, pp. 992-1023
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
103
-
-
84988103838
-
Empirical energy functions for energy minimization and dynamics of nucleic acids
-
Nilsson L and Karplus M 1986 Empirical energy functions for energy minimization and dynamics of nucleic acids J. Comput. Chem. 7 591-616
-
(1986)
J. Comput. Chem.
, vol.7
, pp. 591-616
-
-
Nilsson, L.1
Karplus, M.2
-
104
-
-
33846823909
-
Particle mesh Ewald: An n log(n) method for Ewald sums in large systems
-
Darden T, York D and Pedersen L 1993 Particle mesh Ewald: an n log(n) method for Ewald sums in large systems J. Chem. Phys. 98 10089-92
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
105
-
-
0348244547
-
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data
-
Foloppe N and MacKerrell A D Jr 2000 All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data J. Comput. Chem. 21 86-104
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 86-104
-
-
Foloppe, N.1
MacKerrell, A.D.2
-
106
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
-
Cornell W D, Cieplak P, Bayly C I, Gould I R, Merz K M, Ferguson D M, Spellmeyer D C, Fox T, Caldwell J W and Kollman P A 1995 A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 5179-97
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
107
-
-
84884931806
-
Twenty-five years of nucleic acid simulations
-
Cheatham T E and Case D A 2013 Twenty-five years of nucleic acid simulations Biopolymers 99 969-77
-
(2013)
Biopolymers
, vol.99
, pp. 969-977
-
-
Cheatham, T.E.1
Case, D.A.2
-
108
-
-
0032922174
-
A modified version of the Cornell et al force field with improved sugar pucker phases and helical repeat
-
Cheatham T E, Cieplak P and Kollman P A 1999 A modified version of the Cornell et al force field with improved sugar pucker phases and helical repeat J. Biomol. Struct. Dyn. 16 845-62
-
(1999)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 845-862
-
-
Cheatham, T.E.1
Cieplak, P.2
Kollman, P.A.3
-
110
-
-
34250318638
-
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 and Orozco M 2007 Refinement of the AMBER force field for nucleic acids: improving the description of α/γ conformers Biophys. J. 92 3817-29
-
(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
-
111
-
-
84855661433
-
Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium
-
Hart K, Foloppe N, Baker C M, Denning E J, Nilsson L and MacKerell A D 2012 Optimization of the CHARMM additive force field for DNA: improved treatment of the BI/BII conformational equilibrium J. Chem. Theory Comput. 8 348-62
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 348-362
-
-
Hart, K.1
Foloppe, N.2
Baker, C.M.3
Denning, E.J.4
Nilsson, L.5
MacKerell, A.D.6
-
112
-
-
84865770620
-
Single-stranded DNA within nanopores: Conformational dynamics and implications for sequencing; A molecular dynamics simulation study
-
Guy A T, Piggot T J and Khalid S 2012 Single-stranded DNA within nanopores: conformational dynamics and implications for sequencing; a molecular dynamics simulation study Biophys. J. 103 1028-36
-
(2012)
Biophys. J.
, vol.103
, pp. 1028-1036
-
-
Guy, A.T.1
Piggot, T.J.2
Khalid, S.3
-
113
-
-
75449112058
-
Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in
-
Ditzler M A, Otyepka M, Sponer J and Walter N G 2010 Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in Acc. Chem. Res. 43 40-7
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 40-47
-
-
Ditzler, M.A.1
Otyepka, M.2
Sponer, J.3
Walter, N.G.4
-
114
-
-
78651294111
-
Performance of molecular mechanics force fields for RNA simulations: Stability of UUCG and GNRA hairpins
-
Banás P, Hollas D, Zgarbová M, Jurecka P, Orozco M, Cheatham T E, Sponer J and Otyepka M 2010 Performance of molecular mechanics force fields for RNA simulations: stability of UUCG and GNRA hairpins J. Chem. Theory Comput. 6 3836-49
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 3836-3849
-
-
Banás, P.1
Hollas, D.2
Zgarbová, M.3
Jurecka, P.4
Orozco, M.5
Cheatham, T.E.6
Sponer, J.7
Otyepka, M.8
-
115
-
-
80054698073
-
Noncanonical hydrogen bonding in nucleic acids. Benchmark evaluation of key base phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations
-
Zgarbová M, Jurečka P, Banás P, Otyepka M, Sponer J E, Leontis N B, Zirbel C L and Sponer J 2011 Noncanonical hydrogen bonding in nucleic acids. benchmark evaluation of key base phosphate interactions in folded RNA molecules using quantum-chemical calculations and molecular dynamics simulations J. Phys. Chem. A 115 11277-92
-
(2011)
J. Phys. Chem.
, vol.115
, pp. 11277-11292
-
-
Zgarbová, M.1
Jurečka, P.2
Banás, P.3
Otyepka, M.4
Sponer, J.E.5
Leontis, N.B.6
Zirbel, C.L.7
Sponer, J.8
-
116
-
-
0344796204
-
Ion water interaction potentials derived from free-energy perturbation simulations
-
Åqvist J 1990 Ion water interaction potentials derived from free-energy perturbation simulations J. Phys. Chem. 94 8021-4
-
(1990)
J. Phys. Chem.
, vol.94
, pp. 8021-8024
-
-
Åqvist, J.1
-
117
-
-
0001655657
-
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 9050-63
-
(1994)
J. Chem. Phys.
, vol.100
, pp. 9050-9063
-
-
Beglov, D.1
Roux, B.2
-
118
-
-
35948966376
-
Spontaneous formation of KCl aggregates in biomolecular simulations: A force field issue?
-
Auffinger P, Cheatham T E and Vaiana A C 2007 Spontaneous formation of KCl aggregates in biomolecular simulations: a force field issue? J. Chem. Theory Comput. 3 1851-9
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1851-1859
-
-
Auffinger, P.1
Cheatham, T.E.2
Vaiana, A.C.3
-
119
-
-
77149136136
-
Simulation of osmotic pressure in concentrated aqueous salt solutions
-
Luo Y and Roux B 2009 Simulation of osmotic pressure in concentrated aqueous salt solutions J. Phys. Chem. Lett. 1 183-9
-
(2009)
J. Phys. Chem. Lett.
, vol.1
, pp. 183-189
-
-
Luo, Y.1
Roux, B.2
-
120
-
-
49449085241
-
Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations
-
Joung I S and Cheatham T E 2008 Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations J. Phys. Chem. B 112 9020-41
-
(2008)
J. Phys. Chem.
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
121
-
-
70349956450
-
Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters
-
Joung I S and Cheatham T E 2009 Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters J. Phys. Chem. B 113 13279-90
-
(2009)
J. Phys. Chem.
, vol.113
, pp. 13279-13290
-
-
Joung, I.S.1
Cheatham, T.E.2
-
123
-
-
63449094990
-
Virology pressurized viruses
-
Gelbart W M and Knobler C M 2009 Virology pressurized viruses Science 323 1682-3
-
(2009)
Science
, vol.323
, pp. 1682-1683
-
-
Gelbart, W.M.1
Knobler, C.M.2
-
124
-
-
75649084574
-
Ion selectivity of α-hemolysin with a β-cyclodextrin adapter: I. Single ion potential of mean force and diffusion coefficient
-
Luo Y, Egwolf B, Walters D E and Roux B 2010 Ion selectivity of α-hemolysin with a β-cyclodextrin adapter: I. Single ion potential of mean force and diffusion coefficient J. Phys. Chem. B 144 952-8
-
(2010)
J. Phys. Chem.
, vol.114
, Issue.2
, pp. 952-958
-
-
Luo, Y.1
Egwolf, B.2
Walters, D.E.3
Roux, B.4
-
125
-
-
84868242573
-
Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations
-
Yoo J and Aksimentiev A 2012 Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations J. Phys. Chem. B 116 12946-54
-
(2012)
J. Phys. Chem.
, vol.116
, pp. 12946-12954
-
-
Yoo, J.1
Aksimentiev, A.2
-
126
-
-
36848999901
-
Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
-
Bai Y, Greenfeld M, Travers K J, Chu V B, Lipfert J, Doniach S and Herschlag D 2007 Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids J. Am. Chem. Soc. 129 14981-88
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 14981-14988
-
-
Bai, Y.1
Greenfeld, M.2
Travers, K.J.3
Chu, V.B.4
Lipfert, J.5
Doniach, S.6
Herschlag, D.7
-
127
-
-
34547432557
-
Inter-DNA attraction mediated by divalent counterions
-
Qiu X, Andresen K, Kwok L W, Lamb J S, Park H Y and Pollack L 2007 Inter-DNA attraction mediated by divalent counterions Phys. Rev. Lett. 99 38104
-
(2007)
Phys. Rev. Lett.
, vol.99
, pp. 38104
-
-
Qiu, X.1
Andresen, K.2
Kwok, L.W.3
Lamb, J.S.4
Park, H.Y.5
Pollack, L.6
-
129
-
-
84885818229
-
High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations
-
Chen A A and García A E 2013 High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations Proc. Natl Acad. Sci. USA 110 16820-5
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 16820-16825
-
-
Chen, A.A.1
García, A.E.2
-
131
-
-
0000216904
-
Local dielectric environment of B-DNA in solution: Results from a 14 ns molecular dynamics trajectory
-
Young M A, Jayaram B and Beveridge D L 1998 Local dielectric environment of B-DNA in solution: results from a 14 ns molecular dynamics trajectory J. Phys. Chem. B 102 7666-9
-
(1998)
J. Phys. Chem.
, vol.102
, pp. 7666-7669
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
132
-
-
0036055199
-
Colloquium: The physics of charge inversion in chemical and biological systems
-
Grosberg A Yu, Nguyen T T and Shklovskii B I 2002 Colloquium: the physics of charge inversion in chemical and biological systems Rev. Mod. Phys. 74 329-45
-
(2002)
Rev. Mod. Phys.
, vol.74
, pp. 329-345
-
-
Yu, G.A.1
Nguyen, T.T.2
Shklovskii, B.I.3
-
133
-
-
33847295668
-
Steric effects in the dynamics of electrolytes at large applied voltages: II. Modified Poisson-Nernst-Planck equations
-
Kilic M S, Bazant M Z and Ajdari A 2007 Steric effects in the dynamics of electrolytes at large applied voltages: II. Modified Poisson-Nernst-Planck equations Phys. Rev. E 75 021503
-
(2007)
Phys. Rev.
, vol.75
-
-
Kilic, M.S.1
Bazant, M.Z.2
Ajdari, A.3
-
134
-
-
84887796020
-
A stabilized finite element method for modified Poisson-Nernst-Planck equations to determine ion flow through a nanopore
-
Chaudhry J H, Comer J, Aksimentiev A and Olson L N 2014 A stabilized finite element method for modified Poisson-Nernst-Planck equations to determine ion flow through a nanopore Commun. Comput. Phys 15 93-125
-
(2014)
Commun. Comput. Phys
, vol.15
, pp. 93-125
-
-
Chaudhry, J.H.1
Comer, J.2
Aksimentiev, A.3
Olson, L.N.4
-
135
-
-
84990422191
-
Distribution of counterions around a cylindrical polyelectrolyte and Manning's condensation theory
-
Le Bret M and Zimm B H 1984 Distribution of counterions around a cylindrical polyelectrolyte and Manning's condensation theory Biopolymers 23 287-312
-
(1984)
Biopolymers
, vol.23
, pp. 287-312
-
-
Le Bret, M.1
Zimm, B.H.2
-
137
-
-
33845556449
-
Limiting laws and counterion condensation in polyelectrolyte solutions: VII. Electrophoretic mobility and conductance
-
Manning G 1981 Limiting laws and counterion condensation in polyelectrolyte solutions: VII. Electrophoretic mobility and conductance J. Phys. Chem. 85 1506
-
(1981)
J. Phys. Chem.
, vol.85
, pp. 1506
-
-
Manning, G.1
-
138
-
-
33646903272
-
The critical onset of counterion condensation: A survey of its experimental and theoretical basis
-
Manning G S 1996 The critical onset of counterion condensation: a survey of its experimental and theoretical basis Ber. Bunsenges. Phys. Chem. 100 909-22
-
(1996)
Ber. Bunsenges. Phys. Chem.
, vol.100
, pp. 909-922
-
-
Manning, G.S.1
-
139
-
-
51549093376
-
Approximate solutions to some problems in polyelectrolyte theory involving nonuniform charge distributions
-
Manning G S 2008 Approximate solutions to some problems in polyelectrolyte theory involving nonuniform charge distributions Macromolecules 41 6217-27
-
(2008)
Macromolecules
, vol.41
, pp. 6217-6227
-
-
Manning, G.S.1
-
140
-
-
0035913001
-
Counterion condensation on a helical charge lattice
-
Manning G S 2001 Counterion condensation on a helical charge lattice Macromolecules 34 4650-5
-
(2001)
Macromolecules
, vol.34
, pp. 4650-4655
-
-
Manning, G.S.1
-
141
-
-
0031354944
-
Counterion condensation on ionic oligomers
-
Manning G S and Mohanty U 1997 Counterion condensation on ionic oligomers Physica A 247 196-204
-
(1997)
Physica
, vol.247
, pp. 196-204
-
-
Manning, G.S.1
Mohanty, U.2
-
142
-
-
0000323998
-
A continuum rod model of sequence-dependent DNA structure
-
Manning R S, Maddocks J H and Kahn J D 1996 A continuum rod model of sequence-dependent DNA structure J. Chem. Phys. 105 5626-46
-
(1996)
J. Chem. Phys.
, vol.105
, pp. 5626-5646
-
-
Manning, R.S.1
Maddocks, J.H.2
Kahn, J.D.3
-
143
-
-
36449001060
-
Ionic distribution around simple DNA models: I. Cylindrically averaged properties
-
Montoro J C G and Abascal J L F 1995 Ionic distribution around simple DNA models: I. Cylindrically averaged properties J. Chem. Phys. 103 8273-84
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8273-8284
-
-
Montoro, J.C.G.1
Abascal, J.L.F.2
-
144
-
-
0031769567
-
Electrostatic potential of B-DNA: Effect of interionic correlations
-
Gavryushov S and Zielenkiewicz P 1998 Electrostatic potential of B-DNA: effect of interionic correlations Biophys. J. 75 2732-42
-
(1998)
Biophys. J.
, vol.75
, pp. 2732-2742
-
-
Gavryushov, S.1
Zielenkiewicz, P.2
-
145
-
-
0017895903
-
The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides
-
Manning G S 1978 The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides Quart. Rev. Biophys. 2 179-246
-
(1978)
Quart. Rev. Biophys.
, vol.2
, pp. 179-246
-
-
Manning, G.S.1
-
146
-
-
0038713237
-
A unified model for the origin of DNA sequence-directed curvature
-
Hud N V and Plavec J 2003 A unified model for the origin of DNA sequence-directed curvature Biopolymers 69 144-58
-
(2003)
Biopolymers
, vol.69
, pp. 144-158
-
-
Hud, N.V.1
Plavec, J.2
-
147
-
-
0037928815
-
Counterion distribution around DNA probed by solution x-ray scattering
-
Das R, Mills T T, Kwok L W, Maskel G S, Millett I S, Doniach S, Finkelstein K D, Herschlag D and Pollack L 2003 Counterion distribution around DNA probed by solution x-ray scattering Phys. Rev. Lett. 90 188103
-
(2003)
Phys. Rev. Lett.
, vol.90
-
-
Das, R.1
Mills, T.T.2
Kwok, L.W.3
Maskel, G.S.4
Millett, I.S.5
Doniach, S.6
Finkelstein, K.D.7
Herschlag, D.8
Pollack, L.9
-
148
-
-
42749101028
-
Spatial distribution of competing ions around DNA in solution
-
Andresen K, Das R, Park H Y, Smith H, Kwok L W, Lamb J S, Kirkland E J, Herschlag D, Finkelstein K D and Pollack L 2004 Spatial distribution of competing ions around DNA in solution Phys. Rev. Lett. 93 248103
-
(2004)
Phys. Rev. Lett.
, vol.93
, Issue.24
-
-
Andresen, K.1
Das, R.2
Park, H.Y.3
Smith, H.4
Kwok, L.W.5
Lamb, J.S.6
Kirkland, E.J.7
Herschlag, D.8
Finkelstein, K.D.9
Pollack, L.10
-
149
-
-
46749106335
-
Mono- and trivalent ions around DNA: A small-angle scattering study of competition and interactions
-
Andresen K, Qiu X, Pabit S A, Lamb J S, Park H Y, Kwok L W and Pollack L 2008 Mono- and trivalent ions around DNA: a small-angle scattering study of competition and interactions Biophys. J. 95 287-95
-
(2008)
Biophys. J.
, vol.95
, pp. 287-295
-
-
Andresen, K.1
Qiu, X.2
Pabit, S.A.3
Lamb, J.S.4
Park, H.Y.5
Kwok, L.W.6
Pollack, L.7
-
150
-
-
4143138536
-
Exploring the counterion atmosphere around DNA: What can be learned from molecular dynamics simulations?
-
Rueda M, Cubero E, Laughton C A and Orozco M 2004 Exploring the counterion atmosphere around DNA: what can be learned from molecular dynamics simulations? Biophys. J. 87 800-11
-
(2004)
Biophys. J.
, vol.87
, pp. 800-811
-
-
Rueda, M.1
Cubero, E.2
Laughton, C.A.3
Orozco, M.4
-
151
-
-
4043179941
-
DNA and its counterions: A molecular dynamics study
-
Várnai P and Zakrzewska K 2004 DNA and its counterions: a molecular dynamics study Nucleic Acids Res. 32 4269-80
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4269-4280
-
-
Várnai, P.1
Zakrzewska, K.2
-
154
-
-
0032535607
-
Folding of the four-way RNA junction of the hairpin ribozyme
-
Walter F, Murchie A I H and Lilley D M J 1998 Folding of the four-way RNA junction of the hairpin ribozyme Biochemistry 37 17629-36
-
(1998)
Biochemistry
, vol.37
, pp. 17629-17636
-
-
Walter, F.1
Murchie, A.I.H.2
Lilley, D.M.J.3
-
155
-
-
0029820625
-
Crystal structure of a group i ribozyme domain: Principles of RNA packing
-
Cate J H, Gooding A R, Podell E, Zhou K, Golden B L, Kundrot C E, Cech T R and Doudna J A 1996 Crystal structure of a group i ribozyme domain: principles of RNA packing Science 273 1678-85
-
(1996)
Science
, vol.273
, pp. 1678-1685
-
-
Cate, J.H.1
Gooding, A.R.2
Podell, E.3
Zhou, K.4
Golden, B.L.5
Kundrot, C.E.6
Cech, T.R.7
Doudna, J.A.8
-
157
-
-
35348897239
-
Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction
-
Hohng S, Zhou R, Nahas M K, Yu J, Schulten K, Lilley D M J and Ha T 2007 Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the Holliday junction Science 318 279-83
-
(2007)
Science
, vol.318
, pp. 279-283
-
-
Hohng, S.1
Zhou, R.2
Nahas, M.K.3
Yu, J.4
Schulten, K.5
Lilley, D.M.J.6
Ha, T.7
-
158
-
-
33947425219
-
Tertiary structure of an RNA pseudoknot is stabilized by 'diffuse' Mg2+ ions
-
Soto A M, Misra V and Draper D E 2007 Tertiary structure of an RNA pseudoknot is stabilized by 'diffuse' Mg2+ ions Biochemistry 46 2973-83
-
(2007)
Biochemistry
, vol.46
, pp. 2973-2983
-
-
Soto, A.M.1
Misra, V.2
Draper, D.E.3
-
159
-
-
33749646478
-
Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential
-
Jiao D, King C, Grossfield A, Darden T A and Ren P 2006 Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential J. Phys. Chem. B 110 18553-9
-
(2006)
J. Phys. Chem.
, vol.110
, pp. 18553-18559
-
-
Jiao, D.1
King, C.2
Grossfield, A.3
Darden, T.A.4
Ren, P.5
-
160
-
-
77951134962
-
Solvation of magnesium dication: Molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions
-
Callahan K M, Casillas-Ituarte N N, Roeselová M, Allen H C and Tobias D J 2010 Solvation of magnesium dication: molecular dynamics simulation and vibrational spectroscopic study of magnesium chloride in aqueous solutions J. Phys. Chem. A 114 5141-8
-
(2010)
J. Phys. Chem.
, vol.114
, pp. 5141-5148
-
-
Callahan, K.M.1
Casillas-Ituarte, N.N.2
Roeselová, M.3
Allen, H.C.4
Tobias, D.J.5
-
161
-
-
0031535392
-
Water exchange on magnesium(II) in aqueous solution: A variable temperature and pressure 17o NMR study
-
Bleuzen A, Pittet P-A, Helm L and Merbach A E 1997 Water exchange on magnesium(II) in aqueous solution: a variable temperature and pressure 17o NMR study Magn. Res. Chem. 35 765-73
-
(1997)
Magn. Res. Chem.
, vol.35
, pp. 765-773
-
-
Bleuzen, A.1
Pittet, P.-A.2
Helm, L.3
Merbach, A.E.4
-
162
-
-
33746907422
-
Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure
-
Piquemal J-P, Perera L, Cisneros G A, Ren P, Pedersen L G and Darden T A 2006 Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: from energetics to structure J. Chem. Phys. 125 054511
-
(2006)
J. Chem. Phys.
, vol.125
, Issue.5
-
-
Piquemal, J.-P.1
Perera, L.2
Cisneros, G.A.3
Ren, P.4
Pedersen, L.G.5
Darden, T.A.6
-
163
-
-
84872697347
-
Force fields for divalent cations based on single-ion and ion-pair properties
-
Mamatkulov S, Fyta M and Netz R R 2013 Force fields for divalent cations based on single-ion and ion-pair properties J. Chem. Phys. 138 024505
-
(2013)
J. Chem. Phys.
, vol.138
, Issue.2
-
-
Mamatkulov, S.1
Fyta, M.2
Netz, R.R.3
-
164
-
-
84859603569
-
Magnesium ion-water coordination and exchange in biomolecular simulations
-
Allnér O, Nilsson L and Villa A 2012 Magnesium ion-water coordination and exchange in biomolecular simulations J. Chem. Theory Comput. 8 1493-502
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 1493-1502
-
-
Allnér, O.1
Nilsson, L.2
Villa, A.3
-
165
-
-
84882347869
-
Multisite ion models that improve coordination and free energy calculations in molecular dynamics simulations
-
Saxena A and Sept D 2013 Multisite ion models that improve coordination and free energy calculations in molecular dynamics simulations J. Chem. Theory Comput. 9 3538-42
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3538-3542
-
-
Saxena, A.1
Sept, D.2
-
166
-
-
33846828514
-
Ion conduction through MscS as determined by electrophysiology and simulation
-
Sotomayor M, Vasquez V, Perozo E and Schulten K 2007 Ion conduction through MscS as determined by electrophysiology and simulation Biophys. J. 92 886-902
-
(2007)
Biophys. J.
, vol.92
, pp. 886-902
-
-
Sotomayor, M.1
Vasquez, V.2
Perozo, E.3
Schulten, K.4
-
167
-
-
4143055013
-
Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy
-
Joo C, McKinney S A, Lilley D M J and Ha T 2004 Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy J. Mol. Biol. 341 739-51
-
(2004)
J. Mol. Biol.
, vol.341
, pp. 739-751
-
-
Joo, C.1
McKinney, S.A.2
Lilley, D.M.J.3
Ha, T.4
-
168
-
-
0034725528
-
Water and ion binding around RNA and DNA (c,g) oligomers
-
Auffinger P and Westhof E 2000 Water and ion binding around RNA and DNA (c,g) oligomers J. Mol. Biol. 300 1113-31
-
(2000)
J. Mol. Biol.
, vol.300
, pp. 1113-1131
-
-
Auffinger, P.1
Westhof, E.2
-
169
-
-
32644446799
-
Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study
-
Cheng Y, Korolev N and Nordenskiöld L 2006 Similarities and differences in interaction of K+ and Na+ with condensed ordered DNA. A molecular dynamics computer simulation study Nucleic Acids Res. 34 686-96
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 686-696
-
-
Cheng, Y.1
Korolev, N.2
Nordenskiöld, L.3
-
170
-
-
0030782840
-
Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties
-
MacKerell A D 1997 Influence of magnesium ions on duplex DNA structural, dynamic, and solvation properties J. Phys. Chem. B 101 646-50
-
(1997)
J. Phys. Chem.
, vol.101
, pp. 646-650
-
-
MacKerell, A.D.1
-
171
-
-
83455195615
-
Sequence-specific Mg2+-DNA interactions: A molecular dynamics simulation study
-
Li W, Nordenskiöld L and Mu Y 2011 Sequence-specific Mg2+-DNA interactions: a molecular dynamics simulation study J. Phys. Chem. B 115 14713-20
-
(2011)
J. Phys. Chem.
, vol.115
, pp. 14713-14720
-
-
Li, W.1
Nordenskiöld, L.2
Mu, Y.3
-
172
-
-
45849137851
-
Attractive forces between cation condensed DNA double helices
-
Todd B A, Parsegian V A, Shirahata A, Thomas T J and Rau D C 2008 Attractive forces between cation condensed DNA double helices Biophys. J. 94 4775-82
-
(2008)
Biophys. J.
, vol.94
, pp. 4775-4782
-
-
Todd, B.A.1
Parsegian, V.A.2
Shirahata, A.3
Thomas, T.J.4
Rau, D.C.5
-
173
-
-
84877011320
-
A comparison of DNA compaction by arginine and lysine peptides: A physical basis for arginine rich protamines
-
DeRouchey J, Hoover B and Rau D C 2013 A comparison of DNA compaction by arginine and lysine peptides: a physical basis for arginine rich protamines Biochemistry 52 3000-9
-
(2013)
Biochemistry
, vol.52
, pp. 3000-3009
-
-
Derouchey, J.1
Hoover, B.2
Rau, D.C.3
-
174
-
-
0036106375
-
On the competition between water, sodium ions, and spermine in binding to DNA: A molecular dynamics computer simulation study
-
Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiöld L 2002 On the competition between water, sodium ions, and spermine in binding to DNA: a molecular dynamics computer simulation study Biophys. J. 82 2860-75
-
(2002)
Biophys. J.
, vol.82
, pp. 2860-2875
-
-
Korolev, N.1
Lyubartsev, A.P.2
Laaksonen, A.3
Nordenskiöld, L.4
-
175
-
-
0344011142
-
A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: Diffusion and averaged binding of water and cations
-
Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiöld L 2003 A molecular dynamics simulation study of oriented DNA with polyamine and sodium counterions: diffusion and averaged binding of water and cations Nucleic Acids Res. 31 5971-81
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5971-5981
-
-
Korolev, N.1
Lyubartsev, A.P.2
Laaksonen, A.3
Nordenskiöld, L.4
-
176
-
-
1842683168
-
Molecular dynamics simulation study of oriented polyamine- and Na-DNA: Sequence specific interactions and effects on DNA structure
-
Korolev N, Lyubartsev A P, Laaksonen A and Nordenskiöld L 2004 Molecular dynamics simulation study of oriented polyamine- and Na-DNA: sequence specific interactions and effects on DNA structure Biopolymers 73 542-55
-
(2004)
Biopolymers
, vol.73
, pp. 542-555
-
-
Korolev, N.1
Lyubartsev, A.P.2
Laaksonen, A.3
Nordenskiöld, L.4
-
177
-
-
77957605215
-
Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes
-
Luan B and Aksimentiev A 2010 Electric and electrophoretic inversion of the DNA charge in multivalent electrolytes Soft Matter 6 243-6
-
(2010)
Soft Matter
, vol.6
, pp. 243-246
-
-
Luan, B.1
Aksimentiev, A.2
-
178
-
-
0001301693
-
Screening of a macroion by multivalent ions: Correlation-induced inversion of charge
-
Shklovskii B I 1999 Screening of a macroion by multivalent ions: correlation-induced inversion of charge Phys. Rev. E 60 5802-11
-
(1999)
Phys. Rev.
, vol.60
, pp. 5802-5811
-
-
Shklovskii, B.I.1
-
179
-
-
0000959868
-
Reentrant condensation of DNA induced by multivalent counterions
-
Nguyen T T, Rouzina I and Shklovskii B I 2000 Reentrant condensation of DNA induced by multivalent counterions J. Chem. Phys. 112 2562
-
(2000)
J. Chem. Phys.
, vol.112
, pp. 2562
-
-
Nguyen, T.T.1
Rouzina, I.2
Shklovskii, B.I.3
-
180
-
-
34547344320
-
Detecting SNPs using a synthetic nanopore
-
Zhao Q, Sigalov G, Dimitrov V, Dorvel B, Mirsaidov U, Sligar S, Aksimentiev A and Timp G 2007 Detecting SNPs using a synthetic nanopore Nano Lett. 7 1680-5
-
(2007)
Nano Lett.
, vol.7
, pp. 1680-1685
-
-
Zhao, Q.1
Sigalov, G.2
Dimitrov, V.3
Dorvel, B.4
Mirsaidov, U.5
Sligar, S.6
Aksimentiev, A.7
Timp, G.8
-
181
-
-
67649710352
-
The unique structure of A-tracts and intrinsic DNA bending
-
Haran T E and Mohanty U 2009 The unique structure of A-tracts and intrinsic DNA bending Quart. Rev. Biophys. 42 41-81
-
(2009)
Quart. Rev. Biophys.
, vol.42
, pp. 41-81
-
-
Haran, T.E.1
Mohanty, U.2
-
182
-
-
10044257912
-
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides: I. Research design and results on d(cpg) steps
-
Beveridge D L et al 2004 Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides: I. Research design and results on d(cpg) steps Biophys. J. 87 3799-813
-
(2004)
Biophys. J.
, vol.87
, pp. 3799-3813
-
-
Beveridge, D.L.1
-
184
-
-
0015040327
-
The writhing number of a space curve
-
Fuller F B 1971 The writhing number of a space curve Proc. Natl Acad. Sci. USA 68 815-9
-
(1971)
Proc. Natl Acad. Sci. USA
, vol.68
, pp. 815-819
-
-
Fuller, F.B.1
-
185
-
-
36749121933
-
Theory of twisting and bending of chain macromolecules; Analysis of the fluorescence depolarization of DNA
-
Barkley M D and Zimm B H 1979 Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA J. Chem. Phys. 70 2991-3007
-
(1979)
J. Chem. Phys.
, vol.70
, pp. 2991-3007
-
-
Barkley, M.D.1
Zimm, B.H.2
-
186
-
-
0000545475
-
Ring-closure probabilities for twisted wormlike chains: Application to DNA
-
Shimada J and Yamakawa H 1984 Ring-closure probabilities for twisted wormlike chains: application to DNA Macromolecules 17 689-98
-
(1984)
Macromolecules
, vol.17
, pp. 689-698
-
-
Shimada, J.1
Yamakawa, H.2
-
187
-
-
2942521182
-
Single-molecule manipulation of nucleic acids
-
Bockelmann U 2004 Single-molecule manipulation of nucleic acids Curr. Opin. Struct. Biol. 14 368-73
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 368-373
-
-
Bockelmann, U.1
-
188
-
-
0030064676
-
DNA: An extensible molecule
-
Cluzel P, Lebrun A, Heller C, Lavery R, Viovy J-L, Chatenay D and Caron F 1996 DNA: an extensible molecule Science 271 792-4
-
(1996)
Science
, vol.271
, pp. 792-794
-
-
Cluzel, P.1
Lebrun, A.2
Heller, C.3
Lavery, R.4
Viovy, J.-L.5
Chatenay, D.6
Caron, F.7
-
189
-
-
0942278795
-
The physics of DNA stretching
-
Harris S A 2004 The physics of DNA stretching Contemp. Phys. 45 11
-
(2004)
Contemp. Phys.
, vol.45
, pp. 11
-
-
Harris, S.A.1
-
190
-
-
0029909230
-
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 Bolonick J I 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
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 10989
-
-
Konrad, M.W.1
Bolonick, J.I.2
-
191
-
-
0035146646
-
Force-induced melting of the DNA double heix 1. Thermodynamic analysis
-
Rouzina I and Bloomfield V 2001 Force-induced melting of the DNA double heix 1. Thermodynamic analysis Biophys. J. 80 882-93
-
(2001)
Biophys. J.
, vol.80
, pp. 882-893
-
-
Rouzina, I.1
Bloomfield, V.2
-
192
-
-
37149001327
-
DNA under high tension: Overstretching, undertwisting, and relaxation dynamics
-
Marko J F 1998 DNA under high tension: overstretching, undertwisting, and relaxation dynamics Phys. Rev. E 57 2134-49
-
(1998)
Phys. Rev.
, vol.57
, pp. 2134-2149
-
-
Marko, J.F.1
-
193
-
-
18344386476
-
Structural transitions of a twisted and stretched DNA molecule
-
Léger J F, Romano G, Sarkar A, Robert J, Bourdieu L, Chatenay D and Marko J F 1999 Structural transitions of a twisted and stretched DNA molecule Phys. Rev. Lett. 83 1066-9
-
(1999)
Phys. Rev. Lett.
, vol.83
, pp. 1066-1069
-
-
Léger, J.F.1
Romano, G.2
Sarkar, A.3
Robert, J.4
Bourdieu, L.5
Chatenay, D.6
Marko, J.F.7
-
194
-
-
85015087906
-
Ten years of tension: Single-molecule DNA mechanics
-
Bustamante C, Bryant Z and Smith S B 2003 Ten years of tension: single-molecule DNA mechanics Nature 421 423-7
-
(2003)
Nature
, vol.421
, pp. 423-427
-
-
Bustamante, C.1
Bryant, Z.2
Smith, S.B.3
-
195
-
-
34247643913
-
Pulling geometry induced errors in single molecule force spectroscopy measurements
-
Ke C, Jiang Y, Rivera M, Clark R L and Marszalek P E 2007 Pulling geometry induced errors in single molecule force spectroscopy measurements Biophys. J. 92 76-8
-
(2007)
Biophys. J.
, vol.92
, pp. 76-78
-
-
Ke, C.1
Jiang, Y.2
Rivera, M.3
Clark, R.L.4
Marszalek, P.E.5
-
196
-
-
34147193842
-
Stretching of homopolymeric RNA reveals single-strand helices and base-stacking
-
Seol Y, Skinner G M and Visscher K 2007 Stretching of homopolymeric RNA reveals single-strand helices and base-stacking Phys. Rev. Lett. 98 158103-6
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 158103-158106
-
-
Seol, Y.1
Skinner, G.M.2
Visscher, K.3
-
197
-
-
0030834853
-
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 2972-9
-
(1997)
Biophys. J.
, vol.73
, pp. 2972-2979
-
-
Isralewitz, B.1
Izrailev, S.2
Schulten, K.3
-
198
-
-
84878830185
-
Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA
-
Uzawa T, Isoshima T, Ito Y, Ishimori K, Makarov D E and Plaxco K W 2013 Sequence and temperature dependence of the end-to-end collision dynamics of single-stranded DNA Biophys. J. 104 2485-92
-
(2013)
Biophys. J.
, vol.104
, pp. 2485-2492
-
-
Uzawa, T.1
Isoshima, T.2
Ito, Y.3
Ishimori, K.4
Makarov, D.E.5
Plaxco, K.W.6
-
199
-
-
79952091255
-
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model
-
Ouldridge T E, Louis A A and Doye J P K 2011 Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model J. Chem. Phys. 134 085101
-
(2011)
J. Chem. Phys.
, vol.134
-
-
Ouldridge, T.E.1
Louis, A.A.2
Doye, J.P.K.3
-
200
-
-
21244498669
-
Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA
-
Harris S A, Sands Z A and Laughton C A 2005 Molecular dynamics simulations of duplex stretching reveal the importance of entropy in determining the biomechanical properties of DNA Biophys. J. 88 1684-91
-
(2005)
Biophys. J.
, vol.88
, pp. 1684-1691
-
-
Harris, S.A.1
Sands, Z.A.2
Laughton, C.A.3
-
201
-
-
0031808069
-
Structural equilibrium of DNA represented with different force fields
-
Feig M and Pettitt B M 1998 Structural equilibrium of DNA represented with different force fields Biophys. J. 75 134-49
-
(1998)
Biophys. J.
, vol.75
, pp. 134-149
-
-
Feig, M.1
Pettitt, B.M.2
-
203
-
-
36449003554
-
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 4177-89
-
(1994)
J. Chem. Phys.
, vol.101
, pp. 4177-4189
-
-
Martyna, G.J.1
Tobias, D.J.2
Klein, M.L.3
-
206
-
-
70549099970
-
The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics
-
Brooks T A and Hurley L H 2009 The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics Nature Rev. Cancer 9 849-61
-
(2009)
Nature Rev. Cancer
, vol.9
, Issue.12
, pp. 949-861
-
-
Brooks, T.A.1
Hurley, L.H.2
-
207
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
Lankas F, Sponer J, Langowski J and Cheatham T E 2003 DNA basepair step deformability inferred from molecular dynamics simulations Biophys. J. 85 2872-83
-
(2003)
Biophys. J.
, vol.85
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
208
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
Cloutier T E and Widom J 2004 Spontaneous sharp bending of double-stranded DNA Mol. Cell 14 355-62
-
(2004)
Mol. Cell
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
209
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
Gorin A A, Zhurkin V B and Olson W K 1995 B-DNA twisting correlates with base-pair morphology J. Mol. Biol. 247 34-48
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
210
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson W K, Gorin A A, Lu X-J, Hock L M and Zhurkin V B 1998 DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl Acad. Sci. USA 95 11163-8
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.-J.3
Hock, L.M.4
Zhurkin, V.B.5
-
211
-
-
69449095355
-
Sequence dependencies of DNA deformability and hydration in the minor groove
-
Yonetani Y and Kono H 2009 Sequence dependencies of DNA deformability and hydration in the minor groove Biophys. J. 97 1138-47
-
(2009)
Biophys. J.
, vol.97
, pp. 1138-1147
-
-
Yonetani, Y.1
Kono, H.2
-
212
-
-
0000039979
-
Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion
-
Mazur A K 1999 Symplectic integration of closed chain rigid body dynamics with internal coordinate equations of motion J. Chem. Phys. 111 1407-14
-
(1999)
J. Chem. Phys.
, vol.111
, pp. 1407-1414
-
-
Mazur, A.K.1
-
213
-
-
80051651729
-
Local elasticity of strained DNA studied by all-atom simulations
-
Mazur A K 2011 Local elasticity of strained DNA studied by all-atom simulations Phys. Rev. E 84 021903
-
(2011)
Phys. Rev.
, vol.84
-
-
Mazur, A.K.1
-
214
-
-
84870432003
-
Length scale dependence of DNA mechanical properties
-
Noy A and Golestanian R 2012 Length scale dependence of DNA mechanical properties Phys. Rev. Lett. 109 228101
-
(2012)
Phys. Rev. Lett.
, vol.109
-
-
Noy, A.1
Golestanian, R.2
-
215
-
-
84886780774
-
Comment on Length scale dependence of DNA mechanical properties
-
Mazur A K 2013 Comment on Length scale dependence of DNA mechanical properties Phys. Rev. Lett. 111 179801
-
(2013)
Phys. Rev. Lett.
, vol.111
-
-
Mazur, A.K.1
-
217
-
-
0028375446
-
Bending and twisting elasticity of DNA
-
Marko J F and Siggia E D 1994 Bending and twisting elasticity of DNA Macromolecules 27 981-8
-
(1994)
Macromolecules
, vol.27
, pp. 981-988
-
-
Marko, J.F.1
Siggia, E.D.2
-
218
-
-
33747461393
-
DNA overwinds when stretched
-
Gore J, Bryant Z, Nöllmann M, Le M U, Cozzarelli N R and Bustamante C 2006 DNA overwinds when stretched Nature 442 836-9
-
(2006)
Nature
, vol.442
, pp. 836-839
-
-
Gore, J.1
Bryant, Z.2
Nöllmann, M.3
Le, M.U.4
Cozzarelli, N.R.5
Bustamante, C.6
-
219
-
-
80052442505
-
Quantifying how DNA stretches, melts and changes twist under tension
-
Gross P, Laurens N, Oddershede L B, Bockelmann U, Peterman E J G and Wuite G J L 2011 Quantifying how DNA stretches, melts and changes twist under tension Nature Phys. 7 731-6
-
(2011)
Nature Phys.
, vol.7
, pp. 731-736
-
-
Gross, P.1
Laurens, N.2
Oddershede, L.B.3
Bockelmann, U.4
Peterman, E.J.G.5
Wuite, G.J.L.6
-
220
-
-
0000214231
-
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution
-
MacKerell A D Jr and Banavali N K 2000 All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution J. Comput. Chem. 21 105-20
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 105-120
-
-
MacKerell, A.D.1
Banavali, N.K.2
-
221
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
Olson W K et al 2001 A standard reference frame for the description of nucleic acid base-pair geometry J. Mol. Biol. 313 229-37
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 229-237
-
-
Olson, W.K.1
-
223
-
-
68849118253
-
Twist-stretch coupling and phase transition during DNA supercoiling
-
Sheinin M Y and Wang M D 2009 Twist-stretch coupling and phase transition during DNA supercoiling Phys. Chem. Chem. Phys. 11 4800-3
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 4800-4803
-
-
Sheinin, M.Y.1
Wang, M.D.2
-
224
-
-
70449711324
-
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
-
Randall G L, Zechiedrich L and Pettitt B M 2009 In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form Nucleic Acids Res. 37 5568-77
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5568-5577
-
-
Randall, G.L.1
Zechiedrich, L.2
Pettitt, B.M.3
-
227
-
-
17244362931
-
Cyclization of short DNA fragments and bending fluctuations of the double helix
-
Du Q, Smith C, Shiffeldrim N, Vologodskaia M and Vologodskii A 2005 Cyclization of short DNA fragments and bending fluctuations of the double helix Proc. Natl Acad. Sci. USA 102 5397-402
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Shiffeldrim, N.3
Vologodskaia, M.4
Vologodskii, A.5
-
229
-
-
84861953342
-
Critical torque for kink formation in double-stranded DNA
-
Qu H, Wang Y, Tseng C-Y and Zocchi G 2011 Critical torque for kink formation in double-stranded DNA Phys. Rev. X 1 021008
-
(2011)
Phys. Rev.
, vol.1
-
-
Qu, H.1
Wang, Y.2
Tseng, C.-Y.3
Zocchi, G.4
-
230
-
-
33749259954
-
Kinking occurs during molecular dynamics simulations of small DNA minicircles
-
Lankas F, Lavery R and Maddocks J H 2006 Kinking occurs during molecular dynamics simulations of small DNA minicircles Structure 14 1527-34
-
(2006)
Structure
, vol.14
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
231
-
-
38349173106
-
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
-
Harris S A, Laughton C A and Liverpool T B 2008 Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations Nucleic Acids Res. 36 21-9
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 21-29
-
-
Harris, S.A.1
Laughton, C.A.2
Liverpool, T.B.3
-
232
-
-
79955811415
-
Nucleosome structure(s) and stability: Variations on a theme
-
Andrews A J and Luger K 2011 Nucleosome structure(s) and stability: variations on a theme Annu. Rev. Biophys. 40 99-117
-
(2011)
Annu. Rev. Biophys.
, vol.40
, pp. 99-117
-
-
Andrews, A.J.1
Luger, K.2
-
233
-
-
0037133348
-
Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA
-
Brower-Toland B D, Smith C L, Yeh R C, Lis J T, Peterson C L and Wang M D 2002 Mechanical disruption of individual nucleosomes reveals a reversible multistage release of DNA Proc. Natl Acad. Sci. USA 99 1960-5
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 1960-1965
-
-
Brower-Toland, B.D.1
Smith, C.L.2
Yeh, R.C.3
Lis, J.T.4
Peterson, C.L.5
Wang, M.D.6
-
234
-
-
12344284012
-
Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes
-
Brower-Toland B, Wacker D A, Fulbright R M, Lis J T, Kraus W L and Wang M D 2005 Specific contributions of histone tails and their acetylation to the mechanical stability of nucleosomes J. Mol. Biol. 346 135-46
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 135-146
-
-
Brower-Toland, B.1
Wacker, D.A.2
Fulbright, R.M.3
Lis, J.T.4
Kraus, W.L.5
Wang, M.D.6
-
236
-
-
59649112972
-
High-resolution dynamic mapping of histone-DNA interactions in a nucleosome
-
Hall M A, Shundrovsky A, Bai L, Fulbright R M, Lis J T and Wang M D 2009 High-resolution dynamic mapping of histone-DNA interactions in a nucleosome Nature Struct. Mol. Biol. 16 124-9
-
(2009)
Nature Struct. Mol. Biol.
, vol.16
, pp. 124-129
-
-
Hall, M.A.1
Shundrovsky, A.2
Bai, L.3
Fulbright, R.M.4
Lis, J.T.5
Wang, M.D.6
-
237
-
-
33750807408
-
Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
-
Arya G and Schlick T 2006 Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model Proc. Natl Acad. Sci. USA 103 16236-41
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 16236-16241
-
-
Arya, G.1
Schlick, T.2
-
238
-
-
84863142625
-
Unwrapping of nucleosomal DNA ends: A multiscale molecular dynamics study
-
Voltz K, Trylska J, Calimet N, Smith J C and Langowski J 2012 Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study Biophys. J. 102 849-58
-
(2012)
Biophys. J.
, vol.102
, pp. 849-858
-
-
Voltz, K.1
Trylska, J.2
Calimet, N.3
Smith, J.C.4
Langowski, J.5
-
239
-
-
84873884167
-
An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions
-
Fan Y, Korolev N, Lyubartsev A P and Nordenskiöld L 2013 An advanced coarse-grained nucleosome core particle model for computer simulations of nucleosome-nucleosome interactions under varying ionic conditions PLoS ONE 8 e54228
-
(2013)
PLoS ONE
, vol.8
-
-
Fan, Y.1
Korolev, N.2
Lyubartsev, A.P.3
Nordenskiöld, L.4
-
240
-
-
80054702334
-
Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping
-
Ettig R, Kepper N, Stehr R, Wedemann G and Rippe K 2011 Dissecting DNA-histone interactions in the nucleosome by molecular dynamics simulations of DNA unwrapping Biophys. J. 101 1999-2008
-
(2011)
Biophys. J.
, vol.101
, pp. 1999-2008
-
-
Ettig, R.1
Kepper, N.2
Stehr, R.3
Wedemann, G.4
Rippe, K.5
-
241
-
-
84861892611
-
A rule of seven in Watson-Crick base-pairing of mismatched sequences
-
Cisse I I, Kim H and Ha T 2012 A rule of seven in Watson-Crick base-pairing of mismatched sequences Nature Struct. Mol. Biol. 19 623-7
-
(2012)
Nature Struct. Mol. Biol.
, vol.19
, pp. 623-627
-
-
Cisse, I.I.1
Kim, H.2
Ha, T.3
-
242
-
-
0344270866
-
Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA
-
Hagan M F, Dinner A R, Chandler D and Chakraborty A K 2003 Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA Proc. Natl Acad. Sci. USA 100 13922-7
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 13922-13927
-
-
Hagan, M.F.1
Dinner, A.R.2
Chandler, D.3
Chakraborty, A.K.4
-
243
-
-
0042845840
-
Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations
-
Sorin E J, Rhee Y M, Nakatani B J and Pande V S 2003 Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations Biophys. J. 85 790-803
-
(2003)
Biophys. J.
, vol.85
, pp. 790-803
-
-
Sorin, E.J.1
Rhee, Y.M.2
Nakatani, B.J.3
Pande, V.S.4
-
244
-
-
38349110269
-
Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin
-
Garcia A E and Paschek D 2008 Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin J. Am. Chem. Soc. 130 815-7
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 815-817
-
-
Garcia, A.E.1
Paschek, D.2
-
245
-
-
78249249624
-
Multiple routes to characterize the folding of a small DNA hairpin
-
Portella G and Orozco M 2010 Multiple routes to characterize the folding of a small DNA hairpin Angew. Chem. Int. Edn Engl. 49 7673-6
-
(2010)
Angew. Chem. Int. Edn Engl.
, vol.49
, pp. 7673-7676
-
-
Portella, G.1
Orozco, M.2
-
246
-
-
84893775247
-
Theoretical studies of nucleic acids folding
-
Kara M and Zacharias M 2014 Theoretical studies of nucleic acids folding WIREs Comput. Mol. Sci. 4 116-26
-
(2014)
WIREs Comput. Mol. Sci.
, vol.4
, pp. 116-126
-
-
Kara, M.1
Zacharias, M.2
-
247
-
-
0026558204
-
Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces
-
Rau D C and Parsegian V A 1992 Direct measurement of the intermolecular forces between counterion-condensed DNA double helices. Evidence for long range attractive hydration forces Biophys. J. 61 246-59
-
(1992)
Biophys. J.
, vol.61
, pp. 246-259
-
-
Rau, D.C.1
Parsegian, V.A.2
-
248
-
-
0029975925
-
DNA aggregation induced by polyamines and cobalthexamine
-
Pelta J, Livolant F and Sikorav J L 1996 DNA aggregation induced by polyamines and cobalthexamine J. Biol. Chem. 271 5656-62
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 5656-5662
-
-
Pelta, J.1
Livolant, F.2
Sikorav, J.L.3
-
249
-
-
39149124468
-
Interplay of ion binding and attraction in DNA condensed by multivalent cations
-
Todd B A and Rau D C 2008 Interplay of ion binding and attraction in DNA condensed by multivalent cations Nucleic Acids Res. 36 501-10
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 501-510
-
-
Todd, B.A.1
Rau, D.C.2
-
250
-
-
0022459444
-
Osmotic stress for the direct measurement of intermolecular forces
-
Parsegian V A, Rand R P, Fuller N L and Rau D C 1986 Osmotic stress for the direct measurement of intermolecular forces Methods Enzymol 127 400-16
-
(1986)
Methods Enzymol
, vol.127
, pp. 400-416
-
-
Parsegian, V.A.1
Rand, R.P.2
Fuller, N.L.3
Rau, D.C.4
-
251
-
-
0026608715
-
Direct measurement of temperature-dependent solvation forces between DNA double helices
-
Rau D C and Parsegian V A 1992 Direct measurement of temperature-dependent solvation forces between DNA double helices Biophys. J. 61 260-71
-
(1992)
Biophys. J.
, vol.61
, pp. 260-271
-
-
Rau, D.C.1
Parsegian, V.A.2
-
252
-
-
0001258148
-
Theory of interaction between helical molecules
-
Kornyshev A A and Leikin L 1997 Theory of interaction between helical molecules J. Chem. Phys. 107 3656-74
-
(1997)
J. Chem. Phys.
, vol.107
, pp. 3656-3674
-
-
Kornyshev, A.A.1
Leikin, L.2
-
253
-
-
0032506008
-
Electrostatic interaction between helical macromolecules in dense aggregates: An impetus for DNA poly- and meso-morphism
-
Kornyshev A A and Leikin S 1998 Electrostatic interaction between helical macromolecules in dense aggregates: an impetus for DNA poly- and meso-morphism Proc. Natl Acad. Sci. USA 95 13579-84
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 13579-13584
-
-
Kornyshev, A.A.1
Leikin, S.2
-
254
-
-
18144376538
-
Electrostatic zipper motif for DNA aggregation
-
Kornyshev A A and Leikin S 1999 Electrostatic zipper motif for DNA aggregation Phys. Rev. Lett. 82 4138-41
-
(1999)
Phys. Rev. Lett.
, vol.82
, pp. 4138-4141
-
-
Kornyshev, A.A.1
Leikin, S.2
-
255
-
-
34249041190
-
Inter-DNA electrostatics from explicit solvent molecular dynamics simulations
-
Savelyev A and Papoian G A 2007 Inter-DNA electrostatics from explicit solvent molecular dynamics simulations J. Am. Chem. Soc. 129 6060-1
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 6060-6061
-
-
Savelyev, A.1
Papoian, G.A.2
-
256
-
-
56749160319
-
DNA attraction in monovalent and divalent electrolytes
-
Luan B and Aksimentiev A 2008 DNA attraction in monovalent and divalent electrolytes J. Am. Chem. Soc. 130 15754-5
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 15754-15755
-
-
Luan, B.1
Aksimentiev, A.2
-
257
-
-
0028207587
-
Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations
-
Podgornik R, Rau D C and Parsegian V A 1994 Parametrization of direct and soft steric-undulatory forces between DNA double helical polyelectrolytes in solutions of several different anions and cations Biophys. J. 66 962-71
-
(1994)
Biophys. J.
, vol.66
, pp. 962-971
-
-
Podgornik, R.1
Rau, D.C.2
Parsegian, V.A.3
-
258
-
-
34547430442
-
Ionic effects on viral DNA packaging and portal motor function in bacteriophage φ29
-
Fuller D N, Rickgauer J P, Jardine P J, Grimes S, Anderson D L and Smith D E 2007 Ionic effects on viral DNA packaging and portal motor function in bacteriophage φ29 Proc. Natl Acad. Sci. USA 104 11245-50
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 11245-11250
-
-
Fuller, D.N.1
Rickgauer, J.P.2
Jardine, P.J.3
Grimes, S.4
Anderson, D.L.5
Smith, D.E.6
-
259
-
-
0026053025
-
Spermidine or spermine is essential for the aerobic growth of saccharomyces cerevisiae
-
Balasundaram D, Tabor C W and Tabor H 1991 Spermidine or spermine is essential for the aerobic growth of saccharomyces cerevisiae Proc. Natl Acad. Sci. USA 88 5872-6
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 5872-5876
-
-
Balasundaram, D.1
Tabor, C.W.2
Tabor, H.3
-
260
-
-
70449529855
-
Induction of autophagy by spermidine promotes longevity
-
Eisenberg T et al 2009 Induction of autophagy by spermidine promotes longevity Nature Cell. Biol. 11 1305-14
-
(2009)
Nature Cell. Biol.
, vol.11
, pp. 1305-1314
-
-
Eisenberg, T.1
-
261
-
-
14044271924
-
Toroidal DNA condensates: Unraveling the fine structure and the role of nucleation in determining size
-
Hud N V and Vilfan I D 2005 Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size Annu. Rev. Biophys. Biomol. Struct. 34 295-318
-
(2005)
Annu. Rev. Biophys. Biomol. Struct.
, vol.34
, pp. 295-318
-
-
Hud, N.V.1
Vilfan, I.D.2
-
264
-
-
84907472639
-
Macroion attraction due to electrostatic correlation between screening counterions: I. Mobile surface-adsorbed ions and diffuse ion cloud
-
Rouzina I and Bloomfield V A 1996 Macroion attraction due to electrostatic correlation between screening counterions: I. Mobile surface-adsorbed ions and diffuse ion cloud J. Phys. Chem. 100 9
-
(1996)
J. Phys. Chem.
, vol.100
, pp. 9
-
-
Rouzina, I.1
Bloomfield, V.A.2
-
265
-
-
18344392110
-
Wigner crystal model of counterion induced bundle formation of rod like polyelectrolytes
-
Shklovskii B I 1999 Wigner crystal model of counterion induced bundle formation of rod like polyelectrolytes Phys. Rev. Lett. 82 3268-71
-
(1999)
Phys. Rev. Lett.
, vol.82
, pp. 3268-3271
-
-
Shklovskii, B.I.1
-
266
-
-
41149115685
-
Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules
-
Dai L, Mu Y, Nordenskiöld L and van der Maarel J R C 2008 Molecular dynamics simulation of multivalent-ion mediated attraction between DNA molecules Phys. Rev. Lett. 100 118301
-
(2008)
Phys. Rev. Lett.
, vol.100
-
-
Dai, L.1
Mu, Y.2
Nordenskiöld, L.3
Van Der Maarel, J.R.C.4
-
267
-
-
36448931940
-
End-to-end stacking and liquid crystal condensation of 6 to 20 base pair DNA duplexes
-
Nakata M, Zanchetta G, Chapman B D, Jones C D, Cross J O, Pindak R, Bellini T and Clark N A 2007 End-to-end stacking and liquid crystal condensation of 6 to 20 base pair DNA duplexes Science 318 1276
-
(2007)
Science
, vol.318
, pp. 1276
-
-
Nakata, M.1
Zanchetta, G.2
Chapman, B.D.3
Jones, C.D.4
Cross, J.O.5
Pindak, R.6
Bellini, T.7
Clark, N.A.8
-
268
-
-
58149348585
-
Liquid crystal ordering of DNA and RNA oligomers with partially overlapping sequences
-
Zanchetta G, Nakata M, Buscaglia M, Clark N A and Bellini T 2008 Liquid crystal ordering of DNA and RNA oligomers with partially overlapping sequences J. Phys.: Condens. Matter 20 494214
-
(2008)
J. Phys.: Condens. Matter
, vol.20
, Issue.49
-
-
Zanchetta, G.1
Nakata, M.2
Buscaglia, M.3
Clark, N.A.4
Bellini, T.5
-
271
-
-
18744372751
-
Calculation of absolute protein-ligand binding free energy from computer simulations
-
Woo H-J and Roux B 2005 Calculation of absolute protein-ligand binding free energy from computer simulations Proc. Natl Acad. Sci. USA 102 6825-30
-
(2005)
Proc. Natl Acad. Sci. USA
, vol.102
, pp. 6825-6830
-
-
Woo, H.-J.1
Roux, B.2
-
272
-
-
84864443758
-
Self-assembly of short DNA duplexes: From a coarse-grained model to experiments through a theoretical link
-
De Michele C, Rovigatti L, Bellini T and Sciortino F 2012 Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link Soft Matter 8 8388-98
-
(2012)
Soft Matter
, vol.8
, pp. 8388-8398
-
-
De Michele, C.1
Rovigatti, L.2
Bellini, T.3
Sciortino, F.4
-
273
-
-
0016800090
-
A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase
-
Sanger F and Coulson A R 1975 A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase J. Mol. Biol. 94 441-8
-
(1975)
J. Mol. Biol.
, vol.94
, pp. 441-448
-
-
Sanger, F.1
Coulson, A.R.2
-
274
-
-
53649108801
-
The potential and challenges of nanopore sequencing
-
Branton D et al 2008 The potential and challenges of nanopore sequencing Nature Biotechnol. 26 1146-53
-
(2008)
Nature Biotechnol.
, vol.26
, pp. 1146-1153
-
-
Branton, D.1
-
275
-
-
80455173836
-
Nanopore sensors for nucleic acid analysis
-
Venkatesan B M and Bashir R 2011 Nanopore sensors for nucleic acid analysis Nature Nanotechnol. 6 615-24
-
(2011)
Nature Nanotechnol.
, vol.6
, pp. 615-624
-
-
Venkatesan, B.M.1
Bashir, R.2
-
276
-
-
77952611899
-
Nanopore sequencing: Electrical measurements of the code of life
-
Timp W, Mirsaidov U M, Wang D, Comer J, Aksimentiev A and Timp G 2010 Nanopore sequencing: electrical measurements of the code of life IEEE Trans. Nanotechnol. 9 281-94
-
(2010)
IEEE Trans. Nanotechnol.
, vol.9
, pp. 281-294
-
-
Timp, W.1
Mirsaidov, U.M.2
Wang, D.3
Comer, J.4
Aksimentiev, A.5
Timp, G.6
-
277
-
-
0342918063
-
Capillary electrophoresis measurements of the free solution mobility for several model polyelectrolyte systems
-
Hoagland D A, Arvanitidou E and Welch C 1999 Capillary electrophoresis measurements of the free solution mobility for several model polyelectrolyte systems Macromolecules 32 6180-90
-
(1999)
Macromolecules
, vol.32
, pp. 6180-6190
-
-
Hoagland, D.A.1
Arvanitidou, E.2
Welch, C.3
-
278
-
-
0036672769
-
Determining the electrophoretic mobility and translational diffusion coefficients of DNA molecules in free solution
-
Stellwagen E and Stellwagen N C 2002 Determining the electrophoretic mobility and translational diffusion coefficients of DNA molecules in free solution Electrophoresis 23 2794-803
-
(2002)
Electrophoresis
, vol.23
, pp. 2794-2803
-
-
Stellwagen, E.1
Stellwagen, N.C.2
-
279
-
-
0034898281
-
Diffusion coefficient of DNA molecules during free solution electrophoresis
-
Nkodo A E, Garnier J M, Tinland B, Ren H, Desruissaux C, McCormick L C, Drouin G and Slater G W 2001 Diffusion coefficient of DNA molecules during free solution electrophoresis Electrophoresis 22 2424
-
(2001)
Electrophoresis
, vol.22
, pp. 2424
-
-
Nkodo, A.E.1
Garnier, J.M.2
Tinland, B.3
Ren, H.4
Desruissaux, C.5
McCormick, L.C.6
Drouin, G.7
Slater, G.W.8
-
281
-
-
0141885303
-
Unified description of electrophoresis and diffusion for DNA and other polyions
-
Stellwagen E, Lu Y and Stellwagen N C 2003 Unified description of electrophoresis and diffusion for DNA and other polyions Biochemistry 42 11745-50
-
(2003)
Biochemistry
, vol.42
, pp. 11745-11750
-
-
Stellwagen, E.1
Lu, Y.2
Stellwagen, N.C.3
-
282
-
-
6244226478
-
Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: Motion and deformation
-
Long D, Viovy J L and Ajdari A 1996 Simultaneous action of electric fields and nonelectric forces on a polyelectrolyte: motion and deformation Phys. Rev. Lett. 76 3858-61
-
(1996)
Phys. Rev. Lett.
, vol.76
, pp. 3858-3861
-
-
Long, D.1
Viovy, J.L.2
Ajdari, A.3
-
283
-
-
13844276800
-
End-labeled free-solution electrophoresis of DNA
-
Meagher R J, Won J-I, McCormick L C, Nedelcu S, Bertrand M M, Bertram J L, Drouin G, Barron A E and Slater G W 2005 End-labeled free-solution electrophoresis of DNA Electrophoresis 26 331-50
-
(2005)
Electrophoresis
, vol.26
, pp. 331-350
-
-
Meagher, R.J.1
Won, J.-I.2
McCormick, L.C.3
Nedelcu, S.4
Bertrand, M.M.5
Bertram, J.L.6
Drouin, G.7
Barron, A.E.8
Slater, G.W.9
-
284
-
-
0034335665
-
Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms
-
Viovy J L 2000 Electrophoresis of DNA and other polyelectrolytes: physical mechanisms Rev. Mod. Phys. 72 813
-
(2000)
Rev. Mod. Phys.
, vol.72
, pp. 813
-
-
Viovy, J.L.1
-
286
-
-
36849015843
-
DNA diagnostics by capillary electrophoresis
-
Klepárník K and Bocek P 2007 DNA diagnostics by capillary electrophoresis Chem. Rev. 107 5279-317
-
(2007)
Chem. Rev.
, vol.107
, pp. 5279-5317
-
-
Klepárník, K.1
Bocek, P.2
-
288
-
-
69249203633
-
DNA gel electrophoresis: The reptation model(s)
-
Slater G W 2009 DNA gel electrophoresis: the reptation model(s) Electrophoresis 30 S181-7
-
(2009)
Electrophoresis
, vol.30
, pp. 181-S187
-
-
Slater, G.W.1
-
290
-
-
34248351114
-
Solid-state nanopores
-
Dekker C 2007 Solid-state nanopores Nature Nanotechnol. 2 209-15
-
(2007)
Nature Nanotechnol.
, vol.2
, pp. 209-215
-
-
Dekker, C.1
-
291
-
-
80052258551
-
Controlling molecular transport through nanopores
-
Keyser U F 2011 Controlling molecular transport through nanopores J. R. Soc. Interf. 8 1369-78
-
(2011)
J. R. Soc. Interf.
, vol.8
, pp. 1369-1378
-
-
Keyser, U.F.1
-
292
-
-
0035831563
-
Voltage-driven DNA translocations through a nanopore
-
Meller A, Nivon L and Branton D 2001 Voltage-driven DNA translocations through a nanopore Phys. Rev. Lett. 86 3435-8
-
(2001)
Phys. Rev. Lett.
, vol.86
, pp. 3435-3438
-
-
Meller, A.1
Nivon, L.2
Branton, D.3
-
293
-
-
0035849885
-
Ion-beam sculpting at nanometre length scales
-
Li J, Stein D, McMullan C, Branton D, Aziz M J and Golovchenko J A 2001 Ion-beam sculpting at nanometre length scales Nature 412 166-9
-
(2001)
Nature
, vol.412
, pp. 166-169
-
-
Li, J.1
Stein, D.2
McMullan, C.3
Branton, D.4
Aziz, M.J.5
Golovchenko, J.A.6
-
294
-
-
0042285088
-
Fabrication of solid-state nanopore with single-nanometre precision
-
Storm A J, Chen J H, Ling X S, Zandergen H W and Dekker C 2003 Fabrication of solid-state nanopore with single-nanometre precision Nature Mater. 2 537-40
-
(2003)
Nature Mater.
, vol.2
, pp. 537-540
-
-
Storm, A.J.1
Chen, J.H.2
Ling, X.S.3
Zandergen, H.W.4
Dekker, C.5
-
295
-
-
16644398754
-
Sizing DNA using a nanometer-diameter pore
-
Heng J B, Ho C, Kim T, Timp R, Aksimentiev A, Grinkova Y V, Sligar S, Schulten K and Timp G 2004 Sizing DNA using a nanometer-diameter pore Biophys. J. 87 2905-11
-
(2004)
Biophys. J.
, vol.87
, pp. 2905-2911
-
-
Heng, J.B.1
Ho, C.2
Kim, T.3
Timp, R.4
Aksimentiev, A.5
Grinkova, Y.V.6
Sligar, S.7
Schulten, K.8
Timp, G.9
-
296
-
-
77953677764
-
Deciphering ionic current signatures of DNA transport through a nanopore
-
Aksimentiev A 2010 Deciphering ionic current signatures of DNA transport through a nanopore Nanoscale 2 468-83
-
(2010)
Nanoscale
, vol.2
, pp. 468-483
-
-
Aksimentiev, A.1
-
297
-
-
0034177819
-
Nanopores and nucleic acids: Prospects for ultrarapid sequencing
-
Deamer D W and Akeson M 2000 Nanopores and nucleic acids: prospects for ultrarapid sequencing Trends Biotechnol. 18 147-51
-
(2000)
Trends Biotechnol.
, vol.18
, pp. 147-151
-
-
Deamer, D.W.1
Akeson, M.2
-
298
-
-
31544471731
-
Salt-dependence of ion transport and DNA translocation through solid-state nanopores
-
Smeets R M M, Keyser U F, Krapf D, Wu M-Y, Dekker N H and Dekker C 2006 Salt-dependence of ion transport and DNA translocation through solid-state nanopores Nano Lett. 6 89-95
-
(2006)
Nano Lett.
, vol.6
, pp. 89-95
-
-
Smeets, R.M.M.1
Keyser, U.F.2
Krapf, D.3
Wu, M.-Y.4
Dekker, N.H.5
Dekker, C.6
-
299
-
-
58849087632
-
Microscopic mechanics of hairpin DNA translocation through synthetic nanopores
-
Comer J, Dimitrov V, Zhao Q, Timp G and Aksimentiev A 2009 Microscopic mechanics of hairpin DNA translocation through synthetic nanopores Biophys. J. 96 593-608
-
(2009)
Biophys. J.
, vol.96
, pp. 593-608
-
-
Comer, J.1
Dimitrov, V.2
Zhao, Q.3
Timp, G.4
Aksimentiev, A.5
-
300
-
-
84878271847
-
Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores
-
Venta K, Shemer G, Puster M, Rodríguez-Manzo J A, Balan A, Rosenstein J K, Shepard K and Drndić M 2013 Differentiation of short, single-stranded DNA homopolymers in solid-state nanopores ACS Nano 7 4629-36
-
(2013)
ACS Nano
, vol.7
, Issue.5
, pp. 4629-4636
-
-
Venta, K.1
Shemer, G.2
Puster, M.3
Rodríguez-Manzo, J.A.4
Balan, A.5
Rosenstein, J.K.6
Shepard, K.7
Drndić, M.8
-
301
-
-
84856812308
-
Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics
-
Comer J and Aksimentiev A 2012 Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics J. Phys. Chem. C 116 3376-93
-
(2012)
J. Phys. Chem.
, vol.116
, pp. 3376-3393
-
-
Comer, J.1
Aksimentiev, A.2
-
302
-
-
33746625243
-
Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor
-
Gracheva M E, Aksimentiev A and Leburton J-P 2006 Electrical signatures of single-stranded DNA with single base mutations in a nanopore capacitor Nanotechnology 17 3160-5
-
(2006)
Nanotechnology
, vol.17
, Issue.13
, pp. 3160-3165
-
-
Gracheva, M.E.1
Aksimentiev, A.2
Leburton, J.-P.3
-
303
-
-
38049138721
-
Colloquium: Physical approaches to DNA sequencing and detection
-
Zwolak M and Di Ventra M 2008 Colloquium: physical approaches to DNA sequencing and detection Rev. Mod. Phys. 80 141-65
-
(2008)
Rev. Mod. Phys.
, vol.80
, pp. 141-165
-
-
Zwolak, M.1
Di Ventra, M.2
-
304
-
-
78650009474
-
Identifying single bases in a DNA oligomer with electron tunnelling
-
Huang S, He J, Chang S, Zhang P, Liang F, Li S, Tuchband M, Fuhrmann A, Ros R and Lindsay S 2010 Identifying single bases in a DNA oligomer with electron tunnelling Nature Nanotechnol. 5 868-73
-
(2010)
Nature Nanotechnol.
, vol.5
, pp. 868-873
-
-
Huang, S.1
He, J.2
Chang, S.3
Zhang, P.4
Liang, F.5
Li, S.6
Tuchband, M.7
Fuhrmann, A.8
Ros, R.9
Lindsay, S.10
-
306
-
-
26944479214
-
Translocation of double-strand DNA through a silicon oxide nanopore
-
Storm A J, Chen J H, Zandbergen H W and Dekker C 2005 Translocation of double-strand DNA through a silicon oxide nanopore Phys. Rev. E 71 051903-13
-
(2005)
Phys. Rev.
, vol.71
, pp. 051903-051913
-
-
Storm, A.J.1
Chen, J.H.2
Zandbergen, H.W.3
Dekker, C.4
-
307
-
-
33745774997
-
Direct force measurements on DNA in a solid-state nanopore
-
Keyser U, Koeleman B, Dorp S, Krapf D, Smeets R, Lemay S, Dekker N and Dekker C 2006 Direct force measurements on DNA in a solid-state nanopore Nature Phys. 2 473-77
-
(2006)
Nature Phys.
, vol.2
, pp. 473-477
-
-
Keyser, U.1
Koeleman, B.2
Dorp, S.3
Krapf, D.4
Smeets, R.5
Lemay, S.6
Dekker, N.7
Dekker, C.8
-
308
-
-
33749500050
-
Electrophoresis of a polyelectrolyte through a nanopore
-
Ghosal S 2006 Electrophoresis of a polyelectrolyte through a nanopore Phys. Rev. E 74 041901
-
(2006)
Phys. Rev.
, vol.74
-
-
Ghosal, S.1
-
309
-
-
34547339162
-
Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore
-
Ghosal S 2007 Effect of salt concentration on the electrophoretic speed of a polyelectrolyte through a nanopore Phys. Rev. Lett. 98 238104
-
(2007)
Phys. Rev. Lett.
, vol.98
-
-
Ghosal, S.1
-
310
-
-
50849102996
-
Electro-osmotic screening of the DNA charge in a nanopore
-
Luan B and Aksimentiev A 2008 Electro-osmotic screening of the DNA charge in a nanopore Phys. Rev. E 78 021912
-
(2008)
Phys. Rev.
, vol.78
-
-
Luan, B.1
Aksimentiev, A.2
-
311
-
-
67649206290
-
Origin of the electrophoretic force on DNA in solid-state nanopores
-
van Dorp S, Keyser U F, Dekker N H, Dekker C and Lemay S G 2009 Origin of the electrophoretic force on DNA in solid-state nanopores Nature Phys. 5 347-51
-
(2009)
Nature Phys.
, vol.5
, pp. 347-351
-
-
Van Dorp, S.1
Keyser, U.F.2
Dekker, N.H.3
Dekker, C.4
Lemay, S.G.5
-
312
-
-
78149444505
-
Control and reversal of the electrophoretic force on DNA in a charged nanopore
-
Luan B and Aksimentiev A 2010 Control and reversal of the electrophoretic force on DNA in a charged nanopore J. Phys.: Condens. Matter 22 454123
-
(2010)
J. Phys.: Condens. Matter
, vol.22
, Issue.45
-
-
Luan, B.1
Aksimentiev, A.2
-
313
-
-
84856956993
-
Slowing down DNA translocation through a nanopore in lithium chloride
-
Kowalczyk S W, Wells D B, Aksimentiev A and Dekker C 2012 Slowing down DNA translocation through a nanopore in lithium chloride Nano Lett. 12 1038-44
-
(2012)
Nano Lett.
, vol.12
, pp. 1038-1044
-
-
Kowalczyk, S.W.1
Wells, D.B.2
Aksimentiev, A.3
Dekker, C.4
-
314
-
-
34548414064
-
Charge inversion accompanies DNA condensation by multivalent ions
-
Besteman K, Van Eijk K and Lemay S G 2007 Charge inversion accompanies DNA condensation by multivalent ions Nature Phys. 3 641
-
(2007)
Nature Phys.
, vol.3
, pp. 641
-
-
Besteman, K.1
Van Eijk, K.2
Lemay, S.G.3
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