-
1
-
-
85015106657
-
DNA in a material world
-
DOI 10.1038/nature01406
-
N. C. Seeman, Nature (London) NATUAS 0028-0836 10.1038/nature01406 421, 427 (2003). (Pubitemid 36157949)
-
(2003)
Nature
, vol.421
, Issue.6921
, pp. 427-431
-
-
Seeman, N.C.1
-
2
-
-
0345306761
-
DNA-Templated Carbon Nanotube Field-Effect Transistor
-
DOI 10.1126/science.1091022
-
K. Keren, R. S. Berman, E. Buchstab, U. Sivan, and E. Braun, Science SCIEAS 0036-8075 10.1126/science.1091022 302, 1380 (2003). (Pubitemid 37452176)
-
(2003)
Science
, vol.302
, Issue.5649
, pp. 1380-1382
-
-
Keren, K.1
Berman, R.S.2
Buchstab, E.3
Sivan, U.4
Braun, E.5
-
3
-
-
0344838435
-
DNA molecule provides a computing machine with both data and fuel
-
DOI 10.1073/pnas.0535624100
-
Y. Benenson, R. Adar, T. Paz-Elizur, Z. Livneh, and E. Shapiro, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0535624100 100, 2191 (2003). (Pubitemid 36297475)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.5
, pp. 2191-2196
-
-
Benenson, Y.1
Adart, R.2
Paz-Elizur, T.3
Livneh, Z.4
Shapiro, E.5
-
4
-
-
33751247017
-
Functional DNA nanotechnology: emerging applications of DNAzymes and aptamers
-
DOI 10.1016/j.copbio.2006.10.004, PII S0958166906001480
-
Y. Lu and J. W. Liu, Curr. Opin. Biotechnol. CUOBE3 0958-1669 10.1016/j.copbio.2006.10.004 17, 580 (2006). (Pubitemid 44791909)
-
(2006)
Current Opinion in Biotechnology
, vol.17
, Issue.6
, pp. 580-588
-
-
Lu, Y.1
Liu, J.2
-
5
-
-
33751436653
-
What Drives Proteins into the Major or Minor Grooves of DNA?
-
DOI 10.1016/j.jmb.2006.09.059, PII S0022283606012848
-
P. L. Privalov, A. I. Dragan 1, C. Crane-Robinson, K. J. Breslauer, D. P. Remeta, and C. A. S. A. Minetti, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2006.09.059 365, 1 (2007). (Pubitemid 44821203)
-
(2007)
Journal of Molecular Biology
, vol.365
, Issue.1
, pp. 1-9
-
-
Privalov, P.L.1
Dragan, A.I.2
Crane-Robinson, C.3
Breslauer, K.J.4
Remeta, D.P.5
Minetti, C.A.S.A.6
-
6
-
-
80054714041
-
-
JCPSA6 0021-9606 10.1063/1.3634004
-
S. K. Sinha and S. Bandyopadhyay, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3634004 135, 135101 (2011).
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 135101
-
-
Sinha, S.K.1
Bandyopadhyay, S.2
-
7
-
-
77649270492
-
-
JMOBAK 0022-2836 10.1016/j.jmb.2009.12.050
-
D. Watkins, S. Mohan, G. B. Koudelka, and L. D. Williams, J. Mol. Biol. JMOBAK 0022-2836 10.1016/j.jmb.2009.12.050 396, 1145 (2010).
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 1145
-
-
Watkins, D.1
Mohan, S.2
Koudelka, G.B.3
Williams, L.D.4
-
9
-
-
77952575506
-
-
1756-5901 10.1039/c000429d
-
J. Muller, Metallomics 1756-5901 10.1039/c000429d 2, 318 (2010).
-
(2010)
Metallomics
, vol.2
, pp. 318
-
-
Muller, J.1
-
11
-
-
2942547665
-
Simulation and modeling of nucleic acid structure, dynamics and interactions
-
DOI 10.1016/j.sbi.2004.05.001, PII S0959440X04000752
-
T. E. Cheatham III, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/j.sbi.2004.05.001 14, 360 (2004). (Pubitemid 38749065)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.3
, pp. 360-367
-
-
Cheatham III, T.E.1
-
12
-
-
48449104689
-
-
BOMAF6 1525-7797 10.1021/bm800101x
-
N. Sundaresan, C. H. Suresh, T. Thomas, T. J. Thomas, and C. K. S. Pillai, Biomacromolecules BOMAF6 1525-7797 10.1021/bm800101x 9, 1860 (2008).
-
(2008)
Biomacromolecules
, vol.9
, pp. 1860
-
-
Sundaresan, N.1
Suresh, C.H.2
Thomas, T.3
Thomas, T.J.4
Pillai, C.K.S.5
-
13
-
-
33845727429
-
Exploring DNA groove water dynamics through hydrogen bond lifetime and orientational relaxation
-
DOI 10.1063/1.2403872
-
S. Pal, P. K. Maiti, and B. Bagchi, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.2403872 125, 234903 (2006). (Pubitemid 46013661)
-
(2006)
Journal of Chemical Physics
, vol.125
, Issue.23
, pp. 234903
-
-
Pal, S.1
Maiti, P.K.2
Bagchi, B.3
-
14
-
-
70450248170
-
-
NARHAD 0305-1048 10.1093/nar/gkp834
-
R. Lavery, K. Zakrzewska, D. Beveridge, T. C. Bishop, D. A. Case, T. E. Cheatham III, S. Dixit, B. Jayaram, F. Lankas, C. Laughton, J. H. Maddocks, A. Michon, R. Osman, M. Orozco, A. Perez, T. Singh, N. Spackova, and J. Sponer, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkp834 38, 299 (2010).
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 299
-
-
Lavery, R.1
Zakrzewska, K.2
Beveridge, D.3
Bishop, T.C.4
Case, D.A.5
Cheatham Iii, T.E.6
Dixit, S.7
Jayaram, B.8
Lankas, F.9
Laughton, C.10
Maddocks, J.H.11
Michon, A.12
Osman, R.13
Orozco, M.14
Perez, A.15
Singh, T.16
Spackova, N.17
Sponer, J.18
-
15
-
-
73649101297
-
-
JCPSA6 0021-9606 10.1063/1.3273211
-
J. M. Leveritt III, C. Dibaya, S. Tesar, R. Shrestha, and A. L. Burin, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3273211 131, 245102 (2009).
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 245102
-
-
Leveritt Iii, J.M.1
Dibaya, C.2
Tesar, S.3
Shrestha, R.4
Burin, A.L.5
-
16
-
-
37649028819
-
-
PLEEE8 1539-3755 10.1103/PhysRevE.69.041904
-
E. Allahyarov, G. Gompper, and H. Lowen, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.69.041904 69, 041904 (2004).
-
(2004)
Phys. Rev. e
, vol.69
, pp. 041904
-
-
Allahyarov, E.1
Gompper, G.2
Lowen, H.3
-
17
-
-
34548848587
-
Atomistic model of DNA: Phonons and base-pair opening
-
DOI 10.1103/PhysRevE.76.031917
-
F. Merzel, F. Fontaine-Vive, M. R. Johnson, and G. J. Kearley, Phys. Rev. E PLEEE8 1539-3755 10.1103/PhysRevE.76.031917 76, 031917 (2007). (Pubitemid 47443083)
-
(2007)
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics
, vol.76
, Issue.3
, pp. 031917
-
-
Merzel, F.1
Fontaine-Vive, F.2
Johnson, M.R.3
Kearley, G.J.4
-
18
-
-
41449089219
-
Direct NMR detection of alkali metal ions bound to G-quadruplex DNA
-
DOI 10.1021/ja709975z
-
R. Ida and G. Wu, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja709975z 130, 3590 (2008). (Pubitemid 351456063)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.11
, pp. 3590-3602
-
-
Ida, R.1
Wu, G.2
-
19
-
-
77955438624
-
-
JPCBFK 1520-6106 10.1021/jp105761b
-
K. E. Furse and S. A. Corcelli, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp105761b 114, 9934 (2010).
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 9934
-
-
Furse, K.E.1
Corcelli, S.A.2
-
20
-
-
33746260476
-
+
-
DOI 10.1016/j.cplett.2006.05.120, PII S000926140600813X
-
K. Hibino, Y. Yoshikawa, S. Murata, T. Saito, A. A. Zinchenko, and K. Yoshikawa, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2006.05.120 426, 405 (2006). (Pubitemid 44096938)
-
(2006)
Chemical Physics Letters
, vol.426
, Issue.4-6
, pp. 405-409
-
-
Hibino, K.1
Yoshikawa, Y.2
Murata, S.3
Saito, T.4
Zinchenko, A.A.5
Yoshikawa, K.6
-
22
-
-
0035793210
-
Preferential counterion binding to A-tract DNA oligomers
-
DOI 10.1006/jmbi.2000.4362
-
N. C. Stellwagen, S. Magnusdottir, C. Gelfi, and P. G. Righetti, J. Mol. Biol. JMOBAK 0022-2836 10.1006/jmbi.2000.4362 305, 1025 (2001). (Pubitemid 33027740)
-
(2001)
Journal of Molecular Biology
, vol.305
, Issue.5
, pp. 1025-1033
-
-
Stellwagen, N.C.1
Magnusdottir, S.2
Gelfi, C.3
Righetti, P.G.4
-
23
-
-
0031047279
-
Intrusion of counterions into the spine of hydration in the minor groove of B-DNA: Fractional occupancy of electronegative pockets
-
DOI 10.1021/ja960459m, PII S0002786396004593
-
M. A. Young, B. Jayaram, and D. L. Beveridge, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja960459m 119, 59 (1997). (Pubitemid 27064483)
-
(1997)
Journal of the American Chemical Society
, vol.119
, Issue.1
, pp. 59-69
-
-
Young, M.A.1
Jayaram, B.2
Beveridge, D.L.3
-
24
-
-
32644446799
-
+ with condensed ordered DNA. A molecular dynamics computer simulation study
-
DOI 10.1093/nar/gkj434
-
Y. H. Cheng, N. Korolev, and L. Nordenskiold, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkj434 34, 686 (2006). (Pubitemid 43240255)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.2
, pp. 686-696
-
-
Cheng, Y.1
Korolev, N.2
Nordenskiold, L.3
-
25
-
-
0033594498
-
A 'hydrat-ion' spine in a B-DNA minor groove
-
DOI 10.1021/ja984346+
-
V. Tereshko, G. Minasov, and M. Egli, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja984346+ 121, 3590 (1999). (Pubitemid 29200267)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.15
, pp. 3590-3595
-
-
Tereshko, V.1
Minasov, G.2
Egli, M.3
-
26
-
-
0034005285
-
2 [4]
-
DOI 10.1021/ja9919579
-
K. K. Woods, L. McFail-Isom, C. C. Sines, S. B. Howerton, R. K. Stephens, and L. D. Williams, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja9919579 122, 1546 (2000). (Pubitemid 30120441)
-
(2000)
Journal of the American Chemical Society
, vol.122
, Issue.7
, pp. 1546-1547
-
-
Woods, K.K.1
McFail-Isom, L.2
Sines, C.C.3
Howerton, S.B.4
Stephens, R.K.5
Williams, L.D.6
-
28
-
-
2542583798
-
+ binding in the minor groove of DNA
-
DOI 10.1021/ja049930z
-
F. C. Marincola, V. P. Denisov, and B. Halle, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja049930z 126, 6739 (2004). (Pubitemid 38697373)
-
(2004)
Journal of the American Chemical Society
, vol.126
, Issue.21
, pp. 6739-6750
-
-
Marincola, F.C.1
Denisov, V.P.2
Halle, B.3
-
30
-
-
0035842899
-
Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes
-
DOI 10.1083/jcb.200105026
-
R. Strick, P. L. Strissel, K. Gavrilov, and R. Levi-Setti, J. Cell Biol. JCLBA3 0021-9525 10.1083/jcb.200105026 155, 899 (2001). (Pubitemid 34286242)
-
(2001)
Journal of Cell Biology
, vol.155
, Issue.6
, pp. 899-910
-
-
Strick, R.1
Strissel, P.L.2
Gavrilov, K.3
Levi-Setti, R.4
-
31
-
-
0037381880
-
-
BIOJAU 0006-3495 10.1016/S0006-3495(03)75050-4
-
R. Ahmad, H. Arakawa, and H. A. Tajmir-Riahi, Biophys. J. BIOJAU 0006-3495 10.1016/S0006-3495(03)75050-4 84, 2460 (2003).
-
(2003)
Biophys. J.
, vol.84
, pp. 2460
-
-
Ahmad, R.1
Arakawa, H.2
Tajmir-Riahi, H.A.3
-
32
-
-
0036009329
-
DNA-cation interactions: Quo vadis?
-
DOI 10.1016/S1074-5521(02)00116-3, PII S1074552102001163
-
M. Egli, Chem. Biol. CBOLE2 1074-5521 10.1016/S1074-5521(02)00116-3 9, 277 (2002). (Pubitemid 34253410)
-
(2002)
Chemistry and Biology
, vol.9
, Issue.3
, pp. 277-286
-
-
Egli, M.1
-
33
-
-
0035367927
-
DNA-cation interactions: The major and minor grooves are flexible ionophores
-
DOI 10.1016/S0959-440X(00)00205-0
-
N. V. Hud and M. Polak, Curr. Opin. Struct. Biol. COSBEF 0959-440X 10.1016/S0959-440X(00)00205-0 22, 293 (2001). (Pubitemid 32568268)
-
(2001)
Current Opinion in Structural Biology
, vol.11
, Issue.3
, pp. 293-301
-
-
Hud, N.V.1
Polak, M.2
-
34
-
-
0028020868
-
Solution structure of a DNA dodecamer containing the anti-neoplastic agent arabinosylcytosine: Combined use of NMR, restrained molecular dynamics, and full relaxation matrix refinement
-
DOI 10.1021/bi00204a008
-
B. I. Schweitzer, T. Mikita, G. W. Kellogg, K. H. Gardner, and G. P. Beardsley, Biochem. 0006-2960 10.1021/bi00204a008 33, 11460 (1994). (Pubitemid 24330079)
-
(1994)
Biochemistry
, vol.33
, Issue.38
, pp. 11460-11475
-
-
Schweitzer, B.I.1
Mikita, T.2
Kellogg, G.W.3
Gardner, K.H.4
Beardsley, G.P.5
-
35
-
-
0000333851
-
-
PHBCDQ 0378-4363 10.1016/0378-4363(85)90153-6
-
K. Heinzinger, Physica B PHBCDQ 0378-4363 10.1016/0378-4363(85)90153-6 131, 196 (1985).
-
(1985)
Physica B
, vol.131
, pp. 196
-
-
Heinzinger, K.1
-
37
-
-
17444402471
-
Computational investigation of order, structure, and dynamics in modified water models
-
DOI 10.1021/jp0458553
-
R. M. Lynden-Bell and P. G. Debenedetti, J. Phys. Chem. B JPCBFK 1520-6106 10.1021/jp0458553 109, 6527 (2005). (Pubitemid 40538419)
-
(2005)
Journal of Physical Chemistry B
, vol.109
, Issue.14
, pp. 6527-6534
-
-
Lynden-Bell, R.M.1
Debenedetti, P.G.2
-
38
-
-
0029011701
-
-
JACSAT 0002-7863 10.1021/ja00124a002
-
W. D. Cornell, P. Cieplak, C. I. Bayly, I. Gould, K. M. Merz Jr., D. M. Ferguson, D. C. Spellmeyer, T. Fox, J. W. Caldwell, and P. A. Kollman, J. Am. Chem. Soc. JACSAT 0002-7863 10.1021/ja00124a002 117, 5179 (1995).
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.4
Merz, Jr.K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
39
-
-
4444351490
-
-
JCCHDD 0192-8651 10.1002/jcc.20082
-
A. D. Mackerell, J. Comput. Chem. JCCHDD 0192-8651 10.1002/jcc.20082 25, 1584 (2004).
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584
-
-
MacKerell, A.D.1
-
40
-
-
0001251663
-
-
PRBMDO 1098-0121 10.1103/PhysRevB.31.2643
-
K. Toukan and A. Rahman, Phys. Rev. B PRBMDO 1098-0121 10.1103/PhysRevB.31.2643 31, 2643 (1985).
-
(1985)
Phys. Rev. B
, vol.31
, pp. 2643
-
-
Toukan, K.1
Rahman, A.2
-
41
-
-
0034206682
-
-
CPHCBZ 0010-4655 10.1016/S0010-4655(99)00529-9
-
A. P. Lyubartsev and A. Laaksonen, Comput. Phys. Commun. CPHCBZ 0010-4655 10.1016/S0010-4655(99)00529-9 128, 565 (2000).
-
(2000)
Comput. Phys. Commun.
, vol.128
, pp. 565
-
-
Lyubartsev, A.P.1
Laaksonen, A.2
-
42
-
-
17844399800
-
Molecular dynamics simulation of single DNA stretching reveals a novel structure
-
DOI 10.1016/j.cplett.2005.02.125, PII S0009261405003039
-
R. Lohikoski, J. Timonen, and A. Laaksonen, Chem. Phys. Lett. CHPLBC 0009-2614 10.1016/j.cplett.2005.02.125 427, 23 (2005). (Pubitemid 40584079)
-
(2005)
Chemical Physics Letters
, vol.407
, Issue.1-3
, pp. 23-29
-
-
Lohikoski, R.1
Timonen, J.2
Laaksonen, A.3
-
43
-
-
33646650705
-
-
JCPSA6 0021-9606 10.1063/1.463137
-
M. Tuckerman and B. J. Berne, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.463137 97, 1989 (1992).
-
(1992)
J. Chem. Phys.
, vol.97
, pp. 1989
-
-
Tuckerman, M.1
Berne, B.J.2
-
44
-
-
0028043019
-
-
MOSIEA 0892-7022 10.1080/08927029408022180
-
D. Fincham, Mol. Simul. MOSIEA 0892-7022 10.1080/08927029408022180 13, 1 (1994).
-
(1994)
Mol. Simul.
, vol.13
, pp. 1
-
-
Fincham, D.1
-
46
-
-
0028184697
-
-
BIPMAA 0006-3525 10.1002/bip.360340305
-
E. Stofer and R. Lavery, Biopolymers BIPMAA 0006-3525 10.1002/bip.360340305 34, 337 (1994).
-
(1994)
Biopolymers
, vol.34
, pp. 337
-
-
Stofer, E.1
Lavery, R.2
-
48
-
-
40849099025
-
Solvent-induced DNA conformational transition
-
DOI 10.1103/PhysRevLett.100.088104
-
B. Gu, F. S. Zhang, Z. P. Wang, and H. Y. Zhou, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.100.088104 100, 088104 (2008). (Pubitemid 351393610)
-
(2008)
Physical Review Letters
, vol.100
, Issue.8
, pp. 088104
-
-
Zhang, F.S.1
Gu, B.2
Wang, Z.P.3
Zhou, H.Y.4
-
49
-
-
79960896114
-
-
JCPSA6 0021-9606 10.1063/1.3610549
-
X. Shen, B. Gu, S. A. Che, and F. S. Zhang, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.3610549 135, 034509 (2011).
-
(2011)
J. Chem. Phys.
, vol.135
, pp. 034509
-
-
Shen, X.1
Gu, B.2
Che, S.A.3
Zhang, F.S.4
-
50
-
-
6944220065
-
Ion motions in molecular dynamics simulations on DNA
-
DOI 10.1073/pnas.0406435101
-
S. Y. Ponomarev, K. M. Thayer, and D. L. Beveridge, Proc. Natl. Acad. Sci. USA PNASA6 0027-8424 10.1073/pnas.0406435101 101, 14771 (2004). (Pubitemid 39410750)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.41
, pp. 14771-14775
-
-
Ponornarev, S.Y.1
Thayer, K.M.2
Beveridge, D.L.3
|