-
1
-
-
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, 355-362.
-
(2004)
Mol. Cell
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
2
-
-
0016850069
-
Kinky helix
-
Crick, F.H. and Klug, A. (1975) Kinky helix. Nature, 255, 530-533.
-
(1975)
Nature
, vol.255
, pp. 530-533
-
-
Crick, F.H.1
Klug, A.2
-
3
-
-
0023256126
-
A single mode of DNA base-pair opening drives imino proton exchange
-
Gueron, M., Kochoyan, M. and Leroy, J.L. (1987) A single mode of DNA base-pair opening drives imino proton exchange. Nature, 328, 89-92.
-
(1987)
Nature
, vol.328
, pp. 89-92
-
-
Gueron, M.1
Kochoyan, M.2
Leroy, J.L.3
-
4
-
-
1542269098
-
Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and nuclear magnetic resonance spectroscopy
-
Russu, I.M. (2004) Probing site-specific energetics in proteins and nucleic acids by hydrogen exchange and nuclear magnetic resonance spectroscopy. Methods Enzymol., 379, 152-175.
-
(2004)
Methods Enzymol
, vol.379
, pp. 152-175
-
-
Russu, I.M.1
-
5
-
-
19544379865
-
Localized single-stranded bubble mechanism for cyclization of short double helix DNA
-
Yan, J. and Marko, J.F. (2004) Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93, 108108.
-
(2004)
Phys. Rev. Lett
, vol.93
, pp. 108108
-
-
Yan, J.1
Marko, J.F.2
-
6
-
-
41349084347
-
Exact theory of kinkable elastic polymers
-
Wiggins, P.A., Phillips, R. and Nelson, P.C. (2005) Exact theory of kinkable elastic polymers. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 71, 021909.
-
(2005)
Phys. Rev. E Stat. Nonlin. Soft Matter Phys
, vol.71
, pp. 021909
-
-
Wiggins, P.A.1
Phillips, R.2
Nelson, P.C.3
-
7
-
-
18244404581
-
Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules
-
Ranjith, P., Kumar, P.B. and Menon, G.I. (2005) Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules. Phys. Rev. Lett., 94 138102.
-
(2005)
Phys. Rev. Lett
, vol.94
, pp. 138102
-
-
Ranjith, P.1
Kumar, P.B.2
Menon, G.I.3
-
8
-
-
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, 5397-5402.
-
(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
-
9
-
-
27944487890
-
Statistics of loop formation along double helix DNAs
-
Yan, J., Kawamura, R. and Marko, J.F. (2005) Statistics of loop formation along double helix DNAs. Phys. Rev. E, 71, 17.
-
(2005)
Phys. Rev. E
, vol.71
, pp. 17
-
-
Yan, J.1
Kawamura, R.2
Marko, J.F.3
-
10
-
-
33749986806
-
Spontaneous sharp bending of DNA: Role of melting bubbles
-
Yuan, C., Rhoades, E., Lou, X.W. and Archer, L.A. (2006) Spontaneous sharp bending of DNA: Role of melting bubbles. Nucleic Acids Res., 34, 4554-4560.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4554-4560
-
-
Yuan, C.1
Rhoades, E.2
Lou, X.W.3
Archer, L.A.4
-
11
-
-
33749243974
-
Sequence-dependent effects in the cyclization of short DNA
-
Czapla, L., Swigon, D. and Olson, W.K. (2006) Sequence-dependent effects in the cyclization of short DNA. J. Chem. Theory Comput., 2, 685-695.
-
(2006)
J. Chem. Theory Comput
, vol.2
, pp. 685-695
-
-
Czapla, L.1
Swigon, D.2
Olson, W.K.3
-
12
-
-
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, 1527-1534.
-
(2006)
Structure
, vol.14
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
13
-
-
33645295275
-
Exploring writhe in supercoiled minicircle DNA
-
Fogg, J.M., Kolmakova, N., Rees, I., Magonov, S., Hansma, H., Perona, J.J. and Zechiedrich, E.L. (2006) Exploring writhe in supercoiled minicircle DNA. J. Phys. Condens. Matter, 18, S145-S159.
-
(2006)
J. Phys. Condens. Matter
, vol.18
-
-
Fogg, J.M.1
Kolmakova, N.2
Rees, I.3
Magonov, S.4
Hansma, H.5
Perona, J.J.6
Zechiedrich, E.L.7
-
14
-
-
33845365528
-
A computational study of nucleosomal DNA flexibility
-
Ruscio, J.Z. and Onufriev, A. (2006) A computational study of nucleosomal DNA flexibility. Biophys. J., 91, 4121-4132.
-
(2006)
Biophys. J
, vol.91
, pp. 4121-4132
-
-
Ruscio, J.Z.1
Onufriev, A.2
-
15
-
-
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. Nat. Nanotechnol., 1, 137-141.
-
(2006)
Nat. 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
-
16
-
-
34548770048
-
T4 DNA ligase is more than an effective trap of cyclized dsDNA
-
Yuan, C., Lou, X.W., Rhoades, E., Chen, H. and Archer, L.A. (2007) T4 DNA ligase is more than an effective trap of cyclized dsDNA. Nucleic Acids Res., 35, 5294-5302.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 5294-5302
-
-
Yuan, C.1
Lou, X.W.2
Rhoades, E.3
Chen, H.4
Archer, L.A.5
-
17
-
-
40249090005
-
Kinking the double helix by bending deformation
-
Du, Q., Kotlyar, A. and Vologodskii, A. (2008) Kinking the double helix by bending deformation. Nucleic Acids Res., 36, 1120-1128.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 1120-1128
-
-
Du, Q.1
Kotlyar, A.2
Vologodskii, A.3
-
18
-
-
4444260310
-
Stacked-unstacked equilibrium at the nick site of DNA
-
Protozanova, E., Yakovchuk, P. and Frank-Kamenetskii, M.D. (2004) Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342, 775-785.
-
(2004)
J. Mol. Biol
, vol.342
, pp. 775-785
-
-
Protozanova, E.1
Yakovchuk, P.2
Frank-Kamenetskii, M.D.3
-
19
-
-
0025600461
-
Direct visualization of supercoiled DNA molecules in solution
-
Adrian, M., ten Heggeler-Bordier, B., Wahli, W., Stasiak, A.Z., Stasiak, A. and Dubochet, J. (1990) Direct visualization of supercoiled DNA molecules in solution. EMBO J., 9, 4551-4554.
-
(1990)
EMBO J
, vol.9
, pp. 4551-4554
-
-
Adrian, M.1
ten Heggeler-Bordier, B.2
Wahli, W.3
Stasiak, A.Z.4
Stasiak, A.5
Dubochet, J.6
-
20
-
-
0026630038
-
Cryoelectron microscopy of DNA molecules in solution
-
Dubochet, J., Adrian, M., Dustin, I., Furrer, P. and Stasiak, A. (1992) Cryoelectron microscopy of DNA molecules in solution. Methods Enzymol., 211, 507-518.
-
(1992)
Methods Enzymol
, vol.211
, pp. 507-518
-
-
Dubochet, J.1
Adrian, M.2
Dustin, I.3
Furrer, P.4
Stasiak, A.5
-
21
-
-
0024007766
-
Cryo-electron microscopy of vitrified specimens
-
Dubochet, J., Adrian, M., Chang, J.J., Homo, J.C., Lepault, J., McDowall, A.W. and Schultz, P. (1988) Cryo-electron microscopy of vitrified specimens. Q. Rev. Biophys., 21, 129-228.
-
(1988)
Q. Rev. Biophys
, vol.21
, pp. 129-228
-
-
Dubochet, J.1
Adrian, M.2
Chang, J.J.3
Homo, J.C.4
Lepault, J.5
McDowall, A.W.6
Schultz, P.7
-
22
-
-
0026044516
-
Spatial visualization of DNA in solution
-
Dustin, I., Furrer, P., Stasiak, A., Dubochet, J., Langowski, J. and Egelman, E. (1991) Spatial visualization of DNA in solution. J. Struct. Biol., 107, 15-21.
-
(1991)
J. Struct. Biol
, vol.107
, pp. 15-21
-
-
Dustin, I.1
Furrer, P.2
Stasiak, A.3
Dubochet, J.4
Langowski, J.5
Egelman, E.6
-
23
-
-
0028049305
-
The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo
-
Bednar, J., Furrer, P., Stasiak, A., Dubochet, J., Egelman, E.H. and Bates, A.D. (1994) The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. J. Mol. Biol., 235, 825-847.
-
(1994)
J. Mol. Biol
, vol.235
, pp. 825-847
-
-
Bednar, J.1
Furrer, P.2
Stasiak, A.3
Dubochet, J.4
Egelman, E.H.5
Bates, A.D.6
-
24
-
-
30144441093
-
3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake
-
Jacob, M., Blu, T., Vaillant, C., Maddocks, J.H. and Unser, M. (2006) 3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake. IEEE Trans. Image Process., 15, 214-227.
-
(2006)
IEEE Trans. Image Process
, vol.15
, pp. 214-227
-
-
Jacob, M.1
Blu, T.2
Vaillant, C.3
Maddocks, J.H.4
Unser, M.5
-
25
-
-
33750967917
-
3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy
-
Amzallag, A., Vaillant, C., Jacob, M., Unser, M., Bednar, J., Kahn, J.D., Dubochet, J., Stasiak, A. and Maddocks, J.H. (2006) 3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy. Nucleic Acids Res., 34, e125.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Amzallag, A.1
Vaillant, C.2
Jacob, M.3
Unser, M.4
Bednar, J.5
Kahn, J.D.6
Dubochet, J.7
Stasiak, A.8
Maddocks, J.H.9
-
26
-
-
0020695571
-
Structural features of a phased nucleosome core particle
-
Simpson, R.T. and Stafford, D.W. (1983) Structural features of a phased nucleosome core particle. Proc. Natl Acad. Sci. USA, 80, 51-55.
-
(1983)
Proc. Natl Acad. Sci. USA
, vol.80
, pp. 51-55
-
-
Simpson, R.T.1
Stafford, D.W.2
-
27
-
-
8344246968
-
Using quaternions to calculate RMSD
-
Coutsias, E.A., Seok, C. and Dill, K.A. (2004) Using quaternions to calculate RMSD. J. Comput. Chem., 25, 1849-1857.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1849-1857
-
-
Coutsias, E.A.1
Seok, C.2
Dill, K.A.3
-
28
-
-
19544387813
-
Sorting points into neighborhoods (SPIN): Data analysis and visualization by ordering distance matrices
-
Tsafrir, D., Tsafrir, I., Ein-Dor, L., Zuk, O., Notterman, D.A. and Domany, E. (2005) Sorting points into neighborhoods (SPIN): Data analysis and visualization by ordering distance matrices. Bioinformatics, 21, 2301-2308.
-
(2005)
Bioinformatics
, vol.21
, pp. 2301-2308
-
-
Tsafrir, D.1
Tsafrir, I.2
Ein-Dor, L.3
Zuk, O.4
Notterman, D.A.5
Domany, E.6
-
29
-
-
0017650804
-
A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents
-
Legerski, R.J., Gray, H.B. Jr. and Robberson, D.L. (1977) A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents. J. Biol. Chem., 252, 8740-8746.
-
(1977)
J. Biol. Chem
, vol.252
, pp. 8740-8746
-
-
Legerski, R.J.1
Gray Jr., H.B.2
Robberson, D.L.3
-
30
-
-
0031557391
-
Opposite effect of counterions on the persistence length of nicked and non-nicked DNA
-
Furrer, P., Bednar, J., Stasiak, A.Z., Katritch, V., Michoud, D., Stasiak, A. and Dubochet, J. (1997) Opposite effect of counterions on the persistence length of nicked and non-nicked DNA. J. Mol. Biol. 266, 711-721.
-
(1997)
J. Mol. Biol
, vol.266
, pp. 711-721
-
-
Furrer, P.1
Bednar, J.2
Stasiak, A.Z.3
Katritch, V.4
Michoud, D.5
Stasiak, A.6
Dubochet, J.7
-
31
-
-
32644434270
-
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
-
Yakovchuk, P., Protozanova, E. and Frank-Kamenetskii, M.D. (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res., 34, 564-574.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 564-574
-
-
Yakovchuk, P.1
Protozanova, E.2
Frank-Kamenetskii, M.D.3
-
32
-
-
0025609474
-
Evaporation during preparation of unsupported thin vitrified aqueous layers for cryo-electron microscopy
-
Cyrklaff, M., Adrian, M. and Dubochet, J. (1990) Evaporation during preparation of unsupported thin vitrified aqueous layers for cryo-electron microscopy. J. Electron. Microsc. Tech., 16, 351-355.
-
(1990)
J. Electron. Microsc. Tech
, vol.16
, pp. 351-355
-
-
Cyrklaff, M.1
Adrian, M.2
Dubochet, J.3
-
33
-
-
33645279594
-
Electrostatics of DNA-DNA juxtapositions: Consequences for type II topoisomerase function
-
Randall, G.L., Pettitt, B.M., Buck, G.R. and Zechiedrich, E.L. (2006) Electrostatics of DNA-DNA juxtapositions: Consequences for type II topoisomerase function. J. Phys. Condens. Matter, 18, S173-S185.
-
(2006)
J. Phys. Condens. Matter
, vol.18
-
-
Randall, G.L.1
Pettitt, B.M.2
Buck, G.R.3
Zechiedrich, E.L.4
-
34
-
-
0030581180
-
Helix rigidity of DNA: The meroduplex as an experimental paradigm
-
Hagerman, K.R. and Hagerman, P.J. (1996) Helix rigidity of DNA: The meroduplex as an experimental paradigm. J. Mol. Biol., 260, 207-223.
-
(1996)
J. Mol. Biol
, vol.260
, pp. 207-223
-
-
Hagerman, K.R.1
Hagerman, P.J.2
-
35
-
-
0033534516
-
Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)
-
Mills, J.B., Vacano, E. and Hagerman, P.J. (1999) Flexibility of single-stranded DNA: Use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). J. Mol. Biol., 285, 245-257.
-
(1999)
J. Mol. Biol
, vol.285
, pp. 245-257
-
-
Mills, J.B.1
Vacano, E.2
Hagerman, P.J.3
-
36
-
-
0016766372
-
Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendonuclease and double-strand deoxyriboexonuclease activities
-
Gray, H.B. Jr., Ostrander, D.A., Hodnett, J.L., Legerski, R.J. and Robberson, D.L. (1975) Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendonuclease and double-strand deoxyriboexonuclease activities. Nucleic Acids Res., 2, 1459-1492.
-
(1975)
Nucleic Acids Res
, vol.2
, pp. 1459-1492
-
-
Gray Jr., H.B.1
Ostrander, D.A.2
Hodnett, J.L.3
Legerski, R.J.4
Robberson, D.L.5
-
38
-
-
0021022977
-
Energetics of DNA twisting. I. Relation between twist and cyclization probability
-
Shore, D. and Baldwin, R.L. (1983) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol., 170, 957-981.
-
(1983)
J. Mol. Biol
, vol.170
, pp. 957-981
-
-
Shore, D.1
Baldwin, R.L.2
-
39
-
-
0001191247
-
DNA flexibility studied by covalent closure of short fragments into circles
-
Shore, D., Langowski, J. and Baldwin, R.L. (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl Acad. Sci. USA, 78, 4833-4837.
-
(1981)
Proc. Natl Acad. Sci. USA
, vol.78
, pp. 4833-4837
-
-
Shore, D.1
Langowski, J.2
Baldwin, R.L.3
|