-
1
-
-
0037992395
-
The structure of DNA in the nuclesome core
-
Richmond,T.J. and Davey,C.A. (2003) The structure of DNA in the nuclesome core. Nature, 423, 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
2
-
-
0039837085
-
Sequence motifs and free energies of slected natural and non-natural nucleosome positioning DNA sequence
-
Thastrom,A., Lowary,P.T., Widlund,H.R., Cao,H., Kubista,M. and Widom,J. (1999) Sequence motifs and free energies of slected natural and non-natural nucleosome positioning DNA sequence. J. Mol. Biol., 288, 213-229.
-
(1999)
J. Mol. Biol
, vol.288
, pp. 213-229
-
-
Thastrom, A.1
Lowary, P.T.2
Widlund, H.R.3
Cao, H.4
Kubista, M.5
Widom, J.6
-
3
-
-
0032512794
-
New DNA sequence rules fro high affinity binding to histone octamer and sequence-directed nucleosome positioning
-
Lowary,P.T. and Widom,J. (1999) New DNA sequence rules fro high affinity binding to histone octamer and sequence-directed nucleosome positioning. J. Mol. Biol., 276, 19-42.
-
(1999)
J. Mol. Biol
, vol.276
, pp. 19-42
-
-
Lowary, P.T.1
Widom, J.2
-
4
-
-
0003803285
-
-
University Science Books, Sauslito, California
-
Bloomfield,V.A., Crothers,D.M. and Tinoco,I. (2000) Nucleic Acids: Structures, Properties, and Functions University Science Books, Sauslito, California.
-
(2000)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
-
5
-
-
0019588074
-
Investigation of the flexibility of DNA using transient electric birefringence
-
Hagerman,P.J. (1981) Investigation of the flexibility of DNA using transient electric birefringence. Biopolymers, 7, 1503-1535.
-
(1981)
Biopolymers
, vol.7
, pp. 1503-1535
-
-
Hagerman, P.J.1
-
7
-
-
0028071373
-
Entropic elasticity of lambda-phage DNA
-
Bustamante,C., Marko,J.F., Siggia,E.D. and Smith,S. (1994) Entropic elasticity of lambda-phage DNA. Science, 265, 1599-1600.
-
(1994)
Science
, vol.265
, pp. 1599-1600
-
-
Bustamante, C.1
Marko, J.F.2
Siggia, E.D.3
Smith, S.4
-
8
-
-
0031047888
-
Stretching DNA with optical tweezer
-
Wang,M.D., Yin,H., Landick,R., Gelles,J. and Block,S. (1997) Stretching DNA with optical tweezer. Biophysical J., 72, 1335-1346.
-
(1997)
Biophysical J
, vol.72
, pp. 1335-1346
-
-
Wang, M.D.1
Yin, H.2
Landick, R.3
Gelles, J.4
Block, S.5
-
9
-
-
0032937079
-
Estimating the persistence length of a worm-like chain molecule from force-extension measurements
-
Bouchiat,C., Wang,M.D., Allemand,J.F., Strick,T., Block,S.M. and Croquette,V. (1999) Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophysical J., 76, 409-413.
-
(1999)
Biophysical J
, vol.76
, pp. 409-413
-
-
Bouchiat, C.1
Wang, M.D.2
Allemand, J.F.3
Strick, T.4
Block, S.M.5
Croquette, V.6
-
10
-
-
0026796061
-
DNA bending, flexibility and helical repeat by cyclization kinetics
-
Crothers,D.M., Drak,J., Kahn,J.D. and Levene,S.D. (1992) DNA bending, flexibility and helical repeat by cyclization kinetics. Method Enzymol., 212, 3-29.
-
(1992)
Method Enzymol
, vol.212
, pp. 3-29
-
-
Crothers, D.M.1
Drak, J.2
Kahn, J.D.3
Levene, S.D.4
-
11
-
-
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. PNAS, 78 4833-4837.
-
(1981)
PNAS
, vol.78
, pp. 4833-4837
-
-
Shore, D.1
Langowski, J.2
Baldwin, R.L.3
-
12
-
-
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, 689-698.
-
(1984)
Macromolecules
, vol.17
, pp. 689-698
-
-
Shimada, J.1
Yamakawa, H.2
-
13
-
-
0037215722
-
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
-
Zhang,Y. and Crothers,D.M. (2003) Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophysical J., 84, 136-153.
-
(2003)
Biophysical J
, vol.84
, pp. 136-153
-
-
Zhang, Y.1
Crothers, D.M.2
-
14
-
-
0000816797
-
Elastic model of supercoiling
-
Benham,C.J. (1977) Elastic model of supercoiling. PNAS, 74, 2397-2401.
-
(1977)
PNAS
, vol.74
, pp. 2397-2401
-
-
Benham, C.J.1
-
15
-
-
0024715903
-
Global equilibrium-configurations of supercoiled DNA
-
Hao,M.H. and Olson,W.K. (1989) Global equilibrium-configurations of supercoiled DNA. Macromolecules, 22, 3292-3303.
-
(1989)
Macromolecules
, vol.22
, pp. 3292-3303
-
-
Hao, M.H.1
Olson, W.K.2
-
16
-
-
0027398354
-
Twist and writhe of a DNA loop containing intrinsic bends
-
Bauer,W.R., Lund,R.A. and White,J.H. (1993) Twist and writhe of a DNA loop containing intrinsic bends. PNAS, 90, 833-837.
-
(1993)
PNAS
, vol.90
, pp. 833-837
-
-
Bauer, W.R.1
Lund, R.A.2
White, J.H.3
-
17
-
-
17944383822
-
Elastic rod model of a DNA loop in the LAC operon
-
Balaeff,A., Mahadevan,L. and Schulten,K. (1999) Elastic rod model of a DNA loop in the LAC operon. Phys. Rev. Lett., 83, 4900-4903.
-
(1999)
Phys. Rev. Lett
, vol.83
, pp. 4900-4903
-
-
Balaeff, A.1
Mahadevan, L.2
Schulten, K.3
-
18
-
-
0000091323
-
Finite element analysis of DNA supercoiling
-
Yang,Y., Tobias,I. and Olson,W.K. (1993) Finite element analysis of DNA supercoiling. J. Chem. Phys., 98, 1673-1686.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 1673-1686
-
-
Yang, Y.1
Tobias, I.2
Olson, W.K.3
-
19
-
-
0029087424
-
Effects of localized bending on DNA supercoiling
-
Yang,Y., Westcotts,T.P., Pedersen,S.C., Tobias,I. and Olson,W.K. (1995) Effects of localized bending on DNA supercoiling. Trends Biochem. Sci., 20, 313-319.
-
(1995)
Trends Biochem. Sci
, vol.20
, pp. 313-319
-
-
Yang, Y.1
Westcotts, T.P.2
Pedersen, S.C.3
Tobias, I.4
Olson, W.K.5
-
20
-
-
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
-
21
-
-
14844342574
-
DNA twisting flexibility and the formation of sharply looped protein-DNA complex
-
Cloutier,T.E. and Widom,J. (2005) DNA twisting flexibility and the formation of sharply looped protein-DNA complex. PNAS, 102, 3645-3650.
-
(2005)
PNAS
, vol.102
, pp. 3645-3650
-
-
Cloutier, T.E.1
Widom, J.2
-
22
-
-
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
-
23
-
-
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., 71, 021909.
-
(2005)
Phys. Rev. E
, vol.71
, pp. 021909
-
-
Wiggins, P.A.1
Phillips, R.2
Nelson, P.C.3
-
24
-
-
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, 061905.
-
(2005)
Phys. Rev. E
, vol.71
, pp. 061905
-
-
Yan, J.1
Kawamura, R.2
Marko, J.F.3
-
25
-
-
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. PNAS, 102, 5397-5402.
-
(2005)
PNAS
, vol.102
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Shiffeldrim, N.3
Vologodskaia, M.4
Vologodskii, A.5
-
26
-
-
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
-
27
-
-
33744788870
-
Quantification of α-Synuclein binding to lipid vesicles using fluorescence correlation spectroscopy
-
Rhoades,E., Ramlall,T.F., Webb,W.W. and Eliezer,D. (2006) Quantification of α-Synuclein binding to lipid vesicles using fluorescence correlation spectroscopy. Biophys. J., 90, 4692-4700.
-
(2006)
Biophys. J
, vol.90
, pp. 4692-4700
-
-
Rhoades, E.1
Ramlall, T.F.2
Webb, W.W.3
Eliezer, D.4
-
28
-
-
33745728441
-
Achieving uniform mixing in microfluidic device: Hydrodynamic focusing prior to mixing
-
Park,H.Y., Qiu,X., Rhoades,E., Korlach,J., Kwok,L.W., Zipfel,W.R., Webb,W.W. and Pollack,L. (2006) Achieving uniform mixing in microfluidic device: Hydrodynamic focusing prior to mixing. Analytical Chem., 78, 4465-4473.
-
(2006)
Analytical Chem
, vol.78
, pp. 4465-4473
-
-
Park, H.Y.1
Qiu, X.2
Rhoades, E.3
Korlach, J.4
Kwok, L.W.5
Zipfel, W.R.6
Webb, W.W.7
Pollack, L.8
-
29
-
-
35949038838
-
Thermodynamic fluctuation in a reacting system measurement by fluorescence correlation spectroscopy
-
Magde,D., Elson,E. and Webb,W.W. (1972) Thermodynamic fluctuation in a reacting system measurement by fluorescence correlation spectroscopy. Phys. Rev. Lett., 29, 705-708.
-
(1972)
Phys. Rev. Lett
, vol.29
, pp. 705-708
-
-
Magde, D.1
Elson, E.2
Webb, W.W.3
-
30
-
-
0014669561
-
Fluorescence studies of micleotides and polynucleotides
-
Ward,D.C., Reich,E. and Stryer,L. (1969) Fluorescence studies of micleotides and polynucleotides. J. Biol. Chem., 244, 1228-1237.
-
(1969)
J. Biol. Chem
, vol.244
, pp. 1228-1237
-
-
Ward, D.C.1
Reich, E.2
Stryer, L.3
-
31
-
-
0029992307
-
Fluorescence studies of DNA and RNA structure and dynamics
-
Millar,D.P. (1996) Fluorescence studies of DNA and RNA structure and dynamics. Curr. Opin. in Struct. Biol., 6, 322-326.
-
(1996)
Curr. Opin. in Struct. Biol
, vol.6
, pp. 322-326
-
-
Millar, D.P.1
-
32
-
-
20444480973
-
DNA bending by M. EcoKI methyltransferase is coupled to nucleotide flipping
-
Su,T.J., Tock,M.R., Egelhaaf,S.U., Poon,W.C.K. and Dryden,D.T.F. (2005) DNA bending by M. EcoKI methyltransferase is coupled to nucleotide flipping. Nucleic Acids Res., 10, 3235-3244.
-
(2005)
Nucleic Acids Res
, vol.10
, pp. 3235-3244
-
-
Su, T.J.1
Tock, M.R.2
Egelhaaf, S.U.3
Poon, W.C.K.4
Dryden, D.T.F.5
-
33
-
-
0035804928
-
Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase
-
Liu,C. and Martin,C.T. (2001) Fluorescence characterization of the transcription bubble in elongation complexes of T7 RNA polymerase. J. Mol. Biol., 308, 465-475.
-
(2001)
J. Mol. Biol
, vol.308
, pp. 465-475
-
-
Liu, C.1
Martin, C.T.2
-
34
-
-
0032519379
-
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases
-
Holz,B., Klimasauskas,S., Serva,S. and Weinhold,E. (1998) 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases. Nucleic Acids Res., 26, 1076-1083.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1076-1083
-
-
Holz, B.1
Klimasauskas, S.2
Serva, S.3
Weinhold, E.4
-
35
-
-
0032529485
-
2-Aminopurine fluorescence studies of base stacking interactions at a basic site in DNA: A metal-ion and base sequence effect
-
Stivers,J.T. (1998) 2-Aminopurine fluorescence studies of base stacking interactions at a basic site in DNA: A metal-ion and base sequence effect. Nucleic Acids Res., 26, 3837-3844.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 3837-3844
-
-
Stivers, J.T.1
-
36
-
-
0038750927
-
Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex DNA sequences
-
Rai,P., Cole,J.D., Thompson,E., Millar,D.P. and Linn,S. (2003) Steady-state and time-resolved fluorescence studies indicate an unusual conformation of 2-aminopurine within ATAT and TATA duplex DNA sequences. Nucleic Acids Res., 31, 2323-2332.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2323-2332
-
-
Rai, P.1
Cole, J.D.2
Thompson, E.3
Millar, D.P.4
Linn, S.5
-
37
-
-
0035793105
-
2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking
-
Jean,J.M. and Hall,K.B. (2001) 2-Aminopurine fluorescence quenching and lifetimes: Role of base stacking. PNAS, 98, 37-41.
-
(2001)
PNAS
, vol.98
, pp. 37-41
-
-
Jean, J.M.1
Hall, K.B.2
-
38
-
-
0035969959
-
Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment
-
Rachofsky,E.L., Osman,R. and Ross,J.B.A. (2001) Probing structure and dynamics of DNA with 2-aminopurine: Effects of local environment. Biochemisty, 40, 946-956.
-
(2001)
Biochemisty
, vol.40
, pp. 946-956
-
-
Rachofsky, E.L.1
Osman, R.2
Ross, J.B.A.3
-
39
-
-
3042599013
-
The thermodynamics of DNA structural motifs
-
SantaLucia,J. and Hicks,D. (2004) The thermodynamics of DNA structural motifs. Annu. Rev. Biomol. Struct., 33, 415-420.
-
(2004)
Annu. Rev. Biomol. Struct
, vol.33
, pp. 415-420
-
-
SantaLucia, J.1
Hicks, D.2
-
40
-
-
0029118487
-
A free energy analysis of nucleic acid base stacking in aqueous solution
-
Friedman,R.A. and Honig,B. (1995) A free energy analysis of nucleic acid base stacking in aqueous solution. Biophysical J., 69, 1528-1533.
-
(1995)
Biophysical J
, vol.69
, pp. 1528-1533
-
-
Friedman, R.A.1
Honig, B.2
-
41
-
-
32644434270
-
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
-
Yahovchuk,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
-
-
Yahovchuk, P.1
Protozanova, E.2
Frank-Kamenetskii, M.D.3
-
42
-
-
0016273515
-
DNA ligase: Structure, mechanism, and function
-
Lehman,I.R. (1974) DNA ligase: Structure, mechanism, and function. Science, 186, 790-797.
-
(1974)
Science
, vol.186
, pp. 790-797
-
-
Lehman, I.R.1
-
43
-
-
0030873236
-
Functional characterization of the T4 DNA ligase: A new insight into the mechanism of action
-
Rossi,R, Mohtecucco,A., Ciarrocchi,G. and Biamonti,G. (1997) Functional characterization of the T4 DNA ligase: A new insight into the mechanism of action. Nucleic Acids Res., 25, 2106-2113.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 2106-2113
-
-
Rossi, R.1
Mohtecucco, A.2
Ciarrocchi, G.3
Biamonti, G.4
-
44
-
-
0035204634
-
Binding of Nucleotides by T4 DNA ligase and T4 RNA ligase: Optical absorbance and fluorescence studies
-
Cherpepanov,A.V. and de Vries,S. (2002) Binding of Nucleotides by T4 DNA ligase and T4 RNA ligase: Optical absorbance and fluorescence studies. Biophys. J., 81, 3545-3559.
-
(2002)
Biophys. J
, vol.81
, pp. 3545-3559
-
-
Cherpepanov, A.V.1
de Vries, S.2
-
45
-
-
0029938467
-
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7
-
Subramanya,H.S., Doherty,A.J., Ashford,S.R. and Wigley,D.B. (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell, 85, 607-615.
-
(1996)
Cell
, vol.85
, pp. 607-615
-
-
Subramanya, H.S.1
Doherty, A.J.2
Ashford, S.R.3
Wigley, D.B.4
-
46
-
-
0033555464
-
Structure of the adenylation domain of an NAD (+)-dependent DNA ligase
-
Singleton,M.R., Hakansson,K., Timson,D.J. and Wigley,D.B. (1999) Structure of the adenylation domain of an NAD (+)-dependent DNA ligase. Structure, 7, 35-42.
-
(1999)
Structure
, vol.7
, pp. 35-42
-
-
Singleton, M.R.1
Hakansson, K.2
Timson, D.J.3
Wigley, D.B.4
-
47
-
-
0034161570
-
Crystal structure of NAD (+)-dependent DNA ligase: Modular architecture and functional implications
-
Lee,J.Y., Chang,C., Song,H.K., Moon,J., Yang,J.K.,Kim,H.K., Kwon,S.T. and Suh,S.W. (2000) Crystal structure of NAD (+)-dependent DNA ligase: modular architecture and functional implications. EMBO J., 19 1119-1129.
-
(2000)
EMBO J
, vol.19
, pp. 1119-1129
-
-
Lee, J.Y.1
Chang, C.2
Song, H.K.3
Moon, J.4
Yang, J.K.5
Kim, H.K.6
Kwon, S.T.7
Suh, S.W.8
-
48
-
-
24144449890
-
Single-molecule DNA flexibility in the presence of base-pair mismatch
-
Schallhorn,K.A., Freedman,K.O., Moore,J.M., Lin,J. and Ke,P.C, (2005) Single-molecule DNA flexibility in the presence of base-pair mismatch. App. Phys. Lett., 87, 033901.
-
(2005)
App. Phys. Lett
, vol.87
, pp. 033901
-
-
Schallhorn, K.A.1
Freedman, K.O.2
Moore, J.M.3
Lin, J.4
Ke, P.C.5
-
49
-
-
0028289189
-
Detection of localized DNA flexibility
-
Kahn,J.D., Yun,E. and Crothers,D.M. (1994) Detection of localized DNA flexibility. Nature, 368, 163-166.
-
(1994)
Nature
, vol.368
, pp. 163-166
-
-
Kahn, J.D.1
Yun, E.2
Crothers, D.M.3
|