-
1
-
-
0034923502
-
DNA topoisomerases: Structure, function, and mechanism
-
Champoux,J.J. (2001) DNA topoisomerases: Structure, function, and mechanism. Annu. Rev. Biochem., 70, 369-413.
-
(2001)
Annu. Rev. Biochem.
, vol.70
, pp. 369-413
-
-
Champoux, J.J.1
-
2
-
-
0032549763
-
Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases
-
Cheng,C., Kussie,P., Pavletich,N. and Shuman,S. (1998) Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell, 92, 841-850.
-
(1998)
Cell
, vol.92
, pp. 841-850
-
-
Cheng, C.1
Kussie, P.2
Pavletich, N.3
Shuman, S.4
-
3
-
-
0028641159
-
Requirements for noncovalent binding of vaccinia topoisomerase I to duplex DNA
-
Sekiguchi,J. and Shuman,S. (1994) Requirements for noncovalent binding of vaccinia topoisomerase I to duplex DNA. Nucleic Acids Res., 22, 5360-5365.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5360-5365
-
-
Sekiguchi, J.1
Shuman, S.2
-
4
-
-
0025144958
-
Specific DNA cleavage and binding by vaccinia virus DNA topoisomerase I
-
Shuman,S. and Prescott,J. (1990) Specific DNA cleavage and binding by vaccinia virus DNA topoisomerase I. J. Biol. Chem., 265, 17826-17836.
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 17826-17836
-
-
Shuman, S.1
Prescott, J.2
-
5
-
-
0025735876
-
Site-specific interaction of vaccinia virus topoisomerase I with duplex DNA. Minimal DNA substrate for strand cleavage in vitro
-
Shuman,S. (1991) Site-specific interaction of vaccinia virus topoisomerase I with duplex DNA. Minimal DNA substrate for strand cleavage in vitro. J. Biol. Chem., 266, 11372-11379.
-
(1991)
J. Biol. Chem.
, vol.266
, pp. 11372-11379
-
-
Shuman, S.1
-
6
-
-
0023645150
-
Vaccinia virus encapsidates a novel topoisomerase with the properties of a eucaryotic type I enzyme
-
Shaffer,R. and Traktman,P. (1987) Vaccinia virus encapsidates a novel topoisomerase with the properties of a eucaryotic type I enzyme. J. Biol. Chem., 262, 9309-9315.
-
(1987)
J. Biol. Chem.
, vol.262
, pp. 9309-9315
-
-
Shaffer, R.1
Traktman, P.2
-
7
-
-
0023733467
-
Characterization of vaccinia virus DNA topoisomerase I expressed in Escherichia coli
-
Shuman,S., Golder,M. and Moss,B. (1988) Characterization of vaccinia virus DNA topoisomerase I expressed in Escherichia coli. J. Biol. Chem., 263, 16401-16407.
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 16401-16407
-
-
Shuman, S.1
Golder, M.2
Moss, B.3
-
8
-
-
0023442459
-
Identification of a vaccinia virus gene engoding a type I DNA topoisomerase
-
Shuman,S. and Moss,B. (1987) Identification of a vaccinia virus gene engoding a type I DNA topoisomerase. Proc. Natl Acad. Sci. USA, 84, 7478-7482.
-
(1987)
Proc. Natl Acad. Sci. USA
, vol.84
, pp. 7478-7482
-
-
Shuman, S.1
Moss, B.2
-
9
-
-
0028774040
-
Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution
-
Sharma,A., Hanai,R. and Mondragon,A. (1994) Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution. Structure, 2, 767-777.
-
(1994)
Structure
, vol.2
, pp. 767-777
-
-
Sharma, A.1
Hanai, R.2
Mondragon, A.3
-
10
-
-
0028130224
-
Vaccinia topoisomerase binds circumferentially to DNA
-
Sekiguchi,J. and Shuman,S. (1994) Vaccinia topoisomerase binds circumferentially to DNA. J. Biol. Chem., 269, 31731-31734.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 31731-31734
-
-
Sekiguchi, J.1
Shuman, S.2
-
11
-
-
0033554841
-
Site-specific DNA transesterification by vaccinia topoisomerase: Role of specific phosphates and nucleosides
-
Cheng,C. and Shuman,S. (1999) Site-specific DNA transesterification by vaccinia topoisomerase: Role of specific phosphates and nucleosides. Biochemistry, 38, 16599-16612.
-
(1999)
Biochemistry
, vol.38
, pp. 16599-16612
-
-
Cheng, C.1
Shuman, S.2
-
12
-
-
0025647116
-
Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers
-
Zechiedrich,E.L. and Osheroff,N. (1990) Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. EMBO J., 9, 4555-4562.
-
(1990)
EMBO J.
, vol.9
, pp. 4555-4562
-
-
Zechiedrich, E.L.1
Osheroff, N.2
-
13
-
-
0030774249
-
Intermolecular synapsis of duplex DNA by vaccinia topoisomerase
-
Shuman,S., Bear,D.G. and Sekiguchi,J. (1997) Intermolecular synapsis of duplex DNA by vaccinia topoisomerase. EMBO J., 16, 6584-6589.
-
(1997)
EMBO J.
, vol.16
, pp. 6584-6589
-
-
Shuman, S.1
Bear, D.G.2
Sekiguchi, J.3
-
14
-
-
0012618901
-
Atomic force microscope
-
Binnig,G., Quate,C.F. and Gerber,C. (1986) Atomic force microscope. Phys. Rev. Lett., 56, 930-933.
-
(1986)
Phys. Rev. Lett.
, vol.56
, pp. 930-933
-
-
Binnig, G.1
Quate, C.F.2
Gerber, C.3
-
15
-
-
0033880512
-
Probing protein-protein interactions in real time
-
Viani,M.B., Pietrasanta,L.I., Thompson,J.B., Chand,A., Gebeshuber,I.C., Kindt,J.H., Richter,M., Hansma,H.G. and Hansma,P.K. (2000) Probing protein-protein interactions in real time. Nature Struct. Biol., 7, 644-647.
-
(2000)
Nature Struct. Biol.
, vol.7
, pp. 644-647
-
-
Viani, M.B.1
Pietrasanta, L.I.2
Thompson, J.B.3
Chand, A.4
Gebeshuber, I.C.5
Kindt, J.H.6
Richter, M.7
Hansma, H.G.8
Hansma, P.K.9
-
16
-
-
0034743149
-
Surface biology of DNA by atomic force microscopy
-
Hansma,H.G. (2001) Surface biology of DNA by atomic force microscopy. Annu. Rev. Phys. Chem., 52, 71-92.
-
(2001)
Annu. Rev. Phys. Chem.
, vol.52
, pp. 71-92
-
-
Hansma, H.G.1
-
17
-
-
0031836232
-
Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope
-
van Noort,S.J., van der Werf,K.O., Eker,A.P., Wyman,C., de Grooth,B.G., van Hulst,N.F. and Greve,J. (1998) Direct visualization of dynamic protein-DNA interactions with a dedicated atomic force microscope. Biophys J., 74, 2840-2849.
-
(1998)
Biophys J.
, vol.74
, pp. 2840-2849
-
-
van Noort, S.J.1
van der Werf, K.O.2
Eker, A.P.3
Wyman, C.4
de Grooth, B.G.5
van Hulst, N.F.6
Greve, J.7
-
18
-
-
0034810728
-
Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy
-
Moreno-Herrero,F., Herrero,P., Colchero,J., Baro,A.M. and Moreno,F. (2001) Imaging and mapping protein-binding sites on DNA regulatory regions with atomic force microscopy. Biochem. Biophys. Res. Commun., 280, 151-157.
-
(2001)
Biochem. Biophys. Res. Commun.
, vol.280
, pp. 151-157
-
-
Moreno-Herrero, F.1
Herrero, P.2
Colchero, J.3
Baro, A.M.4
Moreno, F.5
-
19
-
-
0016175370
-
Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice
-
McGhee,J.D. and von Hippel,P.H. (1974) Theoretical aspects of DNA-protein interactions: Co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J. Mol. Biol., 86, 469-489.
-
(1974)
J. Mol. Biol.
, vol.86
, pp. 469-489
-
-
McGhee, J.D.1
von Hippel, P.H.2
-
20
-
-
0022549616
-
Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: Experimental approaches to the determination of thermodynamic parameters
-
Kowalczykowski,S.C., Paul,L.S., Lonberg,N., Newport,J.W., McSwiggen,J.A. and von Hippel,P.H. (1986) Cooperative and noncooperative binding of protein ligands to nucleic acid lattices: Experimental approaches to the determination of thermodynamic parameters. Biochemistry, 25, 1226-1240.
-
(1986)
Biochemistry
, vol.25
, pp. 1226-1240
-
-
Kowalczykowski, S.C.1
Paul, L.S.2
Lonberg, N.3
Newport, J.W.4
McSwiggen, J.A.5
von Hippel, P.H.6
-
21
-
-
2142855641
-
Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution
-
Bussiek,M., Mucke,N. and Langowski,J. (2003) Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution. Nucleic Acids Res., 31, e137.
-
(2003)
Nucleic Acids Res.
, vol.31
-
-
Bussiek, M.1
Mucke, N.2
Langowski, J.3
-
22
-
-
0017499528
-
Use of polylysine for adsorption of nuclei acids and enzymes to electron microscope specimen films
-
Williams,R.C. (1977) Use of polylysine for adsorption of nuclei acids and enzymes to electron microscope specimen films. Proc. Natl Acad. Sci. USA, 74, 2311-2315.
-
(1977)
Proc. Natl Acad. Sci. USA
, vol.74
, pp. 2311-2315
-
-
Williams, R.C.1
-
23
-
-
0030596081
-
Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis
-
Rivetti,C., Guthold,M. and Bustamante,C. (1996) Scanning force microscopy of DNA deposited onto mica: Equilibration versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol., 264, 919-932.
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 919-932
-
-
Rivetti, C.1
Guthold, M.2
Bustamante, C.3
-
24
-
-
0032846225
-
Cationic silanes stabilize intermediates in DNA condensation
-
Fang,Y. and Hoh,J.H. (1999) Cationic silanes stabilize intermediates in DNA condensation. FEBS Lett., 459, 173-176.
-
(1999)
FEBS Lett.
, vol.459
, pp. 173-176
-
-
Fang, Y.1
Hoh, J.H.2
-
25
-
-
28544452770
-
Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA
-
Crampton,N., Bonass,W.A., Kirkham,J. and Thomson,N.H. (2005) Formation of aminosilane-functionalized mica for atomic force microscopy imaging of DNA. Langmuir, 21, 7884-7891.
-
(2005)
Langmuir
, vol.21
, pp. 7884-7891
-
-
Crampton, N.1
Bonass, W.A.2
Kirkham, J.3
Thomson, N.H.4
-
26
-
-
0026500201
-
Circular DNA molecules imaged in air by scanning force microscopy
-
Bustamante,C., Vesenka,J., Tang,C.L., Rees,W., Guthold,M. and Keller,R. (1992) Circular DNA molecules imaged in air by scanning force microscopy. Biochemistry, 31, 22-26.
-
(1992)
Biochemistry
, vol.31
, pp. 22-26
-
-
Bustamante, C.1
Vesenka, J.2
Tang, C.L.3
Rees, W.4
Guthold, M.5
Keller, R.6
-
28
-
-
28544434823
-
-
Chapter 6 Retrieved June, 2005, from the University Bonn website:
-
Brock,I. (2001) Statistical Methods of Data Analysis. Chapter 6 Retrieved June, 2005, from the University Bonn website: http://www-zeus.physik.uni-bonn.de/~brock/stat_ws0001/.
-
(2001)
Statistical Methods of Data Analysis
-
-
Brock, I.1
-
29
-
-
9244248170
-
Accurate height and volume measurements on soft samples with the atomic force microscope
-
Jiao,Y. and Schaffer,T.E. (2004) Accurate height and volume measurements on soft samples with the atomic force microscope. Langmuir, 20, 10038-10045.
-
(2004)
Langmuir
, vol.20
, pp. 10038-10045
-
-
Jiao, Y.1
Schaffer, T.E.2
-
30
-
-
0019350732
-
Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. III. Binding properties of two specific proteolytic digestion products of the protein (G32P*I and G32P*III)
-
Lonberg,N., Kowalczykowski,S.C., Paul,L.S. and von Hippel,P.H. (1981) Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. III. Binding properties of two specific proteolytic digestion products of the protein (G32P*I and G32P*III). J. Mol. Biol., 145, 123-138.
-
(1981)
J. Mol. Biol.
, vol.145
, pp. 123-138
-
-
Lonberg, N.1
Kowalczykowski, S.C.2
Paul, L.S.3
von Hippel, P.H.4
-
31
-
-
0032491470
-
Single-stranded DNA binding properties of the UvsX recombinase of bacteriophage T4: Binding parameters and effects of nucleotides
-
Ando,R.A. and Morrical,S.W. (1998) Single-stranded DNA binding properties of the UvsX recombinase of bacteriophage T4: Binding parameters and effects of nucleotides. J. Mol. Biol., 283, 785-796.
-
(1998)
J. Mol. Biol.
, vol.283
, pp. 785-796
-
-
Ando, R.A.1
Morrical, S.W.2
-
32
-
-
0034814802
-
A novel single-molecule study to determine protein-protein association constants
-
Ratcliff,G.C. and Erie,D.A. (2001) A novel single-molecule study to determine protein-protein association constants. J. Am. Chem. Soc., 123, 5632-5635.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 5632-5635
-
-
Ratcliff, G.C.1
Erie, D.A.2
-
34
-
-
0028091124
-
Vaccinia DNA topoisomerase I: Single-turnover and steady-state kinetic analysis of the DNA strand cleavage and ligation reactions
-
Stivers,J.T., Shuman,S. and Mildvan,A.S. (1994) Vaccinia DNA topoisomerase I: Single-turnover and steady-state kinetic analysis of the DNA strand cleavage and ligation reactions. Biochemistry, 33, 327-339.
-
(1994)
Biochemistry
, vol.33
, pp. 327-339
-
-
Stivers, J.T.1
Shuman, S.2
Mildvan, A.S.3
-
35
-
-
0242576857
-
Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs
-
Boskovic,J., Rivera-Calzada,A., Maman,J.D., Chacon,P., Willison,K.R., Pearl,L.H. and Llorca,O. (2003) Visualization of DNA-induced conformational changes in the DNA repair kinase DNA-PKcs. EMBO J., 22, 5875-5882.
-
(2003)
EMBO J.
, vol.22
, pp. 5875-5882
-
-
Boskovic, J.1
Rivera-Calzada, A.2
Maman, J.D.3
Chacon, P.4
Willison, K.R.5
Pearl, L.H.6
Llorca, O.7
-
36
-
-
24944540931
-
Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon DNA binding
-
Moreno-Herrero,F., de Jager,M., Dekker,N.H., Kanaar,R., Wyman,C. and Dekker,C. (2005) Mesoscale conformational changes in the DNA-repair complex Rad50/Mre11/Nbs1 upon DNA binding. Nature, 437, 440-443.
-
(2005)
Nature
, vol.437
, pp. 440-443
-
-
Moreno-Herrero, F.1
de Jager, M.2
Dekker, N.H.3
Kanaar, R.4
Wyman, C.5
Dekker, C.6
-
37
-
-
0032484232
-
DNA-induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor
-
Holmbeck,S.M., Dyson,H.J. and Wright,P.E. (1998) DNA-induced conformational changes are the basis for cooperative dimerization by the DNA binding domain of the retinoid X receptor. J. Mol. Biol., 284, 533-539.
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 533-539
-
-
Holmbeck, S.M.1
Dyson, H.J.2
Wright, P.E.3
-
38
-
-
0343069462
-
Vaccinia DNA topoisomerase I promotes illegitimate recombination in Escherichia coli
-
Shuman,S. (1989) Vaccinia DNA topoisomerase I promotes illegitimate recombination in Escherichia coli. Proc. Natl Acad. Sci. USA, 86, 3489-3493.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 3489-3493
-
-
Shuman, S.1
-
39
-
-
0025840332
-
Recombination mediated by vaccinia virus DNA topoisomerase I in Escherichia coli is sequence specific
-
Shuman,S. (1991) Recombination mediated by vaccinia virus DNA topoisomerase I in Escherichia coli is sequence specific. Proc. Natl Acad. Sci. USA, 88, 10104-10108.
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 10104-10108
-
-
Shuman, S.1
-
40
-
-
0026657545
-
DNA strand transfer reactions catalyzed by vaccinia topoisomerase I
-
Shuman,S. (1992) DNA strand transfer reactions catalyzed by vaccinia topoisomerase I. J. Biol. Chem., 267, 8620-8627.
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 8620-8627
-
-
Shuman, S.1
-
41
-
-
0026806143
-
Two classes of DNA end-joining reactions catalyzed by vaccinia topoisomerase I
-
Shuman,S. (1992) Two classes of DNA end-joining reactions catalyzed by vaccinia topoisomerase I. J. Biol. Chem., 267, 16755-16758.
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 16755-16758
-
-
Shuman, S.1
-
42
-
-
0028140256
-
Characterization of intra- and intermolecular DNA ligation mediated by eukaryotic topoisomerase I. Role of bipartite DNA interaction in the ligation process
-
Christiansen,K. and Westergaard,O. (1994) Characterization of intra- and intermolecular DNA ligation mediated by eukaryotic topoisomerase I. Role of bipartite DNA interaction in the ligation process. J. Biol. Chem., 269, 721-729.
-
(1994)
J. Biol. Chem.
, vol.269
, pp. 721-729
-
-
Christiansen, K.1
Westergaard, O.2
-
43
-
-
0141594578
-
Poxvirus DNA topoisomerase knockout mutant exhibits decreased infectivity associated with reduced early transcription
-
Da Fonseca,F. and Moss,B. (2003) Poxvirus DNA topoisomerase knockout mutant exhibits decreased infectivity associated with reduced early transcription. Proc. Natl Acad. Sci. USA, 100, 11291-11296.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11291-11296
-
-
Da Fonseca, F.1
Moss, B.2
|