-
1
-
-
14244263426
-
Major nucleoid proteins in the structure and function of the Escherichia coli chromosome
-
Higgins N.P. (Ed), ASM Press, Washington, DC
-
Johnson R.C., Johnson L.M., Schmidt J.W., and Gardner J.F. Major nucleoid proteins in the structure and function of the Escherichia coli chromosome. In: Higgins N.P. (Ed). The Bacterial Chromosome (2005), ASM Press, Washington, DC 65-132
-
(2005)
The Bacterial Chromosome
, pp. 65-132
-
-
Johnson, R.C.1
Johnson, L.M.2
Schmidt, J.W.3
Gardner, J.F.4
-
2
-
-
34247517469
-
DNA-protein interactions and bacterial chromosome architecture
-
Stavans J., and Oppenheim A. DNA-protein interactions and bacterial chromosome architecture. Phys. Biol. 3 (2006) R1-R10
-
(2006)
Phys. Biol.
, vol.3
-
-
Stavans, J.1
Oppenheim, A.2
-
3
-
-
0035283138
-
Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection
-
Frenkiel-Krispin D., Levin-Zaidman S., Shimoni E., Wolf S.G., Wachtel E.J., Arad T., et al. Regulated phase transitions of bacterial chromatin: a non-enzymatic pathway for generic DNA protection. EMBO J. 20 (2001) 1184-1191
-
(2001)
EMBO J.
, vol.20
, pp. 1184-1191
-
-
Frenkiel-Krispin, D.1
Levin-Zaidman, S.2
Shimoni, E.3
Wolf, S.G.4
Wachtel, E.J.5
Arad, T.6
-
4
-
-
3042660143
-
Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy
-
Kim J., Yoshimura S.H., Hizume K., Ohniwa R.L., Ishihama A., and Takeyasu K. Fundamental structural units of the Escherichia coli nucleoid revealed by atomic force microscopy. Nucleic Acids Res. 32 (2004) 1982-1992
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1982-1992
-
-
Kim, J.1
Yoshimura, S.H.2
Hizume, K.3
Ohniwa, R.L.4
Ishihama, A.5
Takeyasu, K.6
-
5
-
-
0033168858
-
DNA protection by stress-induced biocrystallization
-
Wolf S.G., Frenkiel D., Arad T., Finkel S.E., Kolter R., and Minsky A. DNA protection by stress-induced biocrystallization. Nature 400 (1999) 83-85
-
(1999)
Nature
, vol.400
, pp. 83-85
-
-
Wolf, S.G.1
Frenkiel, D.2
Arad, T.3
Finkel, S.E.4
Kolter, R.5
Minsky, A.6
-
6
-
-
0942279510
-
Nucleoid restructuring in stationary-state bacteria
-
Frenkiel-Krispin D., Ben-Avraham I., Englander J., Shimoni E., Wolf S.G., and Minsky A. Nucleoid restructuring in stationary-state bacteria. Mol. Microbiol. 51 (2004) 395-405
-
(2004)
Mol. Microbiol.
, vol.51
, pp. 395-405
-
-
Frenkiel-Krispin, D.1
Ben-Avraham, I.2
Englander, J.3
Shimoni, E.4
Wolf, S.G.5
Minsky, A.6
-
7
-
-
0032716841
-
Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid
-
Ali Azam T., Iwata A., Nishimura A., Ueda S., and Ishihama A. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181 (1999) 6361-6370
-
(1999)
J. Bacteriol.
, vol.181
, pp. 6361-6370
-
-
Ali Azam, T.1
Iwata, A.2
Nishimura, A.3
Ueda, S.4
Ishihama, A.5
-
8
-
-
0025962021
-
Three-dimensional structure of the E. coli DNA-binding protein FIS
-
Kostrewa D., Granzin J., Koch C., Choe H.W., Raghunathan S., Wolf W., et al. Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature 349 (1991) 178-180
-
(1991)
Nature
, vol.349
, pp. 178-180
-
-
Kostrewa, D.1
Granzin, J.2
Koch, C.3
Choe, H.W.4
Raghunathan, S.5
Wolf, W.6
-
9
-
-
0025939520
-
The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding
-
Yuan H.S., Finkel S.E., Feng J.A., Kaczor-Grzeskowiak M., Johnson R.C., and Dickerson R.E. The molecular structure of wild-type and a mutant Fis protein: relationship between mutational changes and recombinational enhancer function or DNA binding. Proc. Natl Acad. Sci. USA 88 (1991) 9558-9562
-
(1991)
Proc. Natl Acad. Sci. USA
, vol.88
, pp. 9558-9562
-
-
Yuan, H.S.1
Finkel, S.E.2
Feng, J.A.3
Kaczor-Grzeskowiak, M.4
Johnson, R.C.5
Dickerson, R.E.6
-
10
-
-
0022545522
-
Host protein requirements for in vitro site-specific DNA inversion
-
Johnson R.C., Bruist M.F., and Simon M.I. Host protein requirements for in vitro site-specific DNA inversion. Cell 46 (1986) 531-539
-
(1986)
Cell
, vol.46
, pp. 531-539
-
-
Johnson, R.C.1
Bruist, M.F.2
Simon, M.I.3
-
11
-
-
18444369954
-
The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin
-
Dame R.T. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 56 (2005) 858-870
-
(2005)
Mol. Microbiol.
, vol.56
, pp. 858-870
-
-
Dame, R.T.1
-
12
-
-
0025895162
-
The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli
-
Gille H., Egan J.B., Roth A., and Messer W. The FIS protein binds and bends the origin of chromosomal DNA replication, oriC, of Escherichia coli. Nucleic Acids Res. 19 (1991) 4167-4172
-
(1991)
Nucleic Acids Res.
, vol.19
, pp. 4167-4172
-
-
Gille, H.1
Egan, J.B.2
Roth, A.3
Messer, W.4
-
13
-
-
0033607776
-
Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter
-
McLeod S.M., Xu J., Cramton S.E., Gaal T., Gourse R.L., and Johnson R.C. Localization of amino acids required for Fis to function as a class II transcriptional activator at the RpoS-dependent proP P2 promoter. J. Mol. Biol. 294 (1999) 333-346
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 333-346
-
-
McLeod, S.M.1
Xu, J.2
Cramton, S.E.3
Gaal, T.4
Gourse, R.L.5
Johnson, R.C.6
-
14
-
-
19244372639
-
Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts
-
Pan C.Q., Finkel S.E., Cramton S.E., Feng J.A., Sigman D.S., and Johnson R.C. Variable structures of Fis-DNA complexes determined by flanking DNA-protein contacts. J. Mol. Biol. 264 (1996) 675-695
-
(1996)
J. Mol. Biol.
, vol.264
, pp. 675-695
-
-
Pan, C.Q.1
Finkel, S.E.2
Cramton, S.E.3
Feng, J.A.4
Sigman, D.S.5
Johnson, R.C.6
-
15
-
-
0023771741
-
Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes
-
Thompson J.F., and Landy A. Empirical estimation of protein-induced DNA bending angles: applications to λ site-specific recombination complexes. Nucleic Acids Res. 16 (1988) 9687-9705
-
(1988)
Nucleic Acids Res.
, vol.16
, pp. 9687-9705
-
-
Thompson, J.F.1
Landy, A.2
-
16
-
-
10244243805
-
DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus
-
Ceci P., Cellai S., Falvo E., Rivetti C., Rossi G.L., and Chiancone E. DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus. Nucleic Acids Res. 32 (2004) 5935-5944
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 5935-5944
-
-
Ceci, P.1
Cellai, S.2
Falvo, E.3
Rivetti, C.4
Rossi, G.L.5
Chiancone, E.6
-
17
-
-
0031959912
-
The crystal structure of Dps, a ferritin homolog that binds and protects DNA
-
Grant R.A., Filman D.J., Finkel S.E., Kolter R., and Hogle J.M. The crystal structure of Dps, a ferritin homolog that binds and protects DNA. Nature Struct. Biol. 5 (1998) 294-303
-
(1998)
Nature Struct. Biol.
, vol.5
, pp. 294-303
-
-
Grant, R.A.1
Filman, D.J.2
Finkel, S.E.3
Kolter, R.4
Hogle, J.M.5
-
18
-
-
33750527566
-
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective
-
Luijsterburg M.S., Noom M.C., Wuite G.J., and Dame R.T. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156 (2006) 262-272
-
(2006)
J. Struct. Biol.
, vol.156
, pp. 262-272
-
-
Luijsterburg, M.S.1
Noom, M.C.2
Wuite, G.J.3
Dame, R.T.4
-
20
-
-
34248370213
-
αβ provides foundation for DNA supercoiling
-
αβ provides foundation for DNA supercoiling. Proc. Natl Acad. Sci. USA 104 (2007) 4309-4314
-
(2007)
Proc. Natl Acad. Sci. USA
, vol.104
, pp. 4309-4314
-
-
Guo, F.1
Adhya, S.2
-
21
-
-
0030451819
-
Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn
-
Rice P.A., Yang S.W., Mizuuchi K., and NAsh H.A. Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn. Cell 87 (1996) 1295-1306
-
(1996)
Cell
, vol.87
, pp. 1295-1306
-
-
Rice, P.A.1
Yang, S.W.2
Mizuuchi, K.3
NAsh, H.A.4
-
22
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
Swinger K.K., Lemberg K.M., Zhang Y., and Rice P.A. Flexible DNA bending in HU-DNA cocrystal structures. EMBO J. 22 (2003) 3749-3760
-
(2003)
EMBO J.
, vol.22
, pp. 3749-3760
-
-
Swinger, K.K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
23
-
-
1342324028
-
IHF and HU: flexible architects of bent DNA
-
Swinger K.K., and Rice P.A. IHF and HU: flexible architects of bent DNA. Curr. Opin. Struct. Biol. 14 (2004) 28-35
-
(2004)
Curr. Opin. Struct. Biol.
, vol.14
, pp. 28-35
-
-
Swinger, K.K.1
Rice, P.A.2
-
24
-
-
0037823447
-
Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure
-
Ramstein J., Hervouet N., Coste F., Zelwer C., Oberto J., and Castaing B. Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J. Mol. Biol. 331 (2003) 101-121
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 101-121
-
-
Ramstein, J.1
Hervouet, N.2
Coste, F.3
Zelwer, C.4
Oberto, J.5
Castaing, B.6
-
25
-
-
39649115803
-
Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H′ DNA
-
Vander Meulen K.A., Saecker R.M., and Record M.T. Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H′ DNA. J. Mol. Biol. 377 (2008) 9-27
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 9-27
-
-
Vander Meulen, K.A.1
Saecker, R.M.2
Record, M.T.3
-
26
-
-
0035816212
-
Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding
-
Holbrook J.A., Tsodikov O.V., Saecker R.M., and Record Jr. M.T. Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding. J. Mol. Biol. 310 (2001) 379-401
-
(2001)
J. Mol. Biol.
, vol.310
, pp. 379-401
-
-
Holbrook, J.A.1
Tsodikov, O.V.2
Saecker, R.M.3
Record Jr., M.T.4
-
27
-
-
0026019440
-
HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments
-
Bonnefoy E., and Rouviere-Yaniv J. HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10 (1991) 687-696
-
(1991)
EMBO J.
, vol.10
, pp. 687-696
-
-
Bonnefoy, E.1
Rouviere-Yaniv, J.2
-
28
-
-
0033515646
-
Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA
-
Pinson V., Takahashi M., and Rouviere-Yaniv J. Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol. 287 (1999) 485-497
-
(1999)
J. Mol. Biol.
, vol.287
, pp. 485-497
-
-
Pinson, V.1
Takahashi, M.2
Rouviere-Yaniv, J.3
-
29
-
-
0035957055
-
HU binding to DNA: evidence for multiple complex formation and DNA bending
-
Wojtuszewski K., Hawkins M.E., Cole J.L., and Mukerji I. HU binding to DNA: evidence for multiple complex formation and DNA bending. Biochemistry 40 (2001) 4892
-
(2001)
Biochemistry
, vol.40
, pp. 4892
-
-
Wojtuszewski, K.1
Hawkins, M.E.2
Cole, J.L.3
Mukerji, I.4
-
30
-
-
0037452946
-
HU binding to bent DNA: A fluorescence resonance energy transfer and anisotropy study
-
Wojtuszewski K., and Mukerji I. HU binding to bent DNA: A fluorescence resonance energy transfer and anisotropy study. Biochemistry 42 (2003) 3096-3104
-
(2003)
Biochemistry
, vol.42
, pp. 3096-3104
-
-
Wojtuszewski, K.1
Mukerji, I.2
-
31
-
-
41149097061
-
Mechanisms of specific and nonspecific binding of architectural proteins in prokaryotic gene regulation
-
Benevides J.M., Danahy J., Kawakami J., and Thomas Jr. G.J. Mechanisms of specific and nonspecific binding of architectural proteins in prokaryotic gene regulation. Biochemistry 47 (2008) 3855-3862
-
(2008)
Biochemistry
, vol.47
, pp. 3855-3862
-
-
Benevides, J.M.1
Danahy, J.2
Kawakami, J.3
Thomas Jr., G.J.4
-
32
-
-
0023041804
-
Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch
-
Broyles S.S., and Pettijohn D.E. Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J. Mol. Biol. 187 (1986) 47-60
-
(1986)
J. Mol. Biol.
, vol.187
, pp. 47-60
-
-
Broyles, S.S.1
Pettijohn, D.E.2
-
33
-
-
0018405881
-
E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA
-
Rouviere-Yaniv J., Yaniv M., and Germond J.E. E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell 17 (1979) 265-274
-
(1979)
Cell
, vol.17
, pp. 265-274
-
-
Rouviere-Yaniv, J.1
Yaniv, M.2
Germond, J.E.3
-
34
-
-
0028901705
-
HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps
-
Castaing B., Zelwer C., Laval J., and Boiteux S. HU protein of Escherichia coli binds specifically to DNA that contains single-strand breaks or gaps. J. Biol. Chem. 270 (1995) 10291-10296
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 10291-10296
-
-
Castaing, B.1
Zelwer, C.2
Laval, J.3
Boiteux, S.4
-
35
-
-
0033214062
-
The binding motif recognized by HU on both nicked and cruciform DNA
-
Kamashev D., Balandina A., and Rouviere-Yaniv J. The binding motif recognized by HU on both nicked and cruciform DNA. EMBO J. 18 (1999) 5434-5444
-
(1999)
EMBO J.
, vol.18
, pp. 5434-5444
-
-
Kamashev, D.1
Balandina, A.2
Rouviere-Yaniv, J.3
-
36
-
-
0034416406
-
The histone-like protein HU binds specifically to DNA recombination and repair intermediates
-
Kamashev D., and Rouviere-Yaniv J. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19 (2000) 6527-6535
-
(2000)
EMBO J.
, vol.19
, pp. 6527-6535
-
-
Kamashev, D.1
Rouviere-Yaniv, J.2
-
37
-
-
7244245362
-
Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes
-
Skoko D., Wong B., Johnson R.C., and Marko J.F. Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes. Biochemistry 43 (2004) 13867-13874
-
(2004)
Biochemistry
, vol.43
, pp. 13867-13874
-
-
Skoko, D.1
Wong, B.2
Johnson, R.C.3
Marko, J.F.4
-
38
-
-
2342454974
-
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
-
van Noort J., Verbrugge S., Goosen N., Dekker C., and Dame R.T. Dual architectural roles of HU: Formation of flexible hinges and rigid filaments. Proc. Natl Acad. Sci. USA 101 (2004) 6969-6974
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 6969-6974
-
-
van Noort, J.1
Verbrugge, S.2
Goosen, N.3
Dekker, C.4
Dame, R.T.5
-
39
-
-
0037048702
-
HU: promoting or counteracting DNA compaction?
-
Dame R.T., and Goosen N. HU: promoting or counteracting DNA compaction?. FEBS Lett. 529 (2002) 151-156
-
(2002)
FEBS Lett.
, vol.529
, pp. 151-156
-
-
Dame, R.T.1
Goosen, N.2
-
40
-
-
0023040461
-
Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA
-
Bujalowski W., and Lohman T.M. Escherichia coli single-strand binding protein forms multiple, distinct complexes with single-stranded DNA. Biochemistry 25 (1986) 7799-7802
-
(1986)
Biochemistry
, vol.25
, pp. 7799-7802
-
-
Bujalowski, W.1
Lohman, T.M.2
-
42
-
-
0021920551
-
Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration
-
Lohman T.M., and Overman L.B. Two binding modes in Escherichia coli single strand binding protein-single stranded DNA complexes. Modulation by NaCl concentration. J. Biol. Chem. 260 (1985) 3594-3603
-
(1985)
J. Biol. Chem.
, vol.260
, pp. 3594-3603
-
-
Lohman, T.M.1
Overman, L.B.2
-
43
-
-
0028246888
-
Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities
-
Lohman T.M., and Ferrari M.E. Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu. Rev. Biochem. 63 (1994) 527-570
-
(1994)
Annu. Rev. Biochem.
, vol.63
, pp. 527-570
-
-
Lohman, T.M.1
Ferrari, M.E.2
-
44
-
-
0032509151
-
Transition between different binding modes in rat DNA polymerase β-ssDNA complexes
-
Jezewska M.J., Rajendran S., and Bujalowski W. Transition between different binding modes in rat DNA polymerase β-ssDNA complexes. J. Mol. Biol. 284 (1998) 1113-1131
-
(1998)
J. Mol. Biol.
, vol.284
, pp. 1113-1131
-
-
Jezewska, M.J.1
Rajendran, S.2
Bujalowski, W.3
-
45
-
-
0032553313
-
Human DNA polymerase β recognizes single-stranded DNA using two different binding modes
-
Rajendran S., Jezewska M.J., and Bujalowski W. Human DNA polymerase β recognizes single-stranded DNA using two different binding modes. J. Biol. Chem. 273 (1998) 31021-31031
-
(1998)
J. Biol. Chem.
, vol.273
, pp. 31021-31031
-
-
Rajendran, S.1
Jezewska, M.J.2
Bujalowski, W.3
-
46
-
-
0018196563
-
Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions
-
Epstein I.R. Cooperative and non-cooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions. Biophys. Chem. 8 (1978) 327-339
-
(1978)
Biophys. Chem.
, vol.8
, pp. 327-339
-
-
Epstein, I.R.1
-
47
-
-
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. 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 (1974) 469-489
-
(1974)
J. Mol. Biol.
, vol.86
, pp. 469-489
-
-
McGhee, J.D.1
von Hippel, P.H.2
-
48
-
-
0000218405
-
Linear cooperative binding of large ligands involving mutual exclusion of different binding modes
-
Schwarz G., and Stankowski S. Linear cooperative binding of large ligands involving mutual exclusion of different binding modes. Biophys. Chem. 10 (1979) 173-181
-
(1979)
Biophys. Chem.
, vol.10
, pp. 173-181
-
-
Schwarz, G.1
Stankowski, S.2
-
49
-
-
33845504065
-
Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF
-
Kuznetsov S.V., Sugimura S., Vivas P., Crothers D.M., and Ansari A. Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc. Natl Acad. Sci. USA 103 (2006) 18515-18520
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 18515-18520
-
-
Kuznetsov, S.V.1
Sugimura, S.2
Vivas, P.3
Crothers, D.M.4
Ansari, A.5
-
50
-
-
0033485813
-
Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer
-
Lorenz M., Hillisch A., Goodman S.D., and Diekmann S. Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer. Nucleic Acids Res. 27 (1999) 4619-4625
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4619-4625
-
-
Lorenz, M.1
Hillisch, A.2
Goodman, S.D.3
Diekmann, S.4
-
51
-
-
33845500268
-
Stepwise binding and bending of DNA by Escherichia coli integration host factor
-
Sugimura S., and Crothers D.M. Stepwise binding and bending of DNA by Escherichia coli integration host factor. Proc. Natl Acad. Sci. USA 103 (2006) 18510-18514
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 18510-18514
-
-
Sugimura, S.1
Crothers, D.M.2
-
52
-
-
0026687952
-
Fluorescence resonance energy transfer and nucleic acids
-
Clegg R.M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211 (1992) 353-388
-
(1992)
Methods Enzymol.
, vol.211
, pp. 353-388
-
-
Clegg, R.M.1
-
53
-
-
0030815232
-
Global structure of three-way DNA junctions with and without additional unpaired bases: a fluorescence resonance energy transfer analysis
-
Stuhmeier F., Welch J.B., Murchie A.I., Lilley D.M., and Clegg R.M. Global structure of three-way DNA junctions with and without additional unpaired bases: a fluorescence resonance energy transfer analysis. Biochemistry 36 (1997) 13530-13538
-
(1997)
Biochemistry
, vol.36
, pp. 13530-13538
-
-
Stuhmeier, F.1
Welch, J.B.2
Murchie, A.I.3
Lilley, D.M.4
Clegg, R.M.5
-
54
-
-
0030928287
-
Repressor induced site-specific binding of HU for transcriptional regulation
-
Aki T., and Adhya S. Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16 (1997) 3666-3674
-
(1997)
EMBO J.
, vol.16
, pp. 3666-3674
-
-
Aki, T.1
Adhya, S.2
-
55
-
-
0037381650
-
Regulation of gene expression by histone-like proteins in bacteria
-
Dorman C.J., and Deighan P. Regulation of gene expression by histone-like proteins in bacteria. Curr. Opin. Genet. Dev. 13 (2003) 179-184
-
(2003)
Curr. Opin. Genet. Dev.
, vol.13
, pp. 179-184
-
-
Dorman, C.J.1
Deighan, P.2
-
56
-
-
0024373965
-
Multiple defects in Escherichia coli mutants lacking HU protein
-
Huisman O., Faelen M., Girard D., Jaffe A., Toussaint A., and Rouviere-Yaniv J. Multiple defects in Escherichia coli mutants lacking HU protein. J. Bacteriol. 171 (1989) 3704-3712
-
(1989)
J. Bacteriol.
, vol.171
, pp. 3704-3712
-
-
Huisman, O.1
Faelen, M.2
Girard, D.3
Jaffe, A.4
Toussaint, A.5
Rouviere-Yaniv, J.6
-
57
-
-
0028970118
-
DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin condensation
-
Paull T.T., and Johnson R.C. DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin condensation. J. Biol. Chem. 270 (1995) 8744-8754
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 8744-8754
-
-
Paull, T.T.1
Johnson, R.C.2
-
58
-
-
0028980296
-
54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR
-
54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR. J. Bacteriol. 177 (1995) 3758-3763
-
(1995)
J. Bacteriol.
, vol.177
, pp. 3758-3763
-
-
Perez-Martin, J.1
de Lorenzo, V.2
-
59
-
-
52949124477
-
-
Vander Meulen, K. A. (2007). The thermodynamics of DNA binding and wrapping by the E. coli DNA-remodeling protein integration host factor. Ph.D. thesis. UW-Madison, Madison, WI.
-
Vander Meulen, K. A. (2007). The thermodynamics of DNA binding and wrapping by the E. coli DNA-remodeling protein integration host factor. Ph.D. thesis. UW-Madison, Madison, WI.
-
-
-
-
60
-
-
0034435652
-
Structural and thermodynamic strategies for site-specific DNA binding proteins
-
Jen-Jacobson L., Engler L.E., and Jacobson L.A. Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure 8 (2000) 1015-1023
-
(2000)
Structure
, vol.8
, pp. 1015-1023
-
-
Jen-Jacobson, L.1
Engler, L.E.2
Jacobson, L.A.3
-
61
-
-
4644342209
-
Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d
-
Peters W.B., Edmondson S.P., and Shriver J.W. Thermodynamics of DNA binding and distortion by the hyperthermophile chromatin protein Sac7d. J. Mol. Biol. 343 (2004) 339-360
-
(2004)
J. Mol. Biol.
, vol.343
, pp. 339-360
-
-
Peters, W.B.1
Edmondson, S.P.2
Shriver, J.W.3
-
62
-
-
33751436653
-
What drives proteins into the major or minor grooves of DNA?
-
Privalov P.L., Dragan A.I., Crane-Robinson C., Breslauer K.J., Remeta D.P., and Minetti C.A. What drives proteins into the major or minor grooves of DNA?. J. Mol. Biol. 365 (2007) 1-9
-
(2007)
J. Mol. Biol.
, vol.365
, 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.6
-
63
-
-
0014413820
-
Flexibility of native DNA from the sedimentation behavior as a function of molecular weight and temperature
-
Gray Jr. H.B., and Hearst J.E. Flexibility of native DNA from the sedimentation behavior as a function of molecular weight and temperature. J. Mol. Biol. 35 (1968) 111-129
-
(1968)
J. Mol. Biol.
, vol.35
, pp. 111-129
-
-
Gray Jr., H.B.1
Hearst, J.E.2
-
64
-
-
0017835397
-
DNA chain flexibility and the structure of chromatin nu-bodies
-
Harrington R.E. DNA chain flexibility and the structure of chromatin nu-bodies. Nucleic Acids Res. 4 (1977) 3519-3535
-
(1977)
Nucleic Acids Res.
, vol.4
, pp. 3519-3535
-
-
Harrington, R.E.1
-
65
-
-
0033614819
-
Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices
-
Holbrook J.A., Capp M.W., Saecker R.M., and Record Jr. M.T. Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices. Biochemistry 38 (1999) 8409-8422
-
(1999)
Biochemistry
, vol.38
, pp. 8409-8422
-
-
Holbrook, J.A.1
Capp, M.W.2
Saecker, R.M.3
Record Jr., M.T.4
-
66
-
-
0042166066
-
DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution
-
Dragan A.I., Klass J., Read C., Churchill M.E., Crane-Robinson C., and Privalov P.L. DNA binding of a non-sequence-specific HMG-D protein is entropy driven with a substantial non-electrostatic contribution. J. Mol. Biol. 331 (2003) 795-813
-
(2003)
J. Mol. Biol.
, vol.331
, pp. 795-813
-
-
Dragan, A.I.1
Klass, J.2
Read, C.3
Churchill, M.E.4
Crane-Robinson, C.5
Privalov, P.L.6
-
67
-
-
0033544727
-
The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5
-
Privalov P.L., Jelesarov I., Read C.M., Dragan A.I., and Crane-Robinson C. The energetics of HMG box interactions with DNA: thermodynamics of the DNA binding of the HMG box from mouse sox-5. J. Mol. Biol. 294 (1999) 997-1013
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 997-1013
-
-
Privalov, P.L.1
Jelesarov, I.2
Read, C.M.3
Dragan, A.I.4
Crane-Robinson, C.5
-
68
-
-
0036600872
-
Protein surface salt bridges and paths for DNA wrapping
-
Saecker R.M., and Record Jr. M.T. Protein surface salt bridges and paths for DNA wrapping. Curr. Opin. Struct. Biol. 12 (2002) 311-319
-
(2002)
Curr. Opin. Struct. Biol.
, vol.12
, pp. 311-319
-
-
Saecker, R.M.1
Record Jr., M.T.2
-
71
-
-
0022542165
-
Salt-dependent changes in the DNA binding co-operativity of Escherichia coli single strand binding protein
-
Lohman T.M., Overman L.B., and Datta S. Salt-dependent changes in the DNA binding co-operativity of Escherichia coli single strand binding protein. J. Mol. Biol. 187 (1986) 603-615
-
(1986)
J. Mol. Biol.
, vol.187
, pp. 603-615
-
-
Lohman, T.M.1
Overman, L.B.2
Datta, S.3
-
72
-
-
0023916373
-
Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects
-
Bujalowski W., Overman L.B., and Lohman T.M. Binding mode transitions of Escherichia coli single strand binding protein-single-stranded DNA complexes. Cation, anion, pH, and binding density effects. J. Biol. Chem. 263 (1988) 4629-4640
-
(1988)
J. Biol. Chem.
, vol.263
, pp. 4629-4640
-
-
Bujalowski, W.1
Overman, L.B.2
Lohman, T.M.3
-
73
-
-
0017701075
-
Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release
-
deHaseth P.L., Lohman T.M., and Record Jr. M.T. Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release. Biochemistry 16 (1977) 4783-4790
-
(1977)
Biochemistry
, vol.16
, pp. 4783-4790
-
-
deHaseth, P.L.1
Lohman, T.M.2
Record Jr., M.T.3
-
75
-
-
0021286693
-
3-Å resolution structure of a protein with histone-like properties in prokaryotes
-
Tanaka I., Appelt K., Dijk J., White S.W., and Wilson K.S. 3-Å resolution structure of a protein with histone-like properties in prokaryotes. Nature 310 (1984) 376-381
-
(1984)
Nature
, vol.310
, pp. 376-381
-
-
Tanaka, I.1
Appelt, K.2
Dijk, J.3
White, S.W.4
Wilson, K.S.5
-
76
-
-
0029973105
-
Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate
-
Lavoie B.D., Shaw G.S., Millner A., and Chaconas G. Anatomy of a flexer-DNA complex inside a higher-order transposition intermediate. Cell 85 (1996) 761-771
-
(1996)
Cell
, vol.85
, pp. 761-771
-
-
Lavoie, B.D.1
Shaw, G.S.2
Millner, A.3
Chaconas, G.4
-
77
-
-
19444387811
-
Bacterial repression loops require enhanced DNA flexibility
-
Becker N.A., Kahn J.D., and Maher III L.J. Bacterial repression loops require enhanced DNA flexibility. J. Mol. Biol. 349 (2005) 716-730
-
(2005)
J. Mol. Biol.
, vol.349
, pp. 716-730
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
78
-
-
0023724433
-
DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU
-
Flashner Y., and Gralla J.D. DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU. Cell 54 (1988) 713-721
-
(1988)
Cell
, vol.54
, pp. 713-721
-
-
Flashner, Y.1
Gralla, J.D.2
-
79
-
-
0027510369
-
In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
-
Law S.M., Bellomy G.R., Schlax P.J., and Record Jr. M.T. In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo. J. Mol. Biol. 230 (1993) 161-173
-
(1993)
J. Mol. Biol.
, vol.230
, pp. 161-173
-
-
Law, S.M.1
Bellomy, G.R.2
Schlax, P.J.3
Record Jr., M.T.4
-
80
-
-
0003803285
-
-
University Science Books, Sausalito, CA
-
Bloomfield V.A., Crothers D.M., and Tinoco I. Nucleic Acids: Structures, Properties, and Functions (2000), University Science Books, Sausalito, CA
-
(2000)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
-
81
-
-
0025297716
-
Large-scale preparation of mononucleosomal DNA from calf thymus for biophysical studies
-
Wang L., Ferrari M., and Bloomfield V.A. Large-scale preparation of mononucleosomal DNA from calf thymus for biophysical studies. Biotechniques 9 24 (1990) 26-27
-
(1990)
Biotechniques
, vol.9
, Issue.24
, pp. 26-27
-
-
Wang, L.1
Ferrari, M.2
Bloomfield, V.A.3
-
82
-
-
52949109232
-
-
Ausubel, F.M. (1997). Curr. Protocols Mol. Biol. Suppl. 44. John Wiley & Sons, New York, NY.
-
Ausubel, F.M. (1997). Curr. Protocols Mol. Biol. Suppl. 44. John Wiley & Sons, New York, NY.
-
-
-
-
84
-
-
77957095245
-
Nonlinear least-squares analysis
-
Johnson M.L., and Frasier S.G. Nonlinear least-squares analysis. Methods Enzymol 117 (1985) 301-342
-
(1985)
Methods Enzymol
, vol.117
, pp. 301-342
-
-
Johnson, M.L.1
Frasier, S.G.2
-
85
-
-
0001576184
-
Partition functions of linear-chain molecules
-
Lifson S. Partition functions of linear-chain molecules. J. Chem. Phys. 40 (1964) 3705-3710
-
(1964)
J. Chem. Phys.
, vol.40
, pp. 3705-3710
-
-
Lifson, S.1
-
86
-
-
84987358412
-
Cooperative multisite binding to DNA
-
Schellman J.A. Cooperative multisite binding to DNA. Isr. J. Chem. 12 (1974) 219-238
-
(1974)
Isr. J. Chem.
, vol.12
, pp. 219-238
-
-
Schellman, J.A.1
-
87
-
-
0024730670
-
On the cooperative binding of large ligands to a one-dimensional homogeneous lattice: the generalized three-state lattice model
-
Bujalowski W., Lohman T.M., and Anderson C.F. On the cooperative binding of large ligands to a one-dimensional homogeneous lattice: the generalized three-state lattice model. Biopolymers 28 (1989) 1637-1643
-
(1989)
Biopolymers
, vol.28
, pp. 1637-1643
-
-
Bujalowski, W.1
Lohman, T.M.2
Anderson, C.F.3
-
88
-
-
0027394243
-
Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer
-
Clegg R.M., Murchie A.I., Zechel A., and Lilley D.M. Observing the helical geometry of double-stranded DNA in solution by fluorescence resonance energy transfer. Proc. Natl Acad. Sci. USA 90 (1993) 2994-2998
-
(1993)
Proc. Natl Acad. Sci. USA
, vol.90
, pp. 2994-2998
-
-
Clegg, R.M.1
Murchie, A.I.2
Zechel, A.3
Lilley, D.M.4
|