-
1
-
-
0025312950
-
Sequence-directed curvature of DNA
-
Hagerman P. Sequence-directed curvature of DNA Annu. Rev. Biochem. 59 1990 755 781
-
(1990)
Annu. Rev. Biochem.
, vol.59
, pp. 755-781
-
-
Hagerman, P.1
-
2
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
Smith S.B., Cui Y.J., and Bustamante C. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules Science 271 1996 795 799
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.J.2
Bustamante, C.3
-
4
-
-
77957240284
-
DNA curvature and flexibility in vitro and in vivo
-
Peters J.P., and Maher L.J. III DNA curvature and flexibility in vitro and in vivo Q. Rev. Biophys. 43 2010 23 63
-
(2010)
Q. Rev. Biophys.
, vol.43
, pp. 23-63
-
-
Peters, J.P.1
Iii, J.M.L.2
-
5
-
-
0000154034
-
Architectural elements in nucleoprotein complexes
-
Crothers D.M. Architectural elements in nucleoprotein complexes Curr. Biol. 3 1993 675 676
-
(1993)
Curr. Biol.
, vol.3
, pp. 675-676
-
-
Crothers, D.M.1
-
6
-
-
33847164986
-
Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity
-
Garcia H.G., Grayson P., Han L., Inamdar M., Kondev J., and Nelson P.C. Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity Biopolymers 85 2007 115 130
-
(2007)
Biopolymers
, vol.85
, pp. 115-130
-
-
Garcia, H.G.1
Grayson, P.2
Han, L.3
Inamdar, M.4
Kondev, J.5
Nelson, P.C.6
-
7
-
-
0027216519
-
The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures
-
Paull T.T., Haykinson M.J., and Johnson R.C. The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures Genes Dev. 7 1993 1521 1534 (Pubitemid 23234346)
-
(1993)
Genes and Development
, vol.7
, Issue.8
, pp. 1521-1534
-
-
Paull, T.T.1
Haykinson, M.J.2
Johnson, R.C.3
-
8
-
-
0028226799
-
DNA chaperones: A solution to a persistence problem?
-
DOI 10.1016/0092-8674(94)90306-9
-
Travers A.A., Ner S.S., and Churchill M.E.A. DNA chaperones: a solution to a persistence problem Cell 77 1994 167 169 (Pubitemid 24138613)
-
(1994)
Cell
, vol.77
, Issue.2
, pp. 167-169
-
-
Travers, A.A.1
Ner, S.S.2
Churchill, M.E.A.3
-
9
-
-
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 (Pubitemid 29512946)
-
(1999)
Journal of Bacteriology
, vol.181
, Issue.20
, pp. 6361-6370
-
-
Azam, T.A.1
Iwata, A.2
Nishimura, A.3
Ueda, S.4
Ishihama, A.5
-
10
-
-
0032731196
-
Twelve species of the nucleoid-associated protein from Escherichia coli: Sequence recognition specificity and DNA binding affinity
-
Azam T.A., and Ishihama A. Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity J. Biol. Chem. 274 1999 33105 33113 (Pubitemid 129535353)
-
(1999)
Journal of Biological Chemistry
, vol.274
, Issue.46
, pp. 33105-33113
-
-
Talukder, A.A.1
Ishihama, A.2
-
11
-
-
33750527566
-
The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective
-
DOI 10.1016/j.jsb.2006.05.006, PII S1047847706001614
-
Luijsterburg M.S., Noom M.C., Wuite G.J.L., 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 (Pubitemid 44666444)
-
(2006)
Journal of Structural Biology
, vol.156
, Issue.2
, pp. 262-272
-
-
Luijsterburg, M.S.1
Noom, M.C.2
Wuite, G.J.L.3
Dame, R.Th.4
-
13
-
-
0025202249
-
DNA looping and unlooping by AraC protein
-
Lobell R.B., and Schleif R.F. DNA looping and unlooping by AraC protein Science 250 1990 528 532 (Pubitemid 120031777)
-
(1990)
Science
, vol.250
, Issue.4980
, pp. 528-532
-
-
Lobell, R.B.1
Schleif, R.F.2
-
15
-
-
15744393452
-
DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
-
DOI 10.1016/j.gde.2005.02.005, Chromosomes and Expression Mechanisms
-
Vilar J.M., and Saiz L. DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise Curr. Opin. Genet. Dev. 15 2005 136 144 (Pubitemid 40410661)
-
(2005)
Current Opinion in Genetics and Development
, vol.15
, Issue.2
, pp. 136-144
-
-
Vilar, J.M.G.1
Saiz, L.2
-
17
-
-
0041312645
-
Flexible DNA bending in HU-DNA cocrystal structures
-
DOI 10.1093/emboj/cdg351
-
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 (Pubitemid 36898351)
-
(2003)
EMBO Journal
, vol.22
, Issue.14
, pp. 3749-3760
-
-
Swinger, K.K.1
Lemberg, K.M.2
Zhang, Y.3
Rice, P.A.4
-
18
-
-
0036404246
-
The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding
-
DOI 10.1016/S0022-2836(02)00938-5
-
Masse J.E., Wong B., Yen Y.M., Allain F.H., Johnson R.C., and Feigon J. The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding J. Mol. Biol. 323 2002 263 284 (Pubitemid 35283691)
-
(2002)
Journal of Molecular Biology
, vol.323
, Issue.2
, pp. 263-284
-
-
Masse, J.E.1
Wong, B.2
Yen, Y.-M.3
Allain, F.H.-T.4
Johnson, R.C.5
Feigon, J.6
-
19
-
-
33745242847
-
Structure of a Complex of Tandem HMG Boxes and DNA
-
DOI 10.1016/j.jmb.2006.04.059, PII S0022283606005535
-
Stott K., Tang G.S., Lee K.B., and Thomas J.O. Structure of a complex of tandem HMG boxes and DNA J. Mol. Biol. 360 2006 90 104 (Pubitemid 43927811)
-
(2006)
Journal of Molecular Biology
, vol.360
, Issue.1
, pp. 90-104
-
-
Stott, K.1
Tang, G.S.F.2
Lee, K.-B.3
Thomas, J.O.4
-
20
-
-
19444387811
-
Bacterial repression loops require enhanced DNA flexibility
-
DOI 10.1016/j.jmb.2005.04.035, PII S0022283605004559
-
Becker N.A., Kahn J.D., and Maher L.J. III Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 349 2005 716 730 (Pubitemid 40725950)
-
(2005)
Journal of Molecular Biology
, vol.349
, Issue.4
, pp. 716-730
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
21
-
-
34547642985
-
Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
-
DOI 10.1093/nar/gkm419
-
Becker N.A., Kahn J.D., and Maher L.J. III Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli Nucleic Acids Res. 35 2007 3988 4000 (Pubitemid 47244620)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.12
, pp. 3988-4000
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
22
-
-
47249091433
-
Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation
-
DOI 10.1093/nar/gkn353
-
Becker N.A., Kahn J.D., and Maher L.J. III Eukaryotic HMGB proteins as replacements for HU in E. coli repression loop formation Nucleic Acids Res. 36 2008 4009 4021 (Pubitemid 351984816)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.12
, pp. 4009-4021
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
23
-
-
23244443772
-
Dual binding modes for an HMG domain from human HMGB2 on DNA
-
DOI 10.1529/biophysj.104.052068
-
McCauley M., Hardwidge P.R., Maher L.J. III, and Williams M.C. Dual binding modes for an HMG domain from human HMGB2 on DNA Biophys. J. 89 2005 353 364 (Pubitemid 41098290)
-
(2005)
Biophysical Journal
, vol.89
, Issue.1
, pp. 353-364
-
-
McCauley, M.1
Hardwidge, P.R.2
Maher III, L.J.3
Williams, M.C.4
-
24
-
-
35748980855
-
HMGB Binding to DNA: Single and Double Box Motifs
-
DOI 10.1016/j.jmb.2007.09.073, PII S0022283607012727
-
McCauley M.J., Zimmerman J., Maher L.J. III, and Williams M.C. HMGB binding to DNA: single and double box motifs J. Mol. Biol. 374 2007 993 1004 (Pubitemid 350052092)
-
(2007)
Journal of Molecular Biology
, vol.374
, Issue.4
, pp. 993-1004
-
-
McCauley, M.J.1
Zimmerman, J.2
Maher III, L.J.3
Williams, M.C.4
-
25
-
-
0028970118
-
DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B
-
Paull T.T., and Johnson R.C. DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B J. Biol. Chem. 270 1995 8744 8754
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 8744-8754
-
-
Paull, T.T.1
Johnson, R.C.2
-
26
-
-
0034815596
-
HMG proteins and DNA flexibility in transcription activation
-
DOI 10.1128/MCB.21.19.6598-6605.2001
-
Ross E.D., Hardwidge P.R., and Maher L.J. III HMG proteins and DNA flexibility in transcription activation Mol. Cell. Biol. 21 2001 6598 6605 (Pubitemid 32927426)
-
(2001)
Molecular and Cellular Biology
, vol.21
, Issue.19
, pp. 6598-6605
-
-
Ross, E.D.1
Hardwidge, P.R.2
Maher III, L.J.3
-
27
-
-
0034708330
-
DNA constraints on transcription activation in vitro
-
Ross E.D. DNA constraints on transcription activation in vitro J. Mol. Biol. 297 2000 321 334
-
(2000)
J. Mol. Biol.
, vol.297
, pp. 321-334
-
-
Ross, E.D.1
-
28
-
-
0032562599
-
DNA bending by the chromosomal protein HMG1 and its high mobility group box domains: Effect of flanking sequences
-
Stros M. DNA bending by the chromosomal protein HMG1 and its high mobility group box domains. Effect of flanking sequences J. Biol. Chem. 273 1998 10355 10361 (Pubitemid 28227642)
-
(1998)
Journal of Biological Chemistry
, vol.273
, Issue.17
, pp. 10355-10361
-
-
Stros, M.1
-
29
-
-
0343794843
-
Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli
-
Rouviere-Yaniv J., and Gros F. Characterization of a novel, low-molecular-weight DNA-binding protein from Escherichia coli Proc. Natl Acad. Sci. USA 72 1975 3428 3432
-
(1975)
Proc. Natl Acad. Sci. USA
, vol.72
, pp. 3428-3432
-
-
Rouviere-Yaniv, J.1
Gros, F.2
-
30
-
-
0018405881
-
E. coli DNA binding protein HU forms nucleosome like 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 (Pubitemid 9230307)
-
(1979)
Cell
, vol.17
, Issue.2
, pp. 265-274
-
-
Rouviere-Yaniv, J.1
Yaniv, M.2
Germond, J.E.3
-
31
-
-
14244263426
-
Major nucleoid proteins in the structure and function of the Escherichia coli chromosome
-
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 N.P. Higgins, 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
-
32
-
-
1342324028
-
IHF and HU: Flexible architects of bent DNA
-
DOI 10.1016/j.sbi.2003.12.003
-
Swinger K.K., and Rice P.A. IHF and HU: flexible architects of bent DNA Curr. Opin. Struct. Biol. 14 2004 28 35 (Pubitemid 38249589)
-
(2004)
Current Opinion in Structural Biology
, vol.14
, Issue.1
, pp. 28-35
-
-
Swinger, K.K.1
Rice, P.A.2
-
33
-
-
0035875344
-
Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips
-
Krylov A.S., Zasedateleva O.A., Prokopenko D.V., Rouviere-Yaniv J., and Mirzabekov A.D. Massive parallel analysis of the binding specificity of histone-like protein HU to single- and double-stranded DNA with generic oligodeoxyribonucleotide microchips Nucleic Acids Res. 29 2001 2654 2660 (Pubitemid 32600323)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.12
, pp. 2654-2660
-
-
Krylov, A.S.1
Zasedateleva, O.A.2
Prokopenko, D.V.3
Rouviere-Yaniv, J.4
Mirzabekov, A.D.5
-
34
-
-
0028136642
-
DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA
-
DOI 10.1006/jmbi.1994.1563
-
Bonnefoy E., Takahashi M., and Yaniv J.R. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA J. Mol. Biol. 242 1994 116 129 (Pubitemid 24298527)
-
(1994)
Journal of Molecular Biology
, vol.242
, Issue.2
, pp. 116-129
-
-
Bonnefoy, E.1
Takahashi, M.2
Yaniv, J.R.3
-
36
-
-
0032945039
-
Role of HU and DNA supercoiling in transcription repression: Specialized nucleoprotein repression complex at gal promoters in Escherichia coli
-
DOI 10.1046/j.1365-2958.1999.01186.x
-
Lewis D.E., Geanacopoulos M., and Adhya S. Role of HU and DNA supercoiling in transcription repression: specialized nucleoprotein repression complex at gal promoters in Escherichia coli Mol. Microbiol. 31 1999 451 461 (Pubitemid 29046088)
-
(1999)
Molecular Microbiology
, vol.31
, Issue.2
, pp. 451-461
-
-
Lewis, D.E.A.1
Geanacopoulos, M.2
Adhya, S.3
-
37
-
-
0027503254
-
Protein HU binds specifically to kinked DNA
-
DOI 10.1111/j.1365-2958.1993.tb01126.x
-
Pontiggia A., Negri A., Beltrame M., and Bianchi M.E. Protein HU binds specifically to kinked DNA Mol. Microbiol. 7 1993 343 350 (Pubitemid 23051199)
-
(1993)
Molecular Microbiology
, vol.7
, Issue.3
, pp. 343-350
-
-
Pontiggia, A.1
Negri, A.2
Beltrame, M.3
Bianchi, M.E.4
-
38
-
-
3342959174
-
Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes
-
DOI 10.1016/j.jmb.2004.06.023, PII S0022283604006916
-
Sagi D., Friedman N., Vorgias C., Oppenheim A.B., and Stavans J. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes J. Mol. Biol. 341 2004 419 428 (Pubitemid 38987779)
-
(2004)
Journal of Molecular Biology
, vol.341
, Issue.2
, pp. 419-428
-
-
Sagi, D.1
Friedman, N.2
Vorgias, C.3
Oppenheim, A.B.4
Stavans, J.5
-
39
-
-
7244245362
-
Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes
-
DOI 10.1021/bi048428o
-
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 (Pubitemid 39431070)
-
(2004)
Biochemistry
, vol.43
, Issue.43
, pp. 13867-13874
-
-
Skoko, D.1
Wong, B.2
Johnson, R.C.3
Marko, J.F.4
-
40
-
-
2342454974
-
Dual architectural roles of HU: Formation of flexible hinges and rigid filaments
-
DOI 10.1073/pnas.0308230101
-
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 (Pubitemid 38596427)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.18
, pp. 6969-6974
-
-
Van Noort, J.1
Verbrugge, S.2
Goosen, N.3
Dekker, C.4
Dame, R.T.5
-
41
-
-
0037452946
-
HU binding to bent DNA: A fluorescence resonance energy transfer and anisotropy study
-
DOI 10.1021/bi0264014
-
Wojtuszewski K., and Mukerji I. HU binding to bent DNA: a fluorescence resonance energy transfer and anisotropy study Biochemistry 42 2003 3096 3104 (Pubitemid 36331555)
-
(2003)
Biochemistry
, vol.42
, Issue.10
, pp. 3096-3104
-
-
Wojtuszewski, K.1
Mukerji, I.2
-
42
-
-
0030928287
-
Repressor induced site-specific binding of HU for transcriptional regulation
-
DOI 10.1093/emboj/16.12.3666
-
Aki T., and Adhya S. Repressor induced site-specific binding of HU for transcriptional regulation EMBO J. 16 1997 3666 3674 (Pubitemid 27250059)
-
(1997)
EMBO Journal
, vol.16
, Issue.12
, pp. 3666-3674
-
-
Aki, T.1
Adhya, S.2
-
43
-
-
0141482089
-
Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping
-
DOI 10.1073/pnas.2034851100
-
Lia G., Bensimon D., Croquette V., Allemand J.F., Dunlap D., and Lewis D.E. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping Proc. Natl Acad. Sci. USA 100 2003 11373 11377 (Pubitemid 37205942)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.20
, pp. 11373-11377
-
-
Lia, G.1
Bensimon, D.2
Croquette, V.3
Allemand, J.-F.4
Dunlap, D.5
Lewis, D.E.A.6
Adhya, S.7
Finzi, L.8
-
44
-
-
52949086418
-
DNA binding mode transitions of Escherichia coli HU(alphabeta): Evidence for formation of a bent DNA-protein complex on intact, linear duplex DNA
-
Koh J., Saecker R.M., and Record M.T. Jr DNA binding mode transitions of Escherichia coli HU(alphabeta): evidence for formation of a bent DNA-protein complex on intact, linear duplex DNA J. Mol. Biol. 383 2008 324 346
-
(2008)
J. Mol. Biol.
, vol.383
, pp. 324-346
-
-
Koh, J.1
Saecker, R.M.2
Record Jr., M.T.3
-
45
-
-
0029991026
-
Histone-like protein HU and bacterial DNA topology: Suppression of an HU deficiency by gyrase mutations
-
DOI 10.1006/jmbi.1996.0068
-
Malik M., Bensaid A., Rouviere-Yaniv J., and Drlica K. Histone-like protein HU and bacterial DNA topology: suppression of an HU deficiency by gyrase mutations J. Mol. Biol. 256 1996 66 76 (Pubitemid 26104210)
-
(1996)
Journal of Molecular Biology
, vol.256
, Issue.1
, pp. 66-76
-
-
Malik, M.1
Bensaid, A.2
Rouviere-Yaniv, J.3
Drlica, K.4
-
46
-
-
0028043678
-
Prokaryotic HU and eukaryotic HMG1: A kinked relationship
-
Bianchi M.E. Prokaryotic HU and eukaryotic HMG1: a kinked relationship Mol. Microbiol. 14 1994 1 5
-
(1994)
Mol. Microbiol.
, vol.14
, pp. 1-5
-
-
Bianchi, M.E.1
-
47
-
-
0033522480
-
Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding
-
DOI 10.1093/emboj/18.9.2563
-
Allain F.H., Yen Y.M., Masse J.E., Schultze P., Dieckmann T., Johnson R.C., and Feigon J. Solution structure of the HMG protein NHP6A and its interaction with DNA reveals the structural determinants for non-sequence-specific binding EMBO J. 18 1999 2563 2579 (Pubitemid 29213287)
-
(1999)
EMBO Journal
, vol.18
, Issue.9
, pp. 2563-2579
-
-
Allain, F.H.-T.1
Yen, Y.-M.2
Masse, J.E.3
Schultze, P.4
Dieckmann, T.5
Johnson, R.C.6
Feigon, J.7
-
48
-
-
0029563931
-
Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy
-
DOI 10.1021/bi00051a007
-
Hardman C.H., Broadhurst R.W., Raine A.R., Grasser K.D., Thomas J.O., and Laue E.D. Structure of the A-domain of HMG1 and its interaction with DNA as studied by heteronuclear three- and four-dimensional NMR spectroscopy Biochemistry 34 1995 16596 16607 (Pubitemid 26011782)
-
(1995)
Biochemistry
, vol.34
, Issue.51
, pp. 16596-16607
-
-
Hardman, C.H.1
Broadhurst, R.W.2
Raine, A.R.C.3
Grasser, K.D.4
Thomas, J.O.5
Laue, E.D.6
-
49
-
-
0034727674
-
Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA
-
He Q., Ohndorf U.M., and Lippard S.J. Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA Biochemistry 39 2000 14426 14435
-
(2000)
Biochemistry
, vol.39
, pp. 14426-14435
-
-
He, Q.1
Ohndorf, U.M.2
Lippard, S.J.3
-
50
-
-
0033617209
-
Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B
-
Jamieson E.R., Jacobson M.P., Barnes C.M., Chow C.S., and Lippard S.J. Structural and kinetic studies of a cisplatin-modified DNA icosamer binding to HMG1 domain B J. Biol. Chem. 274 1999 12346 12354
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 12346-12354
-
-
Jamieson, E.R.1
Jacobson, M.P.2
Barnes, C.M.3
Chow, C.S.4
Lippard, S.J.5
-
51
-
-
0037432325
-
Nature of full-length HMGB1 binding to cisplatin-modified DNA
-
DOI 10.1021/bi026972w
-
Jung Y., and Lippard S.J. Nature of full-length HMGB1 binding to cisplatin-modified DNA Biochemistry 42 2003 2664 2671 (Pubitemid 36330620)
-
(2003)
Biochemistry
, vol.42
, Issue.9
, pp. 2664-2671
-
-
Jung, Y.1
Lippard, S.J.2
-
52
-
-
0033578010
-
Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins
-
DOI 10.1038/21460
-
Ohndorf U.M., Rould M.A., He Q., Pabo C.O., and Lippard S.J. Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins Nature 399 1999 708 712 (Pubitemid 29289069)
-
(1999)
Nature
, vol.399
, Issue.6737
, pp. 708-712
-
-
Ohndorf, U.-M.1
Rould, M.A.2
He, Q.3
Pabo, C.O.4
Lippard, S.J.5
-
53
-
-
0027414641
-
Structure of the HMG box motif in the B-domain of HMG1
-
Weir H.M., Kraulis P.J., Hill C.S., Raine A.R.C., Laue E.D., and Thomas J.O. Structure of the HMG box motif in the B-domain of HMG1 EMBO J. 12 1993 1311 1319 (Pubitemid 23112786)
-
(1993)
EMBO Journal
, vol.12
, Issue.4
, pp. 1311-1319
-
-
Weir, H.M.1
Kraulis, P.J.2
Hill, C.S.3
Raine, A.R.C.4
Laue, E.D.5
Thomas, J.O.6
-
54
-
-
0035281548
-
HMG1 and 2, and related 'architectural' DNA-binding proteins
-
DOI 10.1016/S0968-0004(01)01801-1, PII S0968000401017984
-
Thomas J.O., and Travers A.A. HMG1 and 2, and related 'architectural' DNA-binding proteins Trends Biochem. Sci. 26 2001 167 174 (Pubitemid 32197576)
-
(2001)
Trends in Biochemical Sciences
, vol.26
, Issue.3
, pp. 167-174
-
-
Thomas, J.O.1
Travers, A.A.2
-
55
-
-
4644219557
-
DNA binding and bending by HMG boxes: Energetic determinants of specificity
-
DOI 10.1016/j.jmb.2004.08.035, PII S0022283604010150
-
Dragan A.I., Read C.M., Makeyeva E.N., Milgotina E.I., Churchill M.E., Crane-Robinson C., and Privalov P.L. DNA binding and bending by HMG boxes: energetic determinants of specificity J. Mol. Biol. 343 2004 371 393 (Pubitemid 39296872)
-
(2004)
Journal of Molecular Biology
, vol.343
, Issue.2
, pp. 371-393
-
-
Dragan, A.I.1
Read, C.M.2
Makeyeva, E.N.3
Milgotina, E.I.4
Churchill, M.E.A.5
Crane-Robinson, C.6
Privalov, P.L.7
-
56
-
-
0033554438
-
DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer
-
Lorenz M., Hillisch A., Payet D., Buttinelli M., Travers A., and Diekmann S. DNA bending induced by high mobility group proteins studied by fluorescence resonance energy transfer Biochemistry 38 1999 12150 12158
-
(1999)
Biochemistry
, vol.38
, pp. 12150-12158
-
-
Lorenz, M.1
Hillisch, A.2
Payet, D.3
Buttinelli, M.4
Travers, A.5
Diekmann, S.6
-
57
-
-
0033485515
-
The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition
-
Murphy F., Sweet R.M., and Churchill M.E. The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition EMBO J. 18 1999 6610 6618
-
(1999)
EMBO J.
, vol.18
, pp. 6610-6618
-
-
Murphy, F.1
Sweet, R.M.2
Churchill, M.E.3
-
58
-
-
0000545475
-
Ring-closure probabilities for twisted wormlike chains. Application to DNA
-
Shimada J., and Yamakawa H. Ring-closure probabilities for twisted wormlike chains. Application to DNA Macromolecules 17 1984 689 698
-
(1984)
Macromolecules
, vol.17
, pp. 689-698
-
-
Shimada, J.1
Yamakawa, H.2
-
59
-
-
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
-
60
-
-
78049422210
-
Modulation of HU-DNA interactions by salt concentration and applied force
-
Xiao B., Johnson R.C., and Marko J.F. Modulation of HU-DNA interactions by salt concentration and applied force Nucleic Acids Res. 38 2010 5176 6185
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 5176-6185
-
-
Xiao, B.1
Johnson, R.C.2
Marko, J.F.3
-
61
-
-
0032471965
-
Flexing DNA: HMG-box proteins and their partners
-
DOI 10.1086/302170
-
Bianchi M.E., and Beltrame M. Flexing DNA: HMG-box proteins and their partners Am. J. Hum. Genet. 63 1998 1573 1577 (Pubitemid 30415718)
-
(1998)
American Journal of Human Genetics
, vol.63
, Issue.6
, pp. 1573-1577
-
-
Bianchi, M.E.1
Beltrame, M.2
-
62
-
-
0024584528
-
Specific recognition of cruciform DNA by nuclear protein HMGl
-
Bianchi M.E., Beltrame M., and Paonessa G. Specific recognition of cruciform DNA by nuclear protein HMG1 Science 243 1989 1056 1059 (Pubitemid 19072581)
-
(1989)
Science
, vol.243
, Issue.4894
, pp. 1056-1059
-
-
Bianchi, M.E.1
Beltrame, M.2
Paonessa, G.3
-
63
-
-
0033064093
-
Interactions of high mobility group box proteins with DNA and chromatin
-
DOI 10.1016/S0076-6879(99)04009-4
-
Churchill M.E., Changela A., Dow L.K., and Krieg A.J. Interactions of high mobility group box proteins with DNA and chromatin Methods Enzymol. 304 1999 99 133 (Pubitemid 29268880)
-
(1999)
Methods in Enzymology
, vol.304
, pp. 99-133
-
-
Churchill, M.E.A.1
Changela, A.2
Dow, L.K.3
Krieg, A.J.4
-
64
-
-
46349084382
-
Transient HMGB protein interactions with B-DNA duplexes and complexes
-
Zimmerman J., and Maher L.J. III Transient HMGB protein interactions with B-DNA duplexes and complexes Biochem. Biophys. Res. Commun. 371 2008 79 84
-
(2008)
Biochem. Biophys. Res. Commun.
, vol.371
, pp. 79-84
-
-
Zimmerman, J.1
Iii, J.M.L.2
-
65
-
-
0034081137
-
Mechanism for specificity by HMG-1 in enhanceosome assembly
-
DOI 10.1128/MCB.20.12.4359-4370.2000
-
Ellwood K.B., Yen Y.M., Johnson R.C., and Carey M. Mechanism for specificity by HMG-1 in enhanceosome assembly Mol. Cell. Biol. 20 2000 4359 4370 (Pubitemid 30346630)
-
(2000)
Molecular and Cellular Biology
, vol.20
, Issue.12
, pp. 4359-4370
-
-
Ellwood, K.B.1
Yen, Y.-M.2
Johnson, R.C.3
Carey, M.4
-
66
-
-
0036293430
-
Contribution of the intrinsic curvature to measured DNA persistence length
-
DOI 10.1006/jmbi.2001.5366
-
Vologodskaia M., and Vologodskii A. Contribution of the intrinsic curvature to measured DNA persistence length J. Mol. Biol. 317 2002 205 213 (Pubitemid 34722188)
-
(2002)
Journal of Molecular Biology
, vol.317
, Issue.2
, pp. 205-213
-
-
Vologodskaia, M.1
Vologodskii, A.2
-
67
-
-
78650961101
-
Quantitative methods for measuring DNA flexibility in vitro and in vivo
-
Peters J.P., Becker N.A., Rueter E.M., Bajzer Z., Kahn J.D., and Maher L.J. Quantitative methods for measuring DNA flexibility in vitro and in vivo Methods Enzymol. 488 2011 287 335
-
(2011)
Methods Enzymol.
, vol.488
, pp. 287-335
-
-
Peters, J.P.1
Becker, N.A.2
Rueter, E.M.3
Bajzer, Z.4
Kahn, J.D.5
Maher, L.J.6
-
68
-
-
50249126024
-
Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations
-
Czapla L., Swigon D., and Olson W.K. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations J. Mol. Biol. 382 2008 353 370
-
(2008)
J. Mol. Biol.
, vol.382
, pp. 353-370
-
-
Czapla, L.1
Swigon, D.2
Olson, W.K.3
-
69
-
-
0035957055
-
HU binding to DNA: Evidence for multiple complex formation and dna bending
-
DOI 10.1021/bi002382r
-
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 2588 2598 (Pubitemid 32171734)
-
(2001)
Biochemistry
, vol.40
, Issue.8
, pp. 2588-2598
-
-
Wojtuszewski, K.1
Hawkins, M.E.2
Cole, J.L.3
Mukerji, I.4
-
70
-
-
1542345568
-
Effects of HU Binding on the Equilibrium Cyclization of Mismatched, Curved, and Normal DNA
-
Arthanari H., Wojtuszewski K., Mukerji I., and Bolton P.H. Effects of HU binding on the equilibrium cyclization of mismatched, curved, and normal DNA Biophys. J. 86 2004 1625 1631 (Pubitemid 38295596)
-
(2004)
Biophysical Journal
, vol.86
, Issue.3
, pp. 1625-1631
-
-
Arthanari, H.1
Wojtuszewski, K.2
Mukerji, I.3
Bolton, P.H.4
-
71
-
-
33847348438
-
Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines
-
DOI 10.1093/nar/gkl1093
-
Sarkar T., Vitoc I., Mukerji I., and Hud N.V. Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines Nucleic Acids Res. 35 2007 951 961 (Pubitemid 46344720)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.3
, pp. 951-961
-
-
Sarkar, T.1
Vitoc, I.2
Mukerji, I.3
Hud, N.V.4
-
72
-
-
0037592865
-
The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity
-
DOI 10.1093/nar/gkg389
-
Klass J., Murphy F.V., Fouts S., Serenil M., Changela A., Siple J., and Churchill M.E. The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity Nucleic Acids Res. 31 2003 2852 2864 (Pubitemid 37442129)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.11
, pp. 2852-2864
-
-
Klass, J.1
Murphy IV, F.V.2
Fouts, S.3
Serenil, M.4
Changela, A.5
Siple, J.6
Churchill, M.E.A.7
-
73
-
-
0018196563
-
Cooperative and noncooperative binding of large ligands to a finite one-dimensional lattice. A model for ligand-oligonucleotide interactions
-
DOI 10.1016/0301-4622(78)80015-5
-
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 (Pubitemid 9053702)
-
(1978)
Biophysical Chemistry
, vol.8
, Issue.4
, pp. 327-339
-
-
Epstein, I.R.1
-
74
-
-
17244362931
-
Cyclization of short DNA fragments and bending fluctuations of the double helix
-
DOI 10.1073/pnas.0500983102
-
Du Q., Smith C., Shiffeldrim N., Vologodskaia M., and Vologodskii A. Cyclization of short DNA fragments and bending fluctuations of the double helix Proc. Natl Acad. Sci. USA 102 2005 5397 5402 (Pubitemid 40530269)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.15
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Shiffeldrim, N.3
Vologodskaia, M.4
Vologodskii, A.5
-
75
-
-
33749243974
-
Sequence-dependent effects in the cyclization of short DNA
-
Czapla L., Swigon D., and Olson W. Sequence-dependent effects in the cyclization of short DNA J. Chem. Theory Comput. 2 2006 685 695
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 685-695
-
-
Czapla, L.1
Swigon, D.2
Olson, W.3
-
76
-
-
4444221565
-
UCSF Chimera-A visualization system for exploratory research and analysis
-
Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., and Ferrin T.E. UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
77
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
DOI 10.1093/nar/gkg680
-
Lu X.J., and Olson W.K. 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucleic Acids Res. 31 2003 5108 5121 (Pubitemid 37441878)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.17
, pp. 5108-5121
-
-
Lu, X.-J.1
Olson, W.K.2
-
78
-
-
50349085962
-
3DNA: A versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures
-
Lu X.J., and Olson W.K. 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures Nat. Protoc. 3 2008 1213 1227
-
(2008)
Nat. Protoc.
, vol.3
, pp. 1213-1227
-
-
Lu, X.J.1
Olson, W.K.2
-
79
-
-
0028950413
-
HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG
-
Churchill M.E., Jones D.N., Glaser T., Hefner H., Searles M.A., and Travers A.A. HMG-D is an architecture-specific protein that preferentially binds to DNA containing the dinucleotide TG EMBO J. 14 1995 1264 1275
-
(1995)
EMBO J.
, vol.14
, pp. 1264-1275
-
-
Churchill, M.E.1
Jones, D.N.2
Glaser, T.3
Hefner, H.4
Searles, M.A.5
Travers, A.A.6
-
80
-
-
0027283372
-
Histones H1 and H5 interact preferentially with crossovers of double- helical DNA
-
Krylov D., Leuba S., von Holde K., and Zlatanova J. Histones H1 and H5 interact preferentially with crossovers of double-helical DNA Proc. Natl Acad. Sci. USA 90 1993 5052 5056 (Pubitemid 23182974)
-
(1993)
Proceedings of the National Academy of Sciences of the United States of America
, vol.90
, Issue.11
, pp. 5052-5056
-
-
Krylov, D.1
Leuba, S.2
Van Holde, K.3
Zlatanova, J.4
|