-
1
-
-
0030161428
-
Flexible response: DNA supercoiling, transcription and bacterial adaptation to environmental stress
-
Dorman,C.J. (1996) Flexible response: DNA supercoiling, transcription and bacterial adaptation to environmental stress. Trends Microbiol., 4, 214-216.
-
(1996)
Trends Microbiol.
, vol.4
, pp. 214-216
-
-
Dorman, C.J.1
-
2
-
-
13444288385
-
DNA supercoiling - A global transcriptional regulator for enterobacterial growth?
-
Travers,A. and Muskhelishvili,G. (2005) DNA supercoiling - a global transcriptional regulator for enterobacterial growth? Nature Rev. Microbiol., 3, 157-169.
-
(2005)
Nature Rev. Microbiol.
, vol.3
, pp. 157-169
-
-
Travers, A.1
Muskhelishvili, G.2
-
3
-
-
11344266685
-
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
-
Peter,B.J., Arsuaga,J., Breier,A.M., Khodursky,A.B., Brown,P.O. and Cozzarelli,N.R. (2004) Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol., 5, R87.
-
(2004)
Genome Biol.
, vol.5
-
-
Peter, B.J.1
Arsuaga, J.2
Breier, A.M.3
Khodursky, A.B.4
Brown, P.O.5
Cozzarelli, N.R.6
-
4
-
-
0033518119
-
Influence of promoter DNA topology on sequence-specific DNA binding and transactivation by tumor suppressor p53
-
Kim,E., Rohaly,G., Heinrichs,S., Gimnopoulos,D., Meissner,H. and Deppert,W. (1999) Influence of promoter DNA topology on sequence-specific DNA binding and transactivation by tumor suppressor p53. Oncogene, 18, 7310-7318.
-
(1999)
Oncogene
, vol.18
, pp. 7310-7318
-
-
Kim, E.1
Rohaly, G.2
Heinrichs, S.3
Gimnopoulos, D.4
Meissner, H.5
Deppert, W.6
-
5
-
-
0018843977
-
Phase variation: Genetic analysis of switching mutants
-
Silverman,M. and Simon,M. (1980) Phase variation: Genetic analysis of switching mutants. Cell, 19, 845-854.
-
(1980)
Cell
, vol.19
, pp. 845-854
-
-
Silverman, M.1
Simon, M.2
-
6
-
-
0024411476
-
DNA-binding properties of the Hin recombinase
-
Glasgow,A.C., Bruist,M.F. and Simon,M.I. (1989) DNA-binding properties of the Hin recombinase. J. Biol. Chem., 264, 10072-10082.
-
(1989)
J. Biol. Chem.
, vol.264
, pp. 10072-10082
-
-
Glasgow, A.C.1
Bruist, M.F.2
Simon, M.I.3
-
7
-
-
0028118764
-
Hin recombinase bound to DNA: The origin of specificity in major and minor groove interactions
-
Feng,J.A., Johnson,R.C. and Dickerson,R.E. (1994) Hin recombinase bound to DNA: The origin of specificity in major and minor groove interactions. Science, 263, 348-355.
-
(1994)
Science
, vol.263
, pp. 348-355
-
-
Feng, J.A.1
Johnson, R.C.2
Dickerson, R.E.3
-
8
-
-
0037083987
-
Testing water-mediated DNA recognition by the Hin recombinase
-
Chiu,T.K., Sohn,C., Dickerson,R.E. and Johnson,R.C. (2002) Testing water-mediated DNA recognition by the Hin recombinase. EMBO J., 21, 801-814.
-
(2002)
EMBO J.
, vol.21
, pp. 801-814
-
-
Chiu, T.K.1
Sohn, C.2
Dickerson, R.E.3
Johnson, R.C.4
-
9
-
-
0026645808
-
The effects of symmetrical recombination site hixC on Hin recombinase function
-
Lim,H.M., Hughes,K.T. and Simon,M.I. (1992) The effects of symmetrical recombination site hixC on Hin recombinase function. J. Biol. Chem., 267, 11183-11190.
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 11183-11190
-
-
Lim, H.M.1
Hughes, K.T.2
Simon, M.I.3
-
10
-
-
0024343548
-
Intermediates in Hin-mediated DNA inversion: A role for Fis and the recombinational enhancer in the strand exchange reaction
-
Johnson,R.C. and Bruist,M.F. (1989) Intermediates in Hin-mediated DNA inversion: A role for Fis and the recombinational enhancer in the strand exchange reaction. EMBO J., 8, 1581-1590.
-
(1989)
EMBO J.
, vol.8
, pp. 1581-1590
-
-
Johnson, R.C.1
Bruist, M.F.2
-
11
-
-
0004831176
-
Hin-mediated inversion on positively supercoiled DNA
-
Lim,H.M., Lee,H.J., Jaxel,C. and Nadal,M. (1997) Hin-mediated inversion on positively supercoiled DNA. J. Biol. Chem., 272, 18434-18439.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 18434-18439
-
-
Lim, H.M.1
Lee, H.J.2
Jaxel, C.3
Nadal, M.4
-
12
-
-
0029968460
-
Trinucleotide repeats in neurogenetic disorders
-
Paulson,H.L. and Fischbeck,K.H. (1996) Trinucleotide repeats in neurogenetic disorders. Annu. Rev. Neurosci., 19, 79-107.
-
(1996)
Annu. Rev. Neurosci.
, vol.19
, pp. 79-107
-
-
Paulson, H.L.1
Fischbeck, K.H.2
-
13
-
-
0022006792
-
Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer
-
Johnson,R.C. and Simon,M.I. (1985) Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell, 41, 781-791.
-
(1985)
Cell
, vol.41
, pp. 781-791
-
-
Johnson, R.C.1
Simon, M.I.2
-
14
-
-
0029400480
-
NMRPipe: A multidimensional spectral processing system based on UNIX pipes
-
Delaglio,F., Grzesiek,S., Vuister,G.W., Zhu,G., Pfeifer,J. and Bax,A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR, 6, 277-293.
-
(1995)
J. Biomol. NMR
, vol.6
, pp. 277-293
-
-
Delaglio, F.1
Grzesiek, S.2
Vuister, G.W.3
Zhu, G.4
Pfeifer, J.5
Bax, A.6
-
15
-
-
0024345290
-
Two-dimensional nuclear Overhauser effect: Complete relaxation matrix analysis
-
Borgias,B.A. and James,T.L. (1989) Two-dimensional nuclear Overhauser effect: Complete relaxation matrix analysis. Methods Enzymol., 176, 169-183.
-
(1989)
Methods Enzymol.
, vol.176
, pp. 169-183
-
-
Borgias, B.A.1
James, T.L.2
-
16
-
-
0035742338
-
Measurement of homonuclear proton couplings from regular 2D COSY spectra
-
Delaglio,F., Wu,Z. and Bax,A. (2001) Measurement of homonuclear proton couplings from regular 2D COSY spectra. J. Magn. Reson., 149, 276-281.
-
(2001)
J. Magn. Reson.
, vol.149
, pp. 276-281
-
-
Delaglio, F.1
Wu, Z.2
Bax, A.3
-
17
-
-
0013293280
-
The Xplor-NIH NMR molecular structure determination package
-
Schwieters,C.D., Kuszewski,J.J., Tjandra,N. and Clore,G.M. (2003) The Xplor-NIH NMR molecular structure determination package. J. Magn. Reson., 160, 65-73.
-
(2003)
J. Magn. Reson.
, vol.160
, pp. 65-73
-
-
Schwieters, C.D.1
Kuszewski, J.J.2
Tjandra, N.3
Clore, G.M.4
-
18
-
-
0034794444
-
Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions
-
Kuszewski,J., Schwieters,C. and Clore,G.M. (2001) Improving the accuracy of NMR structures of DNA by means of a database potential of mean force describing base-base positional interactions. J. Am. Chem. Soc., 123, 3903-3918.
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3903-3918
-
-
Kuszewski, J.1
Schwieters, C.2
Clore, G.M.3
-
19
-
-
0024058085
-
The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids
-
Lavery,R. and Sklenar,H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
20
-
-
0242396923
-
3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures
-
Lu,X.J. and Olson,W.K. (2003) 3DNA: A software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 5108-5121
-
-
Lu, X.J.1
Olson, W.K.2
-
21
-
-
0034682870
-
A-Tract bending: Insights into experimental structures by computational models
-
Strahs,D. and Schlick,T. (2000) A-Tract bending: Insights into experimental structures by computational models. J. Mol. Biol., 301, 643-663.
-
(2000)
J. Mol. Biol.
, vol.301
, pp. 643-663
-
-
Strahs, D.1
Schlick, T.2
-
22
-
-
0029881007
-
MOLMOL: A program for display and analysis of macromolecular structures
-
29-32
-
Koradi,R., Billeter,M. and Wuthrich,K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph., 14, 51-55, 29-32.
-
(1996)
J. Mol. Graph.
, vol.14
, pp. 51-55
-
-
Koradi, R.1
Billeter, M.2
Wuthrich, K.3
-
23
-
-
0028864424
-
Studies of base pair kinetics by NMR measurement of proton exchange
-
Gueron,M. and Leroy,J.L. (1995) Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol., 261, 383-413.
-
(1995)
Methods Enzymol.
, vol.261
, pp. 383-413
-
-
Gueron, M.1
Leroy, J.L.2
-
24
-
-
0041829746
-
DNA curvature in solution measured by fluorescence resonance energy transfer
-
Toth,K., Sauermann,V. and Langowski,J. (1998) DNA curvature in solution measured by fluorescence resonance energy transfer. Biochemistry, 37, 8173-8179.
-
(1998)
Biochemistry
, vol.37
, pp. 8173-8179
-
-
Toth, K.1
Sauermann, V.2
Langowski, J.3
-
25
-
-
0024059137
-
Phase variation in Salmonella: Analysis of Hin recombinase and hix recombination site interaction in vivo
-
Hughes,K.T., Youderian,P. and Simon,M.I. (1988) Phase variation in Salmonella: Analysis of Hin recombinase and hix recombination site interaction in vivo. Genes Dev., 2, 937-948.
-
(1988)
Genes Dev.
, vol.2
, pp. 937-948
-
-
Hughes, K.T.1
Youderian, P.2
Simon, M.I.3
-
26
-
-
0035211048
-
Effects of dimer interface mutations in Hin recombinase on DNA binding and recombination
-
Lee,H.J., Lee,S.Y., Lee,H. and Lim,H.M. (2001) Effects of dimer interface mutations in Hin recombinase on DNA binding and recombination. Mol. Genet. Genomics, 266, 598-607.
-
(2001)
Mol. Genet. Genomics
, vol.266
, pp. 598-607
-
-
Lee, H.J.1
Lee, S.Y.2
Lee, H.3
Lim, H.M.4
-
28
-
-
0028931709
-
B-DNA twisting correlates with base-pair morphology
-
Gorin,A.A., Zhurkin,V.B. and Olson,W.K. (1995) B-DNA twisting correlates with base-pair morphology. J. Mol. Biol., 247, 34-48.
-
(1995)
J. Mol. Biol.
, vol.247
, pp. 34-48
-
-
Gorin, A.A.1
Zhurkin, V.B.2
Olson, W.K.3
-
29
-
-
0025914242
-
Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees
-
Schultz,S.C., Shields,G.C. and Steitz,T.A. (1991) Crystal structure of a CAP-DNA complex: The DNA is bent by 90 degrees. Science, 253, 1001-1007.
-
(1991)
Science
, vol.253
, pp. 1001-1007
-
-
Schultz, S.C.1
Shields, G.C.2
Steitz, T.A.3
-
30
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
Kim,Y., Geiger,J.H., Hahn,S. and Sigler,P.B. (1993) Crystal structure of a yeast TBP/TATA-box complex. Nature, 365, 512-520.
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Hahn, S.3
Sigler, P.B.4
-
31
-
-
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
-
32
-
-
0000777707
-
Energetic coupling between DNA bending and base pair opening
-
Ramstein,J. and Lavery,R. (1988) Energetic coupling between DNA bending and base pair opening. Proc. Natl Acad. Sci. USA, 85, 7231-7235.
-
(1988)
Proc. Natl Acad. Sci. USA
, vol.85
, pp. 7231-7235
-
-
Ramstein, J.1
Lavery, R.2
-
33
-
-
0036306349
-
Bending and flexibility of methylated and unmethylated EcoRI DNA
-
Nathan,D. and Crothers,D.M. (2002) Bending and flexibility of methylated and unmethylated EcoRI DNA. J. Mol. Biol., 316, 7-17.
-
(2002)
J. Mol. Biol.
, vol.316
, pp. 7-17
-
-
Nathan, D.1
Crothers, D.M.2
-
34
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
Olson,W.K., Gorin,A.A., Lu,X.J., Hock,L.M. and Zhurkin,V.B. (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl Acad. Sci. USA, 95, 11163-11168.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
35
-
-
0033150892
-
DNA structure: Cations in charge?
-
McFail-Isom,L., Sines,C.C. and Williams,L.D. (1999) DNA structure: cations in charge? Curr. Opin. Struct. Biol., 9, 298-304.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 298-304
-
-
McFail-Isom, L.1
Sines, C.C.2
Williams, L.D.3
-
36
-
-
0023668176
-
Cationic metals promote sequence-directed DNA bending
-
Laundon,C.H. and Griffith,J.D. (1987) Cationic metals promote sequence-directed DNA bending. Biochemistry, 26, 3759-3762.
-
(1987)
Biochemistry
, vol.26
, pp. 3759-3762
-
-
Laundon, C.H.1
Griffith, J.D.2
-
37
-
-
0842299592
-
DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
-
Stefl,R., Wu,H., Ravindranathan,S., Sklenar,V. and Feigon,J. (2004) DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum. Proc. Natl Acad. Sci. USA, 101, 1177-1182.
-
(2004)
Proc. Natl Acad. Sci. USA
, vol.101
, pp. 1177-1182
-
-
Stefl, R.1
Wu, H.2
Ravindranathan, S.3
Sklenar, V.4
Feigon, J.5
-
39
-
-
0027483012
-
Co-crystal structure of TBP recognizing the minor groove of a TATA element
-
Kim,J.L., Nikolov,D.B. and Burley,S.K. (1993) Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature, 365, 520-527.
-
(1993)
Nature
, vol.365
, pp. 520-527
-
-
Kim, J.L.1
Nikolov, D.B.2
Burley, S.K.3
-
40
-
-
0033548682
-
High base pair opening rates in tracts of GC base pairs
-
Dornberger,U., Leijon,M. and Fritzsche,H. (1999) High base pair opening rates in tracts of GC base pairs. J. Biol. Chem., 274, 6957-6962.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 6957-6962
-
-
Dornberger, U.1
Leijon, M.2
Fritzsche, H.3
-
41
-
-
0032559372
-
CTG repeats associated with human genetic disease are inherently flexible
-
Chastain,P.D. and Sinden,R.R. (1998) CTG repeats associated with human genetic disease are inherently flexible. J. Mol. Biol., 275, 405-411.
-
(1998)
J. Mol. Biol.
, vol.275
, pp. 405-411
-
-
Chastain, P.D.1
Sinden, R.R.2
-
42
-
-
0028932050
-
Expanded CTG triplet blocks from the myotonic dystrophy gene create the strongest known natural nucleosome positioning elements
-
Wang,Y.H. and Griffith,J. (1995) Expanded CTG triplet blocks from the myotonic dystrophy gene create the strongest known natural nucleosome positioning elements. Genomics, 25, 570-573.
-
(1995)
Genomics
, vol.25
, pp. 570-573
-
-
Wang, Y.H.1
Griffith, J.2
-
43
-
-
0030814020
-
Triplet repeat instability and DNA topology: An expansion model based on statistical mechanics
-
Gellibolian,R., Bacolla,A. and Wells,R.D. (1997) Triplet repeat instability and DNA topology: An expansion model based on statistical mechanics. J. Biol. Chem., 272, 16793-16797.
-
(1997)
J. Biol. Chem.
, vol.272
, pp. 16793-16797
-
-
Gellibolian, R.1
Bacolla, A.2
Wells, R.D.3
-
44
-
-
0023649576
-
The gamma delta resolvase induces an unusual DNA structure at the recombinational crossover point
-
Hatfull,G.F., Noble,S.M. and Grindley,N.D. (1987) The gamma delta resolvase induces an unusual DNA structure at the recombinational crossover point. Cell, 49, 103-110.
-
(1987)
Cell
, vol.49
, pp. 103-110
-
-
Hatfull, G.F.1
Noble, S.M.2
Grindley, N.D.3
-
45
-
-
0023992694
-
Site-specific recombination in bacteriophage Mu: Characterization of binding sites for the DNA invertase Gin
-
Mertens,G., Klippel,A., Fuss,H., Blocker,H., Frank,R. and Kahmann,R. (1988) Site-specific recombination in bacteriophage Mu: Characterization of binding sites for the DNA invertase Gin. EMBO J., 7, 1219-1227.
-
(1988)
EMBO J.
, vol.7
, pp. 1219-1227
-
-
Mertens, G.1
Klippel, A.2
Fuss, H.3
Blocker, H.4
Frank, R.5
Kahmann, R.6
-
46
-
-
0028820166
-
DNA twist, flexibility and transcription of the osmoregulated proU promoter of Salmonella typhimurium
-
Jordi,B.J., Owen-Hughes,T.A., Hulton,C.S. and Higgins,C.F. (1995) DNA twist, flexibility and transcription of the osmoregulated proU promoter of Salmonella typhimurium. EMBO J., 14, 5690-5700.
-
(1995)
EMBO J.
, vol.14
, pp. 5690-5700
-
-
Jordi, B.J.1
Owen-Hughes, T.A.2
Hulton, C.S.3
Higgins, C.F.4
-
47
-
-
0037453011
-
High-throughput approach for detection of DNA bending and flexibility based on cyclization
-
Zhang,Y. and Crothers,D.M. (2003) High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc. Natl Acad. Sci. USA, 100, 3161-3166.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 3161-3166
-
-
Zhang, Y.1
Crothers, D.M.2
-
48
-
-
17544367055
-
Nucleosome assembly on CTG triplet repeats
-
Godde,J.S. and Wolffe,A.P. (1996) Nucleosome assembly on CTG triplet repeats. J. Biol. Chem., 271, 15222-15229.
-
(1996)
J. Biol. Chem.
, vol.271
, pp. 15222-15229
-
-
Godde, J.S.1
Wolffe, A.P.2
-
49
-
-
0028606859
-
p53 oligomerization and DNA looping are linked with transcriptional activation
-
Stenger,J.E., Tegtmeyer,P., Mayr,G.A., Reed,M., Wang,Y., Wang,P., Hough,P.V. and Mastrangelo,I.A. (1994) p53 oligomerization and DNA looping are linked with transcriptional activation. EMBO J., 13, 6011-6020.
-
(1994)
EMBO J.
, vol.13
, pp. 6011-6020
-
-
Stenger, J.E.1
Tegtmeyer, P.2
Mayr, G.A.3
Reed, M.4
Wang, Y.5
Wang, P.6
Hough, P.V.7
Mastrangelo, I.A.8
-
50
-
-
0032575756
-
DNA structure in human RNA polymerase II promoters
-
Pedersen,A.G., Baldi,P., Chauvin,Y. and Brunak,S. (1998) DNA structure in human RNA polymerase II promoters. J. Mol. Biol., 281, 663-673.
-
(1998)
J. Mol. Biol.
, vol.281
, pp. 663-673
-
-
Pedersen, A.G.1
Baldi, P.2
Chauvin, Y.3
Brunak, S.4
|