Indirect Readout of DNA Sequence by Proteins: The Roles of DNA Sequence-Dependent Intrinsic and Extrinsic Forces

Progress in Nucleic Acid Research and Molecular Biology

Volumn 81, Issue , 2006, Pages 143-177

  Koudelka, Gerald B ^a   Mauro, Steven A ^a   Ciubotaru, Mihai ^a  

^a UNIVERSITY AT BUFFALO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA BINDING PROTEIN; REPRESSOR PROTEIN;

BACTERIOPHAGE; CONFORMATION; ENZYME SPECIFICITY; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; NUCLEOTIDE SEQUENCE; REVIEW;

BACTERIOPHAGES; BASE SEQUENCE; DNA; DNA-BINDING PROTEINS; NUCLEIC ACID CONFORMATION; REPRESSOR PROTEINS; SUBSTRATE SPECIFICITY;

EID: 33750621840     PISSN: 00796603     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0079-6603(06)81004-4     Document Type: Review

References (128)

1. Kim Y., Geiger J.H., Hahn S., and Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature 365 (1993) 512-520
2. Scheviz R.W., Otwinowski Z., Joachimiak A., Lawson C.L., and Sigler P.B. The three dimensional structure of trp repressor. Nature 317 (1985) 782-786
3. Wu L., Vertino A., and Koudelka G.B. Non-contacted bases affect the affinity of synthetic P22 operators for P22 repressor. J. Biol. Chem. 267 (1992) 9134-9135
4. Hegde R.S., Grossman S.R., Laimins L.A., and Sigler P.B. Crystal structure at 1.7 Å of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature 359 (1992) 505-512
5. Yang C.C., and Nash H.A. The interaction of E. coli IHF protein with its specific binding sites. Cell 57 (1989) 869-880
6. Somers W.S., and Phillips S.E.V. Crystal structure of the met repressor-operator complex at 2.8 Å resolution reveals DNA recognition by β-strands. Nature 359 (1992) 387-393
7. Gabrielsen O.S., Sentenac A., and Fromageot P. Specific DNA binding by c-Myb: Evidence for a double helix- turn-helix-related motif. Science 253 (1991) 1140-1143
8. Dangi B., Pelupessey P., Martin R.G., Rosner J.L., Louis J.M., and Gronenborn A.M. Structure and dynamics of MarA-DNA complexes: An NMR investigation. J. Mol. Biol. 314 (2001) 113-127
9. Schwabe J.W.R., Chapman L., Finch J.T., and Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements. Cell 75 (1993) 567-578
10. Jeltsch A., Alves J., Wolfes H., Maass G., and Pingoud A. Pausing of the restriction endonuclease EcoRI during linear diffusion on DNA. Biochemistry 33 (1994) 10215-10219
11. Jeltsch A., Wenz C., Stahl F., and Pingoud A. Linear diffusion of the restriction endonuclease EcoRV on DNA is essential for the in vivo function of the enzyme. EMBO J. 15 (1996) 5104-5111
12. Hegde R.S., and Androphy E.J. Crystal structure of the E2 DNA-binding domain from human papillomavirus type 16: Implications for its DNA binding-site selection mechanism. J. Mol. Biol. 284 (1998) 1479-1489
13. Rodgers D.W., and Harrison S.C. The complex between phage 434 repressor DNA-binding domain and operator site OR3: Structural differences between consensus and non-consensus half-sites. Structure 1 (1993) 227-240
14. Widlund H.R., Cao H., Simonsson S., Magnusson E., Simonsson T., Nielsen P.E., Kahn J.D., Crothers D.M., and Kubista M. Identification and characterization of genomic nucleosome-positioning sequences. J. Mol. Biol. 267 (1997) 807-817
15. Thastrom A., Lowary P.T., Widlund H.R., Cao H., Kubista M., and Widom J. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J. Mol. Biol. 288 (1999) 213-229
16. Widlund H.R., Kuduvalli P.N., Bengtsson M., Cao H., Tullius T.D., and Kubista M. Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence. J. Biol. Chem. 274 (1999) 31847-31852
17. Gartenberg M.R., and Crothers D.M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature 333 (1986) 824-829
18. Craig N.L., and Nash H.A. E. coli integration host factor binds to specific sites in DNA. Cell 39 (1984) 707-716
19. Goodman S.D., Nicholson S.C., and Nash H.A. Deformation of DNA during site-specific recombination of bacteriophage lambda: Replacement of IHF protein by HU protein or sequence-directed bends. Proc. Natl. Acad. Sci. USA 89 (1992) 11910-11914
20. Segall A.M., Goodman S.D., and Nash H.A. Architectural elements in nucleoprotein complexes: Interchangeability of specific and non-specific DNA binding proteins. EMBO J. 13 (1994) 4536-4548
21. Blomquist P., Belikov S., and Wrange O. Increased nuclear factor 1 binding to its nucleosomal site mediated by sequence-dependent DNA structure. Nucleic Acids Res. 27 (1999) 517-525
22. Tisne C., Delepierre M., and Hartmann B. How NF-kappaB can be attracted by its cognate DNA. J. Mol. Biol. 293 (1999) 139-150
23. Sierk M.L., Zhao Q., and Rastinejad F. DNA deformability as a recognition feature in the reverb response element. Biochemistry 40 (2001) 12833-12843
24. Moitoso de Vargas L., Pargellis C.A., Hasan N.M., Bushman E.W., and Landy A. Autonomous DNA binding domains of lambda integrase recognize two different sequence families. Cell 54 (1988) 923-929
25. Kwon H.J., Tirumalai R., Landy A., and Ellenberger T. Flexibility in DNA recombination: Structure of the lambda integrase catalytic core. Science 276 (1997) 126-131
26. Werel W., Schickor P., and Heumann H. Flexibility of the DNA enhances promoter affinity of Escherichia coli RNA polymerase. EMBO J. 10 (1991) 2589-2594
27. Auble D.T., Allen T.L., and DeHaseth P.L. Promoter recognition by Escherichia coli RNA polymerase. J. Biol. Chem. 261 (1986) 11202-11206
28. Sasmor H.M., and Betz J.L. Specific binding of lac repressor to linear versus circular polyoperator molecules. Biochemistry 29 (1990) 9023-9028
29. Sasmor H.M., and Betz J.L. Symmetric lac operator derivatives: Effects of half-operator sequence and spacing on repressor affinity. Gene 89 (1990) 1-6
30. Hines C.S., Meghoo C., Shetty S., Biburger M., Brenowitz M., and Hegde R.S. DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins. J. Mol. Biol. 276 (1998) 809-818
31. Rohs R., Sklenar H., and Shakked Z. Structural and energetic origins of sequence-specific DNA bending: Monte carlo simulations of papillomavirus E2-DNA binding sites. Structure (Camb.) 13 (2005) 1499-1509
32. Szymczyna B.R., and Arrowsmith C.H. DNA binding specificity studies of four ETS proteins support an indirect read-out mechanism of protein-DNA recognition. J. Biol. Chem. 275 (2000) 28363-28370
33. Kodandapani R., Pio F., Ni C.Z., Piccialli G., Klemsz M., McKercher S., Maki R.A., and Ely K.R. A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature 380 (1996) 456-460
34. Batchelor A.H., Piper D.E., de la Brousse F.C., McKnight S.L., and Wolberger C. The structure of GABPalpha/beta: An ETS domain-ankyrin repeat heterodimer bound to DNA. Science 279 (1998) 1037-1041
35. Mo Y., Vaessen B., Johnston K., and Marmorstein R. Structures of SAP-1 bound to DNA targets from the E74 and c-fos promoters: Insights into DNA sequence discrimination by Ets proteins. Mol. Cell 2 (1998) 201-212
36. Mo Y., Vaessen B., Johnston K., and Marmorstein R. Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA. Nat. Struct. Biol. 7 (2000) 292-297
37. Bareket-Samish A., Cohen I., and Haran T.E. Signals for TBP/TATA box recognition. J. Mol. Biol. 299 (2000) 965-977
38. Patel L.R., Curran T., and Kerppola T.K. Energy transfer analysis of Fos-Jun dimerization and DNA binding. Proc. Natl. Acad. Sci. USA 91 (1994) 7360-7364
39. RM function in vitro. Modulation by the bacteriophage λ cI protein. J. Biol. Chem. 268 (1993) 8943-8948
40. La Baer J., and Yamamoto K.R. Analysis of the DNA-binding affinity, sequence specificity and context dependence of the glucocorticoid receptor zinc finger region. J. Mol. Biol. 239 (1994) 664-688
41. Lefstin J.A., Thomas J.R., and Yamamoto K.R. Influence of a steroid receptor DNA-binding domain on transcriptional regulatory functions. Genes Dev. 8 (1994) 2842-2856
42. Lefstin J.A., and Yamamoto K.R. Allosteric effects of DNA on transcriptional regulators. Nature 392 (1998) 885-888
43. van Tilborg M.A., Lefstin J.A., Kruiskamp M., Teuben J., Boelens R., Yamamoto K.R., and Kaptein R. Mutations in the glucocorticoid receptor DNA-binding domain mimic an allosteric effect of DNA. J. Mol. Biol. 301 (2000) 947-958
44. Spiro C., Bazett-Jones D.P., Wu X., and McMurray C.T. DNA structure determines protein binding and transcriptional efficiency of the proenkephalin cAMP-responsive enhancer. J. Biol. Chem. 270 (1995) 27702-27710
45. Watson J.D., and Crick F.H. Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171 (1953) 737-738
46. Arnott S., and Hukins D.W. Refinement of the structure of B-DNA and implications for the analysis of x-ray diffraction data from fibers of biopolymers. J. Mol. Biol. 81 (1973) 93-105
47. Fuller W., Wilkins M.H., Wilson H.R., and Hamilton L.D. The molecular configuration of deoxyribonucleic acid. IV. X-ray diffraction study of the A form. J. Mol. Biol. 12 (1965) 60-76
48. Bugg C.E., Thomas J.M., Sundaralingam M., and Rao S.T. Stereochemistry of nucleic acids and their constituents. X. Solid-state base-stacking patterns in nucleic acid constituents and polynucleotides. Biopolymers 10 (1971) 175-219
49. Wing R., Drew H., Takano T., Broka C., Tanaka S., Itakura K., and Dickerson R.E. Crystal structure analysis of a complete turn of B-DNA. Nature 287 (1980) 755-758
50. Drew H.R., Wing R.M., Takano T., Broka C., Tanaka S., Itakura K., and Dickerson R.E. Structure of a B-DNA dodecamer: Conformation and dynamics. Proc. Natl. Acad. Sci. USA 78 (1981) 2179-2183
51. Grzeskowiak K., Yanagi K., Prive G.G., and Dickerson R.E. The structure of B-helical C-G-A-T-C-G-A-T-C-G and comparison with C-C-A-A-C-G-T-T-G-G. The effect of base pair reversals. J. Biol. Chem. 266 (1991) 8861-8883
52. Chiu T.K., Kaczor-Grzeskowiak M., and Dickerson R.E. Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G. J. Mol. Biol. 292 (1999) 589-608
53. Shui X., McFail-Isom L., Hu G.G., and Williams L.D. The B-DNA dodecamer at high resolution reveals a spine of water on sodium. Biochemistry 37 (1998) 8341-8355
54. Calladine C.R. Mechanics of sequence-dependent stacking of bases in B-DNA. J. Mol. Biol. 161 (1982) 343-352
55. Packer M.J., Dauncey M.P., and Hunter C.A. Sequence-dependent DNA structure: Tetranucleotide conformational maps. J. Mol. Biol. 295 (2000) 85-103
56. Packer M.J., Dauncey M.P., and Hunter C.A. Sequence-dependent DNA structure: Dinucleotide conformational maps. J. Mol. Biol. 295 (2000) 71-83
57. Dlakic M., and Harrington R.E. Bending and torsional flexibility of G/C-rich sequences as determined by cyclization assays. J. Biol. Chem. 270 (1995) 29945-29952
58. Dlakic M., and Harrington R.E. The effects of sequence context on DNA curvature. Proc. Natl. Acad. Sci. USA 93 (1996) 3847-3852
59. Dlakic M., and Harrington R.E. Unconventional helical phasing of repetitive DNA motifs reveals their relative bending contributions. Nucleic Acids Res. 26 (1998) 4274-4279
60. Saenger W. "Principles of Nucleic Acid Structure." (1984), Springer-Verlag, Inc., New York
61. Nelson H.C.M., Finch J.T., Luisi B.F., and Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature 330 (1987) 221-226
62. el Hassan M.A., and Calladine C.R. The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. J. Mol. Biol. 251 (1995) 648-664
63. el Hassan M.A., and Calladine C.R. Propeller-twisting of base-pairs and the conformational mobility of dinucleotide steps in DNA. J. Mol. Biol. 259 (1996) 95-103
64. el Hassan M.A., and Calladine C.R. Structural mechanics of bent DNA. Endeavour 20 (1996) 61-67
65. Suzuki M., Amano N., Kakinuma J., and Tateno M. Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA. J. Mol. Biol. 274 (1997) 421-435
66. Hud N.V., and Feigon J. Localization of divalent metal ions in the minor groove of DNA A-tracts. J. Am. Chem. Soc. 119 (1997) 5756-5757
67. Shui X., Sines C.C., McFail-Isom L., VanDerveer D., and Williams L.D. Structure of the potassium form of CGCGAATTCGCG: DNA deformation by electrostatic collapse around inorganic cations. Biochemistry 37 (1998) 16877-16887
68. Hud N.V., Sklenar V., and Feigon J. Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending. J. Mol. Biol. 286 (1999) 651-660
69. McFail-Isom L., Sines C.C., and Williams L.D. DNA structure: Cations in charge?. Curr. Opin. Struct. Biol. 9 (1999) 298-304
70. Rouzina I., and Bloomfield V.A. DNA bending by small, mobile multivalent cations. Biophys. J. 74 (1998) 3152-3164
71. Rouzina I., and Bloomfield V.A. Force-induced melting of the DNA double helix. 2. Effect of solution conditions. Biophys. J. 80 (2001) 894-900
72. Rosenberg J.M., Seeman N.C., Kim J.J., Suddath F.L., Nicholas H.B., and Rich A. Double helix at atomic resolution. Nature 243 (1973) 150-154
73. Quigley G.J., Teeter M.M., and Rich A. Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA. Proc. Natl. Acad. Sci. USA 75 (1978) 64-68
74. Howerton S.B., Sines C.C., VanDerveer D., and Williams L.D. Locating monovalent cations in the grooves of B-DNA. Biochemistry 40 (2001) 10023-10031
75. Minasov G., Tereshko V., and Egli M. Atomic-resolution crystal structures of B-DNA reveal specific influences of divalent metal ions on conformation and packing. J. Mol. Biol. 291 (1999) 83-99
76. Woods K., McFail-Isom L., Sines C.C., Howerton S.B., Stephens R.K., and Williams L.D. Monovalent cations sequester within the A-Tract minor groove of [d(CGCGAATTCGCG)]2. J. Am. Chem. Soc. 122 (2001) 1546-1547
77. Hud N.V., and Polak M. DNA-cation interactions: The major and minor grooves are flexible ionophores. Curr. Opin. Struct. Biol. 11 (2001) 293-301
78. Chiu T.K., and Dickerson R.E. 1 angstrom crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium. J. Mol. Biol. 301 (2000) 915-945
79. Davey C.A., and Richmond T.J. DNA-dependent divalent cation binding in the nucleosome core particle. Proc. Natl. Acad. Sci. USA 99 (2002) 11169-11174
80. Davey C.A., Sargent D.F., Luger K., Maeder A.W., and Richmond T.J. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. J. Mol. Biol. 319 (2002) 1097-1113
81. Sauer R.T., Yocum R.R., Doolittle R.F., Lewis M., and Pabo C.O. Homology among DNA-binding proteins suggests use of a conserved supersecondary structure. Nature 298 (1982) 447-451
82. Ptashne M. "A Genetic Switch." (1986), Blackwell Press, Palo Alto
83. Xu J., and Koudelka G.B. Repression of transcription initiation at 434 P(R) by 434 repressor: Effects on transition of a closed to an open promoter complex. J. Mol. Biol. 309 (2001) 573-587
84. Shang Z., Isaac V.E., Li H., Patel L., Catron K.M., Curran T., Montelione G.T., and Abate C. Design of a "minimal" homeodomain: The N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure. Proc. Natl. Acad. Sci. USA 91 (1994) 8373-8377
85. Hochschild A., Irwin N., and Ptashne M. Repressor structure and the mechanism of positive control. Cell 32 (1983) 319-325
86. RM transcription by 434 repressor. DNA Cell Biol. 19 (2000) 621-630
87. RM promoter. Implications for an indirect mechanism of transcriptional activation by lambda repressor. J. Mol. Biol. 222 (1991) 479-494
88. Xu J., and Koudelka G.B. Mutually exclusive utilization of P(R) and P(RM) promoters in bacteriophage 434 O(R). J. Bacteriol. 182 (2000) 3165-3174
89. Jacob F., and Monod J. Genetic regulatory mechanisms in the synthesis of proteins. J. Mol. Biol. 3 (1961) 318-356
90. Bushman F.D. The bacteriophage 434 right operator. Roles of O(R)1, O(R)2 and O(R)3. J. Mol. Biol. 230 (1993) 28-40
91. Choy H.E., and Adhya S. RNA polymerase idling and clearance in gal promoters: Use of supercoiled minicircle DNA template made in vivo. Proc. Natl. Acad. Sci. USA 90 (1993) 472-476
92. Johnson A.D., Pabo C.O., and Sauer R.T. Bacteriophage lambda repressor and cro protein: Interactions with operator DNA. Methods Enzymol. 65 (1982) 839-856
93. DeAnda J., Poteete A.R., and Sauer R.T. P22 c2 repressor-domain structure and function. J. Biol. Chem. 258 (1983) 10536-10542
94. Pabo C.O., Sauer R.T., Sturtevant J.M., and Ptashne M. The lambda repressor contains two domains. Proc. Natl. Acad. Sci. USA 76 (1979) 1608-1612
95. Anderson J.E. (1984), Harvard University, Cambridge Ph.D. thesis.
96. Aggarwal A., Rodgers D.W., Drottar M., Ptashne M., and Harrison S.C. Recognition of a DNA operator by the repressor of phage 434: A view at high resolution. Science 242 (1988) 899-907
97. Anderson J.E., Harrison S.C., and Ptashne M. A phage repressor-operator complex at 7# resolution. Nature 326 (1987) 888-891
98. Mondragon A., Subbiah S., Almo S.C., Drottar M., and Harrison S.C. Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution. J. Mol. Biol. 205 (1989) 189-200
99. Fattah K.R., Mizutani S., Fattah F.J., Matsushiro A., and Sugino Y. A comparative study of the immunity region of lambdoid phages including shiga-toxin-converting phages: Molecular basis for cross immunity. Genes Genet. Syst. 75 (2000) 223-232
100. Harrison S.C. A structural taxonomy of DNA-binding domains. Nature 353 (1991) 715-719
101. Johnson A.D., Meyer B.J., and Ptashne M. Interaction between DNA-bound repressors govern regulation by the lambda repressor. Proc. Natl. Acad. Sci. USA 76 (1979) 5061-5065
102. Luo Y., Pfuetzner R.A., Mosimann S., Paetzel M., Frey E.A., Cherney M., Kim B., Little J.W., and Strynadka N.C. Crystal structure of LexA: A conformational switch for regulation of self-cleavage. Cell 106 (2001) 585-594
103. Donner A.L., and Koudelka G.B. Carboxyl-teminal domain dimer interface mutant 434 repressors have altered dimerization and DNA binding specificities. J. Mol. Biol. 283 (1998) 931-946
104. Ciubotaru M., Bright F.V., Ingersoll C.M., and Koudelka G.B. DNA-induced conformational changes in bacteriophage 434 repressor. J. Mol. Biol. 294 (1999) 859-873
105. Koudelka G.B., Harrison S.C., and Ptashne M. Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 326 (1987) 886-888
106. Anderson J.E., Ptashne M., and Harrison S.C. Structure of the repressor-operator complex of bacteriophage 434. Nature 326 (1987) 846-852
107. Koudelka G.B., and Carlson P. DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor. Nature 355 (1992) 89-91
108. R2/R1-69 complex at 2•5 Å resolution. J. Mol. Biol. 232 (1993) 826-838
109. Barkley M.D., and Zimm B.H. Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization. J. Chem. Phys. 70 (1979) 2991-3007
110. Koudelka G.B. Bending of synthetic bacteriophage 434 operators by bacteriophage 434 proteins. Nucleic Acids Res. 19 (1991) 4115-4119
111. Koudelka G.B. Recognition of DNA structure by 434 repressor. Nucleic Acids Res. 26 (1998) 669-675
112. Fujimoto B.S., and Schurr J.M. Dependence of the torsional rigidity of DNA on base composition. Nature 344 (1990) 175-178
113. Donner A.L., Carlson P.A., and Koudelka G.B. Dimerization specificity of P22 and 434 repressors is determined by multiple polypeptide segments. J. Bacteriol. 179 (1997) 1253-1261
114. Mauro S.A., Pawlowski D., and Koudelka G.B. The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor. J. Biol. Chem. 278 (2004) 12955-12960
115. Koudelka G.B., Harbury P.H., Harrison S.C., and Ptashne M. DNA twisting and the affinity of bacteriophage 434 operator for bacteriophage 434 repressor. Proc. Natl. Acad. Sci. USA 85 (1988) 4633-4637
116. R3. The influence of contacted and noncontacted base pairs. J. Biol. Chem. 270 (1995) 1205-1212
117. Bell A.C., and Koudelka G.B. Operator sequence context influences amino acid-base-pair interactions in 434 repressor-operator complexes. J. Mol. Biol. 234 (1993) 542-553
118. Duong T.H., and Zakrzewska K. Sequence specificity of bacteriophage 434 repressor-operator complexation. J. Mol. Biol. 280 (1998) 31-39
119. Higgins C.F., Dorman C.J., Stirling D.A., Waddell L., Booth I.R., May G., and Bremer E. A physiological role for DNA supercoiling in the osmotic regulation of gene expression in S. typhimurium and E. coli. Cell 52 (1988) 569-584
120. Jordi B.J., and Higgins C.F. The downstream regulatory element of the proU operon of Salmonella typhimurium inhibits open complex formation by RNA polymerase at a distance. J. Biol. Chem. 275 (2000) 12123-12128
121. Conter A., Menchon C., and Gutierrez C. Role of DNA supercoiling and rpoS sigma factor in the osmotic and growth phase-dependent induction of the gene osmE of Escherichia coli K12. J. Mol. Biol. 273 (1997) 75-83
122. Graeme-Cook K.A., May G., Bremer E., and Higgins C.F. Osmotic regulation of porin expression: A role for DNA supercoiling. Mol. Microbiol. 3 (1989) 1287-1294
123. Record M.T., Courtenay E.S., Cayley D.S., and Guttman H.J. Responses of E-coli to osmotic stress: Large changes in amounts of cytoplasmic solutes and water. Trends Biochem. Sci. 23 (1998) 143-148
124. Record M.T., Courtenay E.S., Cayley S., and Guttman H.J. Biophysical compensation mechanisms buffering E-coli protein-nucleic acid interactions against changing environments. Trends Biochem. Sci. 23 (1998) 190-194
125. Mauro S.A., and Koudelka G.B. Monovalent cations regulate DNA sequence recognition by 434 repressor. J. Mol. Biol. 340 (2004) 445-457
126. Daniels D.I., Schroeder J.L., Szybalski W., Sanger F., Coulson A.R., Hong G.F., Hill D.F., Petersen G.F., and Blattner F.R. Lambda II (1983), Cold Spring Harbor Laboratory, Cold Spring Harbor 519-676
127. Sauer R.T., Nelson H.C., Hehir K., Hecht M.H., Gimble F.S., DeAnda J., and Poteete A.R. The lambda and P22 phage repressors. J. Biomol. Struct. Dyn. 1 (1983) 1011-1022
128. 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