DNA recognition and bending

Chemistry and Biology

Volumn 4, Issue 9, 1997, Pages 643-650

  Allemann, Rudolf K ^a   Egli, Martin ^b  

^a ETH ZURICH   (Switzerland)

^b NORTHWESTERN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMALIA;

EID: 0031238604     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1074-5521(97)90218-0     Document Type: Review

References (72)

1. Klug, A., Jack, A., Viswamitra, M.A. Kennard, O., Shakked, Z. & Steitz, T.A. (1979). A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lacrepressor protein. J. Mol. Biol. 131, 669-680.
2. Dickerson, R.E., Goodsell, D. & Neidle, S. (1994). "...the tyranny of the lattice ...". Proc. Natl Acad. Sci. USA 91, 3579-3583.
3. Dickerson, R.E., Goodsell, D. & Kopka, M.L. (1996). MPD and DNA bending in crystals and in solution. J. Mol. Biol. 256, 108-125.
4. Kahn, J.D., Yun, E. & Crothers, D.M. (1994). Detection of localised DNA flexibility. Nature 368, 163-166.
5. Koo, H-S., Wu, H.-M. & Crothers, D.M. (1986). DNA bending at adenine thymine tracts. Nature 320, 501-506.
6. Wu, H.-M. & Crothers, D.M. (1984). The locus of sequence-directed and protein-induced DNA bending. Nature 308, 509-513.
7. Zinkel, S.S., & Crothers, D.M. (1987). DNA bend direction by phase sensitive detection. Nature 328, 178-181.
8. Goodsell, D.M., Kopka, M.L., Cascio, D. & Dickerson, R.E. (1993). Crystal structure of CATGGCATG and its implications for A-tract bending models. Proc. Natl Acad. Sci. USA 90, 2930-2934.
9. Dickerson, R.E. (1983). The DNA helix and how it is read. Sci. Am. 249, 94-102.
10. Calladine, C.R. & Drew, H.R. (1997). Understanding DNA. The Molecule and How it Works. Academic Press Inc., San Diego, CA.
11. Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R.E. (1980). Crystal structure analysis of a complete turn of B-DNA. Nature 287, 755-758.
12. Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K. & Dickerson, R.E. (1981). Structure of a B-DNA dodecamer: conformation and dynamics. Proc. Natl Acad. Sci. USA 78, 2179-2183.
13. Nelson, H.C.M., Finch, J.T., Luisi, B.F. & Klug, A. (1987). The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature 330, 221-226.
14. Coll, M., Frederick, C.A., Wang, A., H.-J. & Rich, A. (1987). A bifurcated hydrogen-bonded conformation in the d(A-T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin. Proc. Natl Acad. Sci. USA 84, 8385-8389.
15. DiGabriele, A.D., Sanderson, M.R. & Steitz, T.A. (1989). Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. Proc. Natl Acad. Sci. USA 86, 11816-11819.
16. DiGabriele, M.R. & Steitz, T.A. (1993). A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend. J. Mol. Biol. 231, 1024-1039.
17. Shatzky-Schwartz, M., et al., & Shakked, Z. (1997). X-ray and solution studies of DNA oligomers and implications for the structural basis of a-tract dependent curvature. J. Mol. Biol. 267, 595-623.
18. Diekmann, S., Mazzarelli, J.M., McLaughlin, L.W., von Kitzing, E. & Travers, A.A. (1992). DNA curvature does not require bifurcated hydrogen bonds or pyrimidine methyl groups. J. Mol. Biol. 225, 729-738.
19. Yoon, C., Privé, G.G., Goodsell, D.S. & Dickerson, R.E. (1988). Structure of an alternating B-DNA helix and its relationship to A-tract DNA. Proc. Natl Acad. Sci. USA 85, 6332-6336.
20. Kopka, M.L & Larsen, T.A. (1992). Netropsin and the lexitropins. The search for sequence-specific minor-groove-binding ligands. In Nucleic Acid Targeted Drug Design. (Probst, C.L. & Perun, T.J., eds) pp. 303-374, Marcel Dekker, Inc., New York.
21. Brown, D.G., Sanderson, M.R., Garman, E. & Neidle, S. (1992). Crystal structure of a berenil-d(CGCAAATTTGCG) complex: an example of drug-DNA recognition based on sequence-dependent structural features. J. Mol. Biol. 226, 481-490.
22. Goodsell, D.S., Kopka, M.L. & Dickerson, R.E. (1995). Refinement of netropsin bound to DNA: bias and feedback in electron density map interpretation. Biochemistry 34, 4983-4993.
23. Nunn, C.M., Garman, E. & Neidle, S. (1997). Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin. Biochemistry 36, 4792-4799.
24. Neidle, S. (1997). Crystallographic insights into DNA minor groove recognition by drugs. Biopolymers 44, 105-121.
25. Bailly, C., Waring, M.J. & Travers, A.A. (1995). Effects of base substitutions on the binding of a DNA-bending protein. J. Mol. Biol. 253, 1-7.
26. Chen, X., Ramakrishnan, B., Rao, S.T. & Sundaralingam, M. (1994). Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex. Nat. Struct. Biol. 1, 169-175.
27. Suzuki, M., Yagi, N. & Finch, J.T. (1996). Role of base-backbone and base-base interactions in alternating DNA conformations. FEBS Lett. 379, 148-152.
28. Aggarwal, A.K., Rogers, D.W., Drottar, M., Ptashne, M. & Harrison, S.C. (1988). Recognition of a DNA operator by the repressor of Phage 434: a view at high resolution. Science 242, 899-907.
29. Jordan, S.R. & Pabo, C.O. (1988). Structure of the lambda complex at 2.5 A resolution: details of the repressor-operator interactions. Science 242, 893-899.
30. Beamer, L.J. & Pabo, C.O. (1992). Refined 1.8 Å crystal structure of the λ repressor-operator complex. J. Mol. Biol. 227, 177-196.
31. Brennan, R.G., Roderick, S.L., Takeda, Y. & Matthews, B.W. (1990). Protein-DNA conformational changes in the crystal structure of a λ Cro-operator complex. Proc. Natl Acad. Sci. USA 87, 8165-8169.
32. Schultz, S.C., Shields, G.C. & Steitz, T.A. (1991). Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science 253, 1001-1007.
33. Norman, C., Runswick, M., Pollock, R. & Treisman, R. (1988). Isolation and properties of cDNA clones encoding SRF, a transcription factor that binds to the c-fos serum response element. Cell 55, 989-1003.
34. Pellegrini, L., Tan, S. & Richmond, T.J. (1995). Structure of serum response factor core bound to DNA. Nature 376, 490-498.
35. Pollock, R. & Treisman, R. (1990). A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 18, 6197-6204.
36. Rich, A. (1978). Localised positive charges can bend double helical nucleic acid. Fed. Eur. Biochem. Soc. 51, 71-81.
37. Strauss, J.K. & Maher III, L.J. (1994). DNA bending by asymmetric phosphate neutralisation. Science 266, 1829-1834.
38. Shore, P. & Sharrock, A.D. (1995). The MADS-box family of transcription factors. Eur. J. Biochem. 229, 1-13.
39. Gosset, L.A., Kelvin, D.J., Sternberg, E.A. & Olson, E.N. (1989). A new myocyte-specific enhancer-binding factor that recognizes a conserved element associated with multiple muscle-specific genes. Mol. Cell. Biol. 9, 5022-5033.
40. Werner, M.H., Gronenborn, A.M. & Clore, G.M. (1996). Intercalation, DNA kinking, and the control of transcription. Science 271, 778-784.
41. Sharp, P.A. (1992). TATA-binding protein is a classless factor. Cell 68, 819-821.
42. Rigby, P.W.J. (1993). Three in one and one in three: it all depends on TBP. Cell 72, 7-10.
43. Tansey, W.P. & Herr, W. (1997). TAFs: guilt by association? Cell 88, 729-732.
44. Marsh, T.L., Reich, C.I., Whitelock, R.B. & Olsen, G.J. (1992). Transcription factor IID in the archaea: sequences in the thermococcus celer genome would encode a product closely related to the TATA-binding protein of eukaryotes. Proc. Natl Acad. Sci. USA 91, 4180-4184.
45. Bucher, P. (1990). Weight matrix description of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578.
46. Juo, Z.S., Chiu, T.K., Leiberman, P.M., Baikalov, I., Berk, A.J. & Dickerson, R.E. (1996). How proteins recognize the TATA box. J. Mol. Biol. 261, 239-254.
47. Kim, Y., Geiger, J.H., Hahn, S. & Sigler, P.B. (1993). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-529.
48. Kim, J.L., Nikolov, D.B. & Burley, S.K. (1993). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
49. Starr, D.B., Hobbs, B.C. & Hawley, D.K. (1995). DNA bending is an important component of site-specific recognition by the TATA binding protein. J. Mol. Biol. 250, 434-446.
50. Wobbe, C.R. & Struhl, K. (1990). Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. Mol. Cell. Biol. 10, 3859-3867.
51. Roberts, R.J. & Halford, S.S. (1993). Type II restriction endonucleases, In Nucleases. (Linn, S.M., Lloyd, R.S. & Roberts, R.J., eds), pp. 35-88, Cold Spring Harbor Laboratory Press, New York.
52. Kim, Y., Grable, J.C., Love, R., Greene, P.J. & Rosenberg, J.M. (1990). Refinement of EcoRI endonuclease crystal structure: a revised protein chain tracing. Science 249, 1307-1309.
53. Winkler, F.K., et al., & Wilson, K.S. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and noncognate DNA fragments. EMBO J. 12, 1781-1795.
54. Lesser, D.R., Kurpiewski, M.R., Waters, T., Connolly, B.A. & Jen Jacobson, L. (1993). Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition. Proc. Natl Acad. Sci. USA 90, 7548-7552.
55. Wah, D.A., Hirsch, J.A., Dorner, L.F., Schildkraut, I. & Aggarwal, A.K. (1997). Structure of the multimodular endonuclease Fokl bound to DNA. Nature 388, 97-100.
56. Allan, B.W. & Reich, N.O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757-14762.
57. Klimasauskas, S., Kumar, S., Roberts, R.J. & Cheng, X. (1994). Hhal methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
58. 6 DNA methyltransferases requires different deformations of DNA. Proc. Natl Acad. Sci. USA 93, 7618-7622.
59. Huth, J.R., et al., & Clore, G.M. (1997). The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif. Nat. Struct. Biol. 4, 657-665.
60. Falvo, J.V., Thanos, D. & Maniatis, T. (1995). Reversal of intrinsic DNA bends in the IFNβ gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell 83, 1101-1111.
61. Ellenberger,T., Fass, D., Arnaud, M. & Harrison, S.C. (1994). Crystal structure of transcription factor E47: E-box recognition by a basic region helix-loop-helix dimer. Genes Dev. 8, 970-980.
62. Ferré-D'Amaré, A.R., Prendergast, G.C., Ziff, E.B. & Burley, S.K. (1993). Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363, 38-45.
63. Ferré-D'Amaré, A.R., Pognonec, P., Roeder, R.G. & Burley, S.K. (1994). Structure and function of the b/HLH/Z domain of USF. EMBO J. 13, 180-189.
64. Zalkin, H. & Dixon, J.E. (1992). De novo purine nucleotide biosynthesis. Prog. Nucleic Acid. Res. Mol. Biol. 42, 259-287.
65. Schumacher, M.A., Choi, K.Y., Zalkin, H. & Brennan, R.G. (1994). Crystal structure of Lacl member, PurR, bound to DNA: minor groove binding by α helices. Science 266, 763-770.
66. Werner, M.H., Huth, J.R., Gronenborn, A.M. & Clore, G.M. (1995). Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell 81, 705-714.
67. Werner, M.H., et al., & Gronenborn, A.M. (1995). The solution structure of the human ETS1-DNA complex reveals a novel mode of binding and true side chain interaction. Cell 83, 761-771.
68. Richmond, T.J., Finch, J.T., Rhodes, D. & Klug, A. (1984). Structure of the nucleosome core particle at 7 A resolution. Nature 311, 532-537.
69. Rice, P.A., Yang, S.-W., Mizuuchi, K. & Nash, H.A. (1996). Crystal structure of an IHF-DNA complex: a protein-induced DNA U-Turn. Cell 87, 1295-1306.
70. Yang, S.-W. & Nash, H.A. (1995). Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target. EMBO J. 14, 6292-6300.
71. Nash, H.A. (1996). The HU and IHF proteins: accessory factors for complex protein-DNA assemblies. In Regulation of Gene Expression in Escherichia coli. (Lin, E.C.C. & Lynch, A.S., eds), pp. 149-179, R.G. Landes Company, Austin, TX.
72. Goosen, N. & van de Putte, P. (1995). The regulation of transcription initiation by integration host factor. Mol. Microbiol. 16, 1-7.