Intercalation, DNA kinking, and the control of transcription

Science

Volumn 271, Issue 5250, 1996, Pages 778-784

  Werner, Milton H ^a   Gronenborn, Angela M ^a   Clore, G Marius ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA B; INTERCALATING AGENT;

ARTICLE; DNA HELIX; DNA PROTEIN COMPLEX; DNA STRUCTURE; HYDROPHOBICITY; PRIORITY JOURNAL; STRUCTURE ACTIVITY RELATION; TRANSCRIPTION REGULATION;

EID: 0030046809     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.271.5250.778     Document Type: Article

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88. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
89. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
90. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
91. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
92. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
93. Bending without intercalation or exclusive minor groove binding occurs in the protein-DNA complexes of several transcription factors from prokaryotes and eukaryotes, for example, E coli CAP protein [S. C. Schulte, G. C. Shields, T. A. Steitz, Science 253, 101 (1991)], HNF3/forkhead [K. L. Clark, E. D. Halay, E Lai, S K Burley, Nature 364, 412 (1993)], and the a1/α2 homeodomain [T. Li, M. R. Stark, A. D. Johnson, C. Wolberger, Science 270, 262 (1995)]. Kinking occurs in several DNA enzymes without intercalation, for example, deoxyribonuclease 1 [S. A Weston, A. Lahm, D. Suck, J. Mol Biol. 226, 1237 (1992)], Eco RV [F. K. Winkler et al., EMBO J 12, 1781 (1993)], and Eco RI [J A. McClarin et al., Science 234, 1526 (1986)]
94. R. Lavery and H Sklenar, J Biomol. Struct Dyn. 6, 655 (1989).
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97. The coordinates for the LEF-1-DNA complex of Love et al. (7) were not made available to us at the time of writing The structure ot both the protein and the DNA, however, are nearly identical to the structured the SRY-DNA complex (6) at the site of intercalation.
98. N Boutonnet, X Hui, K. Zakrzewska, Biopolymers 33, 479 (1993); E Stofer and R. Lavery, ibid 34, 337 (1994).
99. N Boutonnet, X Hui, K. Zakrzewska, Biopolymers 33, 479 (1993); E Stofer and R. Lavery, ibid 34, 337 (1994).
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103. The style of base representations is adapted from C. R Calladine and H. R. Drew, Understanding DNA: The Molecule and How It Works (Academic Press, New York, 1992).
104. We wish to acknowledge W. A. Eaton, A. Szabo, H A Nash, and V. Zhurkin for critical reading of the manuscript; J. Aarons for help with the art work in Fig. 3; V. Zhurkin for assistance with the analysis of distorted DNA structures and many stimulating discussions, A. A. Gonn, V. Zhurkin, and W. K. Olson for the use of CompDNA; R. G. Brennan, W. I. Lipscomb, S. K. Burley, and X. Cheng for providing crystal structure coordinates; and M. Summers, R J. Fisher, M. Brenowitz, P. Rice, S.-W. Yang, K. Mizuuchi, and H. A Nash for communicating information before publication Supported by the AIDS Targeted Antiviral Program of the Office of the Director of the National Institutes of Health (G.M.C and A.M.G.)