Abstract
Gel electrophoresis of DNA and protein–DNA complexes has been a key method used in studies of sequence-directed and protein-induced DNA bending1,2. Natural DNA sequences can have protein binding sites adjacent to A-tract bending sites3–5, resulting in the potential for the formation of topologically complex shapes in a localized DNA regulatory domain. An essential first step in deducing the structure and functional significance of such domains is elucidation of the relative direction of bending, which can be determined from the electrophoretic mobilities of isomers having varied helical phasing between the bends. Taking DNA bent around CAP protein as a standard, we conclude that the junction bending model correctly predicts the direction of bending at A5–6 tracts in kinetoplast DNA. The overall direction of the bend is towards the minor groove at the centre of the A tract.
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References
1. Marini, J. C., Levene, S. D., Crothers, D. M. & Englund, P. T. Proc. natn. Acad. Sci. U.S.A. 79, 7664–7668 (1982). 2. Wu, H. M. & Crothers, D. M. Nature 308, 509–513 (1984). 3. Zahn, K. & Blattner, F. R. EMBO J. 44, 3605–3615 (1985). 4. Mukherjee, I. P. & Bastia, D. Cell 43, 189–197 (1985). 5. Ryder, K., Silver, S., DeLucia, A. L., Fanning, E. & Tegtmeyer, P. Cell 44, 719–725 (1986). 6. Lerman, L. S. & Frisch, H. L. Biopolymers 21, 995–997 (1982). 7. Lumpkin, O. J. & Zimm, B. H. Biopolymers 21, 2315–2316 (1982). 8. Koo, H.-S., Wu, H.–M. & Crothers, D. M. Nature 320, 501–506 (1986). 9. Majors, J. thesis, Harvard Univ. (1977). 10. Simpson, R. B. Nucleic Acids Res. 8, 759–766 (1980). 11. Schmitz, A. Nucleic Acids Res. 9, 272–292 (1981). 12. Weber, I. T. & Steitz, T. A. Proc. natn. Acad. Sci. U.S.A. 81, 3973–3977 (1984). 13. Liu-Johnson, H.-N., Gartenberg, M. R. & Crothers, D. M. Cell 47, 995–1005 (1986). 14. Kolb, A. & Buc, H. Nucleic Acids Res. 10, 473–485 (1982). 15. Warwicker, J., Engelman, B. P. & Steitz, T. A. Proteins (submitted). 16. Gronenborn, A. M., Nermut, M. V., Eason, P. & Clore, G. M. J. molec. Biol. 179, 751–757 (1984). 17. Rhodes, D. & Klug, A. Nature 386, 573–578 (1980). 18. Rhodes, D. & Klug, A. Nature 292, 378–380 (1981). 19. Wang, J. C. Proc. natn. Aacd. Sci. U.S.A 76, 200–203 (1979). 20. Peck, L. J. & Wang, J. C. Nature 292, 375–278 (1981). 21. Levene, S. D. & Crothers, D. M. / Biomolec. Str. Dynam, 1, 429–435 (1983). 22. Trifonov, E. N. & Sussman, J. L. Proc. natn. Acad. Sci. U.S.A. 77, 3816–3820 (1980). 23. Ulanovsky, L., Bodner, M., Trifonov, E. N. & Choder, M. Proc. natn. Acad. Sci. U.S.A. 83, 862–866 (1986). 24. Ulanovsky, L. & Trifonov, E. N. Nature (in the press). 25. Hagerman, P. J. Nature 321, 449–450 (1986). 26. Arnott, S., Chandrasekaran, R., Hall, I. H. & Puigjaner, L. C. Nucleic Acids Res. 11, 4141–4155 (1983). 27. Alexeev, D. G., Lipanov, A. A. & Skuratovskii, I. Ya. Nature 325, 831–823 (1987). 28. LeBret, M. Biopolymers 18, 1709–1795 (1979). 29. Shore, D. & Baldwin, R. L. /. molec. Biol. 170, 983–1007 (1983). 30. Horowitz, D. & Wang, J. C. J. molec. Biol. 173, 75–91 (1984). 31. Levene, S. L. & Crothers, D. M. /. molec. Biol.. 189, 73–83 (1986).
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Zinkel, S., Crothers, D. DNA bend direction by phase sensitive detection. Nature 328, 178–181 (1987). https://doi.org/10.1038/328178a0
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DOI: https://doi.org/10.1038/328178a0
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