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Chemical crosshairs on the central dogma

As cellular machines and processes that regulate the flow of genomic information have come into sharper focus, a new level of chemical control has become possible. The scope of such chemical intervention extends from the mechanistic dissection of biochemical processes in living cells to the targeted control of gene networks and cell fate.

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Figure 1: The view of RNA polymerase II since its discovery in 1969.
Figure 2: α-Amanitin binding site in the yeast RNA polymerase II.
Figure 3: Biological concepts that have influenced the design of chemical ligands.
Figure 4: Chemical control of the central dogma.

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References

  1. Kornberg, R.D. Biol. Chem. 382, 1103–1107 (2001).

    Article  CAS  Google Scholar 

  2. Fire, A. et al. Nature 391, 806–811 (1998).

    Article  CAS  Google Scholar 

  3. Boeger, H. et al. FEBS Lett. 579, 899–903 (2005).

    Article  CAS  Google Scholar 

  4. Zhang, G. et al. Cell 98, 811–824 (1999).

    Article  CAS  Google Scholar 

  5. Gnatt, A.L., Cramer, P., Fu, J., Bushnell, D.A. & Kornberg, R.D. Science 292, 1876–1882 (2001).

    Article  CAS  Google Scholar 

  6. Khorana, H.G. Biochem. J. 109, 709–725 (1968).

    Article  CAS  Google Scholar 

  7. Roeder, R.G. & Rutter, W.J. Nature 224, 234–237 (1969).

    Article  CAS  Google Scholar 

  8. Weinmann, R., Raskas, H.J. & Roeder, R.G. Cold Spring Harb. Symp. Quant. Biol. 39, 495–499 (1975).

    Article  Google Scholar 

  9. Bushnell, D.A., Cramer, P. & Kornberg, R.D. Proc. Natl. Acad. Sci. USA 99, 1218–1222 (2002).

    Article  CAS  Google Scholar 

  10. Darst, S.A. Trends Biochem. Sci. 29, 159–160 (2004).

    Article  CAS  Google Scholar 

  11. Grozinger, C.M. & Schreiber, S.L. Chem. Biol. 9, 3–16 (2002).

    Article  CAS  Google Scholar 

  12. Marks, P.A., Richon, V.M., Breslow, R. & Rifkind, R.A. Curr. Opin. Oncol. 13, 477–483 (2001).

    Article  CAS  Google Scholar 

  13. Lau, O.D. et al. Mol. Cell 5, 589–595 (2000).

    Article  CAS  Google Scholar 

  14. Greiner, D., Bonaldi, T., Eskeland, R., Roemer, E. & Imhof, A. Nat. Chem. Biol. 1, 143–145 (2005).

    Article  CAS  Google Scholar 

  15. Kornberg, R.D. & Lorch, Y. Cell 98, 285–294 (1999).

    Article  CAS  Google Scholar 

  16. McNally, J.G., Muller, W.G., Walker, D., Wolford, R. & Hager, G.L. Science 287, 1262–1265 (2000).

    Article  CAS  Google Scholar 

  17. Yao, J., Munson, K.M., Webb, W.W. & Lis, J.T. Nature 442, 1050–1053 (2006).

    Article  CAS  Google Scholar 

  18. Kodadek, T., Sikder, D. & Nalley, K. Cell 127, 261–264 (2006).

    Article  CAS  Google Scholar 

  19. Vermeulen, W. & Houtsmuller, A.B. Mol. Cell 10, 1264–1266 (2002).

    Article  CAS  Google Scholar 

  20. Xie, X.S., Yu, J. & Yang, W.Y. Science 312, 228–230 (2006).

    Article  CAS  Google Scholar 

  21. Raser, J.M. & O'Shea, E.K. Science 309, 2010–2013 (2005).

    Article  CAS  Google Scholar 

  22. Wang, L., Xie, J. & Schultz, P.G. Annu. Rev. Biophys. Biomol. Struct. 35, 225–249 (2006).

    Article  Google Scholar 

  23. Giepmans, B.N., Adams, S.R., Ellisman, M.H. & Tsien, R.Y. Science 312, 217–224 (2006).

    Article  CAS  Google Scholar 

  24. Chen, I. & Ting, A.Y. Curr. Opin. Biotechnol. 16, 35–40 (2005).

    Article  CAS  Google Scholar 

  25. Prescher, J.A. & Bertozzi, C.R. Nat. Chem. Biol. 1, 13–21 (2005).

    Article  CAS  Google Scholar 

  26. Rothman, D.M., Shults, M.D. & Imperiali, B. Trends Cell Biol. 15, 502–510 (2005).

    Article  CAS  Google Scholar 

  27. Massoud, T.F. & Gambhir, S.S. Genes Dev. 17, 545–580 (2003).

    Article  CAS  Google Scholar 

  28. Corey, D.R. Ann. NY Acad. Sci. 1058, 16–25 (2005).

    Article  CAS  Google Scholar 

  29. Nielsen, P.E. Methods Mol. Biol. 288, 343–358 (2005).

    CAS  PubMed  Google Scholar 

  30. Kalish, J.M. & Glazer, P.M. Ann. NY Acad. Sci. 1058, 151–161 (2005).

    Article  CAS  Google Scholar 

  31. Pei, Y. & Tuschl, T. Nat. Methods 3, 670–676 (2006).

    Article  CAS  Google Scholar 

  32. Novina, C.D. & Sharp, P.A. Nature 430, 161–164 (2004).

    Article  CAS  Google Scholar 

  33. Zimmermann, T.S. et al. Nature 441, 111–114 (2006).

    Article  CAS  Google Scholar 

  34. Puthenveetil, S. et al. Nucleic Acids Res. 34, 4900–4911 (2006).

    Article  CAS  Google Scholar 

  35. Grundy, F.J. & Henkin, T.M. Curr. Opin. Microbiol. 7, 126–131 (2004).

    Article  CAS  Google Scholar 

  36. Winkler, W.C. & Breaker, R.R. Annu. Rev. Microbiol. 59, 487–517 (2005).

    Article  CAS  Google Scholar 

  37. Nudler, E. Cell 126, 19–22 (2006).

    Article  CAS  Google Scholar 

  38. Ansari, A.Z. & Mapp, A.K. Curr. Opin. Chem. Biol. 6, 765–772 (2002).

    Article  CAS  Google Scholar 

  39. Dervan, P.B., Doss, R.M. & Marques, M.A. Curr. Med. Chem. Anticancer Agents 5, 373–387 (2005).

    Article  CAS  Google Scholar 

  40. Mandell, J.G. & Barbas, C.F. III. Nucleic Acids Res. 34, W516–W523 (2006).

    Article  CAS  Google Scholar 

  41. Majmudar, C.Y. & Mapp, A.K. Curr. Opin. Chem. Biol. 9, 467–474 (2005).

    Article  CAS  Google Scholar 

  42. Cartegni, L. & Krainer, A.R. Nat. Struct. Biol. 10, 120–125 (2003).

    Article  CAS  Google Scholar 

  43. Schneekloth, J.S. Jr. et al. J. Am. Chem. Soc. 126, 3748–3754 (2004).

    Article  CAS  Google Scholar 

  44. Boger, D.L., Desharnais, J. & Capps, K. Angew. Chem. Int. Edn. Engl. 42, 4138–4176 (2003).

    Article  CAS  Google Scholar 

  45. Sprinzak, D. & Elowitz, M.B. Nature 438, 443–448 (2005).

    Article  CAS  Google Scholar 

  46. Lindell, T.J., Weinberg, F., Morris, P.W., Roeder, R.G. & Rutter, W.J. Science 170, 447–449 (1970).

    Article  CAS  Google Scholar 

  47. Darst, S.A., Edwards, A.M., Kubalek, E.W. & Kornberg, R.D. Cell 66, 121–128 (1991).

    Article  CAS  Google Scholar 

  48. Ptashne, M. & Gann, A. Genes & Signals (Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, 2001).

    Google Scholar 

  49. Arndt, H.D. et al. J. Am. Chem. Soc. 125, 13322–13323 (2003).

    Article  CAS  Google Scholar 

  50. Passner, J.M., Ryoo, H.D., Shen, L., Mann, R.S. & Aggarwal, A.K. Nature 397, 714–719 (1999).

    Article  CAS  Google Scholar 

  51. Hauschild, K.E. et al. Proc. Natl. Acad. Sci. USA 102, 5008–5013 (2005).

    Article  CAS  Google Scholar 

  52. Schreiber, S.L. Science 287, 1964–1969 (2000).

    Article  CAS  Google Scholar 

  53. Johns, G.C. & Joyce, G.F. J. Mol. Evol. 61, 253–263 (2005).

    Article  CAS  Google Scholar 

  54. Shuker, S.B., Hajduk, P.J., Meadows, R.P. & Fesik, S.W. Science 274, 1531–1534 (1996).

    Article  CAS  Google Scholar 

  55. Erlanson, D.A., Wells, J.A. & Braisted, A.C. Annu. Rev. Biophys. Biomol. Struct. 33, 199–223 (2004).

    Article  CAS  Google Scholar 

  56. Chin, J.W. Nat. Chem. Biol. 2, 304–311 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

I apologize to many friends and colleagues whom I could not reference, and I thank those who generously helped in assembling this commentary. The support of the US National Institutes of Health and the Shaw and Keck foundations is gratefully acknowledged.

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Ansari, A. Chemical crosshairs on the central dogma. Nat Chem Biol 3, 2–7 (2007). https://doi.org/10.1038/nchembio0107-2

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