Regulation of gene expression by small molecules


Small molecules that target specific DNA sequences have the potential to control gene expression. Ligands designed for therapeutic application must bind any predetermined DNA sequence with high affinity and permeate living cells. Synthetic polyamides containing N-methylimidazole and N-methylpyrrole amino acids have an affinity and specificity for DNA comparable to naturally occurring DNA-binding proteins1. We report here that an eight-ring polyamide targeted to a specific region of the transcription factor TFIIIA binding site interferes with 5S RNA gene expression in Xenopus kidney cells. Our results indicate that pyrrole-imida-zole polyamides are cell-permeable and can inhibit the transcription of specific genes.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.


  1. 1

    1. Trauger, J. W., Baird, E. E. & Dervan, P. B. Recognition of DNA by designed ligands at subnanomolar concentrations. Nature 382, 559-561 (1996). 2. Moser, H. E. & Dervan, P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238, 645-650 (1987). 3. Thuong, N. T. & Helene, C. Sequence-specific recognition and modification of double-helical DNA by oligonucleotides. Angew. Chem. Int. Ed. Engl. 32, 666-690 (1993). 4. Maher, J. L., Dervan, P. B. & Wold, B. Analysis of promoter-specific repression by triple-helical DNA complexes in a eukaryotic cell-free transcription system. Biochemistry 31, 70-81 (1992). 5. Duvalvalentin, G., Thuong, N. T. & Helene, C. Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc. Natl Acad. Sci. USA 89, 504-508 (1992). 6. Ho, S. N., Boyer, S. H., Schreiber, S. L., Danishefsky, S. J. & Crabtree, G. R. Specific inhibition of formation of transcription complexes by a calicheamicin oligosaccharide-a paradigm for the development of transcriptional antagonists. Proc. Natl Acad. Sci. USA 91, 9203-9207 (1994). 7. Liu, C. et al. Sequence-selective carbohydrate DNA interaction-dimeric and monomeric forms of the calicheamicin oligosaccharide interfere with transcription factor function. Proc. Natl Acad. Sci. USA 93, 940-944 (1996). 8. Wade, W. S., Mrksich, M. & Dervan, P. B. Design of peptides that bind in the minor groove of DNA at 5'-(A,T)5G(A,T)C(A,T) sequences by a dimeric side-by-side motif. /. Am. Chem. Soc. 114, 8784-8794 (1992). 9. Mrksich, M. et al. Antiparallel side-by-side dimeric motif for sequence-specific recognition in the minor groove of DNA by the designed peptide l-methylimidazole-2-carboxamidenetropsin. Proc. Natl Acad. Sci. USA 89, 7586-7590 (1992). 10. Pelton, J. G. & Wemmer, D. E. Structural characterization of a 2-1 distamycin A-d(CGCAAATTTG GC) complex by two-dimensional NMR. Proc. Natl Acad. Sci. USA 86, 5723-5727 (1989). 11. White, S., Baird, E. E. & Dervan, P. B. Effects of the A-T/T-A degeneracy of pyrrole-imidazole polyamide recognition in the minor groove of DNA. Biochemistry 35, 12532-12537 (1996). 12. Parks, M. E., Baird, E. E. & Dervan, P. B. Optimization of the hairpin polyamide design for recognition of the minor groove of DNA. /. Am. Chem. Soc. 118, 6147-6152 (1996). 13. Trauger, J. W., Baird, E. E., Mrksich, M. & Dervan, P. B. Extension of sequence-specific recognition in the minor groove of DNA by pyrrole-imidazole polyamides to 9-13 base pairs. /. Am. Chem. Soc. 118, 6160-6166 (1996). 14. Kelly, J. J., Baird, E. E. & Dervan, P. B. Binding site size limit of the 2:1 pyrrole-imidazole polyamide-DNA motif. Proc. Natl Acad. Sci. USA 93, 6981-6985 (1996). 15. Geierstanger, B. H., Mrksich, M., Dervan, P. B. & Wemmer, D. E. Design of a G-C-specific minor groove-binding peptide. Science 266, 646-650 (1994). 16. Schlissel, M. S. & Brown, D. D. The transcriptional regulation of Xenopus 5S RNA genes in chromatin-the roles of active stable transcription complexes and histone HI. Cell 37, 903-913 (1984). 17. Engelke, D. R., Ng, S.-Y., Shastry, B. S. & Roeder, R. G. Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes. Cell 19, 717-728 (1980). 18. Wolffe, A. P. & Brown, D. D. Developmental regulation of two 5S ribosomal RNA genes. Science 241, 1626-1632 (1988). 19. Fairall, L., Rhodes, D. & Klug, A. Mapping of the sites of protection on a 5S-RNA gene by the Xenopus transcription factor-IIIA-a model for the interaction. /. Mol. Biol. 192, 577-591 (1986). 20. Sakonju, S. & Brown, D. D. Contact points between a positive transcription factor and the Xenopus 5S RNA gene. Cell 31, 395-405 (1982). 21. Clemens, K. R., Liao, X. B., Wolf, V., Wright, P. E. & Gottesfeld, J. M. Definition of the binding sites of individual zinc fingers in the transcription factor-IIIA-5S RNA gene complex. Proc. Natl Acad. Sci. USA 89, 10822-10826 (1992). 22. Hayes, J. J. & Tullius, T. D. Structure of the TFIIIA 5S DNA complex./. Mol. Biol. 227,407-417 (1992). 23. Clemens, K. R. et al. Relative contributions of the zinc fingers of transcription factor IIIA to the energetics of DNA binding. /. Mol. Biol. 244, 23-35 (1994). 24. Stutz, E, Gouilloud, E. & Clarkson, S. G. Oocyte and somatic tyrosine transfer-RNA genes in Xenopus laevis. Genes Dev. 3, 1190-1198 (1989). 25. Baird, E. E. & Dervan, P. B. Solid-phase synthesis of polyamides containing imidazole and pyrrole amino-acids. /. Am. Chem. Soc. 118, 6141-6146 (1996). 26. Hartl, P., Gottesfeld, J. M. & Forbes, D. J. Mitotic repression of transcription in vitro. J. Cell Biol. 120, 613-624 (1993). 27. Peterson, R. C., Doering, J. L. & Brown, D. D. Characterization of two Xenopus somatic DNAs and one minor oocyte specific 5S DNA. Cell 20, 131-141 (1980). 28. Smith, D. R., Jackson, I. J. & Brown, D. D. Domains of the positive transcription factor specific for the Xenopus 5S-RNA gene. Cell 37, 645-652 (1984). 29. Roeder, R. G. Multiple forms of DNA-dependent RNA-polymerases in Xenopus laevis-properties, purification, and subunit structure of class III RNA polymerases. /. Biol. Chem. 258, 1932-1941 (1983).

Download references

Author information

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Gottesfeld, J., Neely, L., Trauger, J. et al. Regulation of gene expression by small molecules. Nature 387, 202–205 (1997).

Download citation

Further reading


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.