Skip to main content
PMC home page
Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1994 Nov 8;91(23):11163–11167. doi: 10.1073/pnas.91.23.11163

Toward a code for the interactions of zinc fingers with DNA: selection of randomized fingers displayed on phage.

Y Choo 1, A Klug 1
PMCID: PMC45187  PMID: 7972027

Abstract

We have used two selection techniques to study sequence-specific DNA recognition by the zinc finger, a small, modular DNA-binding minidomain. We have chosen zinc fingers because they bind as independent modules and so can be linked together in a peptide designed to bind a predetermined DNA site. In this paper, we describe how a library of zinc fingers displayed on the surface of bacteriophage enables selection of fingers capable of binding to given DNA triplets. The amino acid sequences of selected fingers which bind the same triplet are compared to examine how sequence-specific DNA recognition occurs. Our results can be rationalized in terms of coded interactions between zinc fingers and DNA, involving base contacts from a few alpha-helical positions. In the paper following this one, we describe a complementary technique which confirms the identity of amino acids capable of DNA sequence discrimination from these positions.

Full text

PDF
11163

Images in this article

11165Image
on p.11165
11166Image
on p.11166

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bass S., Greene R., Wells J. A. Hormone phage: an enrichment method for variant proteins with altered binding properties. Proteins. 1990;8(4):309–314. doi: 10.1002/prot.340080405. [DOI] [PubMed] [Google Scholar]
  2. Berg J. M. Proposed structure for the zinc-binding domains from transcription factor IIIA and related proteins. Proc Natl Acad Sci U S A. 1988 Jan;85(1):99–102. doi: 10.1073/pnas.85.1.99. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Berg J. M. Sp1 and the subfamily of zinc finger proteins with guanine-rich binding sites. Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11109–11110. doi: 10.1073/pnas.89.23.11109. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Choo Y., Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11168–11172. doi: 10.1073/pnas.91.23.11168. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Christy B. A., Lau L. F., Nathans D. A gene activated in mouse 3T3 cells by serum growth factors encodes a protein with "zinc finger" sequences. Proc Natl Acad Sci U S A. 1988 Nov;85(21):7857–7861. doi: 10.1073/pnas.85.21.7857. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Christy B., Nathans D. DNA binding site of the growth factor-inducible protein Zif268. Proc Natl Acad Sci U S A. 1989 Nov;86(22):8737–8741. doi: 10.1073/pnas.86.22.8737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Desjarlais, Berg J. M. Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach. Proteins. 1992 Jul;13(3):272–272. doi: 10.1002/prot.340130309. [DOI] [PubMed] [Google Scholar]
  8. Desjarlais J. R., Berg J. M. Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7345–7349. doi: 10.1073/pnas.89.16.7345. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Dickerson R. E., Drew H. R. Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. J Mol Biol. 1981 Jul 15;149(4):761–786. doi: 10.1016/0022-2836(81)90357-0. [DOI] [PubMed] [Google Scholar]
  10. Fairall L., Schwabe J. W., Chapman L., Finch J. T., Rhodes D. The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature. 1993 Dec 2;366(6454):483–487. doi: 10.1038/366483a0. [DOI] [PubMed] [Google Scholar]
  11. Ginsberg A. M., King B. O., Roeder R. G. Xenopus 5S gene transcription factor, TFIIIA: characterization of a cDNA clone and measurement of RNA levels throughout development. Cell. 1984 Dec;39(3 Pt 2):479–489. doi: 10.1016/0092-8674(84)90455-0. [DOI] [PubMed] [Google Scholar]
  12. Harrison S. C. A structural taxonomy of DNA-binding domains. Nature. 1991 Oct 24;353(6346):715–719. doi: 10.1038/353715a0. [DOI] [PubMed] [Google Scholar]
  13. Harrison S. D., Travers A. A. The tramtrack gene encodes a Drosophila finger protein that interacts with the ftz transcriptional regulatory region and shows a novel embryonic expression pattern. EMBO J. 1990 Jan;9(1):207–216. doi: 10.1002/j.1460-2075.1990.tb08097.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hoogenboom H. R., Griffiths A. D., Johnson K. S., Chiswell D. J., Hudson P., Winter G. Multi-subunit proteins on the surface of filamentous phage: methodologies for displaying antibody (Fab) heavy and light chains. Nucleic Acids Res. 1991 Aug 11;19(15):4133–4137. doi: 10.1093/nar/19.15.4133. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hunter C. A. Sequence-dependent DNA structure. The role of base stacking interactions. J Mol Biol. 1993 Apr 5;230(3):1025–1054. doi: 10.1006/jmbi.1993.1217. [DOI] [PubMed] [Google Scholar]
  16. Jacobs G. H. Determination of the base recognition positions of zinc fingers from sequence analysis. EMBO J. 1992 Dec;11(12):4507–4517. doi: 10.1002/j.1460-2075.1992.tb05552.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kinzler K. W., Ruppert J. M., Bigner S. H., Vogelstein B. The GLI gene is a member of the Kruppel family of zinc finger proteins. Nature. 1988 Mar 24;332(6162):371–374. doi: 10.1038/332371a0. [DOI] [PubMed] [Google Scholar]
  18. Klug A. Co-chairman's remarks: protein designs for the specific recognition of DNA. Gene. 1993 Dec 15;135(1-2):83–92. doi: 10.1016/0378-1119(93)90052-5. [DOI] [PubMed] [Google Scholar]
  19. Lee M. S., Gippert G. P., Soman K. V., Case D. A., Wright P. E. Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science. 1989 Aug 11;245(4918):635–637. doi: 10.1126/science.2503871. [DOI] [PubMed] [Google Scholar]
  20. Marks J. D., Hoogenboom H. R., Griffiths A. D., Winter G. Molecular evolution of proteins on filamentous phage. Mimicking the strategy of the immune system. J Biol Chem. 1992 Aug 15;267(23):16007–16010. [PubMed] [Google Scholar]
  21. Matthews B. W. Protein-DNA interaction. No code for recognition. Nature. 1988 Sep 22;335(6188):294–295. doi: 10.1038/335294a0. [DOI] [PubMed] [Google Scholar]
  22. McCafferty J., Griffiths A. D., Winter G., Chiswell D. J. Phage antibodies: filamentous phage displaying antibody variable domains. Nature. 1990 Dec 6;348(6301):552–554. doi: 10.1038/348552a0. [DOI] [PubMed] [Google Scholar]
  23. Miller J., McLachlan A. D., Klug A. Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. EMBO J. 1985 Jun;4(6):1609–1614. doi: 10.1002/j.1460-2075.1985.tb03825.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Nardelli J., Gibson T. J., Vesque C., Charnay P. Base sequence discrimination by zinc-finger DNA-binding domains. Nature. 1991 Jan 10;349(6305):175–178. doi: 10.1038/349175a0. [DOI] [PubMed] [Google Scholar]
  25. Nardelli J., Gibson T., Charnay P. Zinc finger-DNA recognition: analysis of base specificity by site-directed mutagenesis. Nucleic Acids Res. 1992 Aug 25;20(16):4137–4144. doi: 10.1093/nar/20.16.4137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Pabo C. O., Sauer R. T. Transcription factors: structural families and principles of DNA recognition. Annu Rev Biochem. 1992;61:1053–1095. doi: 10.1146/annurev.bi.61.070192.005201. [DOI] [PubMed] [Google Scholar]
  27. Pavletich N. P., Pabo C. O. Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. Science. 1993 Sep 24;261(5129):1701–1707. doi: 10.1126/science.8378770. [DOI] [PubMed] [Google Scholar]
  28. Pavletich N. P., Pabo C. O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 A. Science. 1991 May 10;252(5007):809–817. doi: 10.1126/science.2028256. [DOI] [PubMed] [Google Scholar]
  29. Rebar E. J., Pabo C. O. Zinc finger phage: affinity selection of fingers with new DNA-binding specificities. Science. 1994 Feb 4;263(5147):671–673. doi: 10.1126/science.8303274. [DOI] [PubMed] [Google Scholar]
  30. Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. doi: 10.1073/pnas.73.3.804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Smith G. P. Filamentous fusion phage: novel expression vectors that display cloned antigens on the virion surface. Science. 1985 Jun 14;228(4705):1315–1317. doi: 10.1126/science.4001944. [DOI] [PubMed] [Google Scholar]
  32. Stengele I., Bross P., Garcés X., Giray J., Rasched I. Dissection of functional domains in phage fd adsorption protein. Discrimination between attachment and penetration sites. J Mol Biol. 1990 Mar 5;212(1):143–149. doi: 10.1016/0022-2836(90)90311-9. [DOI] [PubMed] [Google Scholar]
  33. Suzuki M. A framework for the DNA-protein recognition code of the probe helix in transcription factors: the chemical and stereochemical rules. Structure. 1994 Apr 15;2(4):317–326. doi: 10.1016/s0969-2126(00)00033-2. [DOI] [PubMed] [Google Scholar]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES