Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1994 Aug 25;22(16):3397–3405. doi: 10.1093/nar/22.16.3397

Stereochemical basis of DNA recognition by Zn fingers.

M Suzuki 1, M Gerstein 1, N Yagi 1
PMCID: PMC523735  PMID: 8078776

Abstract

DNA-recognition rules for Zn fingers are discussed in terms of crystal structures. The rules can explain the DNA-binding characteristics of a number of Zn finger proteins for which there are no crystal structures. The rules have two parts: chemical rules, which list the possible pairings between the 4 DNA bases and the 20 amino acid residues, and stereochemical rules, which describe the specific base positions contacted by several amino acid positions in the Zn finger. It is discussed that to maintain the correct binding geometry, in which the N-terminus of the recognition helix is closer to the DNA than the C-terminus, the residues facing the DNA on the helix must be larger near the C-terminus, and that two different types of fingers (A and B) bind to DNA in distinctly different ways and cover different numbers of base pairs.

Full text

PDF
3397

Selected References

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

  1. Baldwin A. S., Jr, LeClair K. P., Singh H., Sharp P. A. A large protein containing zinc finger domains binds to related sequence elements in the enhancers of the class I major histocompatibility complex and kappa immunoglobulin genes. Mol Cell Biol. 1990 Apr;10(4):1406–1414. doi: 10.1128/mcb.10.4.1406. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Blumberg H., Eisen A., Sledziewski A., Bader D., Young E. T. Two zinc fingers of a yeast regulatory protein shown by genetic evidence to be essential for its function. 1987 Jul 30-Aug 5Nature. 328(6129):443–445. doi: 10.1038/328443a0. [DOI] [PubMed] [Google Scholar]
  4. Bossone S. A., Asselin C., Patel A. J., Marcu K. B. MAZ, a zinc finger protein, binds to c-MYC and C2 gene sequences regulating transcriptional initiation and termination. Proc Natl Acad Sci U S A. 1992 Aug 15;89(16):7452–7456. doi: 10.1073/pnas.89.16.7452. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Call K. M., Glaser T., Ito C. Y., Buckler A. J., Pelletier J., Haber D. A., Rose E. A., Kral A., Yeger H., Lewis W. H. Isolation and characterization of a zinc finger polypeptide gene at the human chromosome 11 Wilms' tumor locus. Cell. 1990 Feb 9;60(3):509–520. doi: 10.1016/0092-8674(90)90601-a. [DOI] [PubMed] [Google Scholar]
  6. Choo Y., Klug A. A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA. Nucleic Acids Res. 1993 Jul 25;21(15):3341–3346. doi: 10.1093/nar/21.15.3341. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Christensen J. H., Hansen P. K., Lillelund O., Thøgersen H. C. Sequence-specific binding of the N-terminal three-finger fragment of Xenopus transcription factor IIIA to the internal control region of a 5S RNA gene. FEBS Lett. 1991 Apr 9;281(1-2):181–184. doi: 10.1016/0014-5793(91)80388-j. [DOI] [PubMed] [Google Scholar]
  8. 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]
  9. Churchill M. E., Tullius T. D., Klug A. Mode of interaction of the zinc finger protein TFIIIA with a 5S RNA gene of Xenopus. Proc Natl Acad Sci U S A. 1990 Jul;87(14):5528–5532. doi: 10.1073/pnas.87.14.5528. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Delwel R., Funabiki T., Kreider B. L., Morishita K., Ihle J. N. Four of the seven zinc fingers of the Evi-1 myeloid-transforming gene are required for sequence-specific binding to GA(C/T)AAGA(T/C)AAGATAA. Mol Cell Biol. 1993 Jul;13(7):4291–4300. doi: 10.1128/mcb.13.7.4291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Desjarlais J. R., Berg J. M. Redesigning the DNA-binding specificity of a zinc finger protein: a data base-guided approach. Proteins. 1992 Feb;12(2):101–104. doi: 10.1002/prot.340120202. [DOI] [PubMed] [Google Scholar]
  12. Desjarlais J. R., Berg J. M. Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. Proc Natl Acad Sci U S A. 1993 Mar 15;90(6):2256–2260. doi: 10.1073/pnas.90.6.2256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Ebright R. H., Cossart P., Gicquel-Sanzey B., Beckwith J. Molecular basis of DNA sequence recognition by the catabolite gene activator protein: detailed inferences from three mutations that alter DNA sequence specificity. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7274–7278. doi: 10.1073/pnas.81.23.7274. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fairall L., Harrison S. D., Travers A. A., Rhodes D. Sequence-specific DNA binding by a two zinc-finger peptide from the Drosophila melanogaster Tramtrack protein. J Mol Biol. 1992 Jul 20;226(2):349–366. doi: 10.1016/0022-2836(92)90952-g. [DOI] [PubMed] [Google Scholar]
  15. Fairall L., Rhodes D. A new approach to the analysis of DNase I footprinting data and its application to the TFIIIA/5S DNA complex. Nucleic Acids Res. 1992 Sep 25;20(18):4727–4731. doi: 10.1093/nar/20.18.4727. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Fairall L., Rhodes D., Klug A. Mapping of the sites of protection on a 5 S RNA gene by the Xenopus transcription factor IIIA. A model for the interaction. J Mol Biol. 1986 Dec 5;192(3):577–591. doi: 10.1016/0022-2836(86)90278-0. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. Fan C. M., Maniatis T. A DNA-binding protein containing two widely separated zinc finger motifs that recognize the same DNA sequence. Genes Dev. 1990 Jan;4(1):29–42. doi: 10.1101/gad.4.1.29. [DOI] [PubMed] [Google Scholar]
  19. Gibson T. J., Postma J. P., Brown R. S., Argos P. A model for the tertiary structure of the 28 residue DNA-binding motif ('zinc finger') common to many eukaryotic transcriptional regulatory proteins. Protein Eng. 1988 Sep;2(3):209–218. doi: 10.1093/protein/2.3.209. [DOI] [PubMed] [Google Scholar]
  20. Gogos J. A., Hsu T., Bolton J., Kafatos F. C. Sequence discrimination by alternatively spliced isoforms of a DNA binding zinc finger domain. Science. 1992 Sep 25;257(5078):1951–1955. doi: 10.1126/science.1290524. [DOI] [PubMed] [Google Scholar]
  21. Hansen P. K., Christensen J. H., Nyborg J., Lillelund O., Thøgersen H. C. Dissection of the DNA-binding domain of Xenopus laevis TFIIIA. Quantitative DNase I footprinting analysis of specific complexes between a 5 S RNA gene fragment and N-terminal fragments of TFIIIA containing three, four or five zinc-finger domains. J Mol Biol. 1993 Sep 20;233(2):191–202. doi: 10.1006/jmbi.1993.1499. [DOI] [PubMed] [Google Scholar]
  22. Hartshorne T. A., Blumberg H., Young E. T. Sequence homology of the yeast regulatory protein ADR1 with Xenopus transcription factor TFIIIA. Nature. 1986 Mar 20;320(6059):283–287. doi: 10.1038/320283a0. [DOI] [PubMed] [Google Scholar]
  23. Hayes J. J., Tullius T. D. Structure of the TFIIIA-5 S DNA complex. J Mol Biol. 1992 Sep 20;227(2):407–417. doi: 10.1016/0022-2836(92)90897-s. [DOI] [PubMed] [Google Scholar]
  24. Henseling U., Schmidt W., Schöler H. R., Gruss P., Hatzopoulos A. K. A transcription factor interacting with the class I gene enhancer is inactive in tumorigenic cell lines which suppress major histocompatibility complex class I genes. Mol Cell Biol. 1990 Aug;10(8):4100–4109. doi: 10.1128/mcb.10.8.4100. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ip Y. T., Park R. E., Kosman D., Bier E., Levine M. The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo. Genes Dev. 1992 Sep;6(9):1728–1739. doi: 10.1101/gad.6.9.1728. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. Kasai Y., Nambu J. R., Lieberman P. M., Crews S. T. Dorsal-ventral patterning in Drosophila: DNA binding of snail protein to the single-minded gene. Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3414–3418. doi: 10.1073/pnas.89.8.3414. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Keller A. D., Maniatis T. Identification and characterization of a novel repressor of beta-interferon gene expression. Genes Dev. 1991 May;5(5):868–879. doi: 10.1101/gad.5.5.868. [DOI] [PubMed] [Google Scholar]
  29. Keller A. D., Maniatis T. Only two of the five zinc fingers of the eukaryotic transcriptional repressor PRDI-BF1 are required for sequence-specific DNA binding. Mol Cell Biol. 1992 May;12(5):1940–1949. doi: 10.1128/mcb.12.5.1940. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Kinzler K. W., Vogelstein B. The GLI gene encodes a nuclear protein which binds specific sequences in the human genome. Mol Cell Biol. 1990 Feb;10(2):634–642. doi: 10.1128/mcb.10.2.634. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Klevit R. E., Herriott J. R., Horvath S. J. Solution structure of a zinc finger domain of yeast ADR1. Proteins. 1990;7(3):215–226. doi: 10.1002/prot.340070303. [DOI] [PubMed] [Google Scholar]
  32. Klevit R. E. Recognition of DNA by Cys2,His2 zinc fingers. Science. 1991 Sep 20;253(5026):1367–1393. doi: 10.1126/science.1896847. [DOI] [PubMed] [Google Scholar]
  33. Kochoyan M., Keutmann H. T., Weiss M. A. Alternating zinc fingers in the human male associated protein ZFY: refinement of the NMR structure of an even finger by selective deuterium labeling and implications for DNA recognition. Biochemistry. 1991 Jul 23;30(29):7063–7072. doi: 10.1021/bi00243a005. [DOI] [PubMed] [Google Scholar]
  34. Kriwacki R. W., Schultz S. C., Steitz T. A., Caradonna J. P. Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Sp1. Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9759–9763. doi: 10.1073/pnas.89.20.9759. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. 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]
  36. Lemaire P., Vesque C., Schmitt J., Stunnenberg H., Frank R., Charnay P. The serum-inducible mouse gene Krox-24 encodes a sequence-specific transcriptional activator. Mol Cell Biol. 1990 Jul;10(7):3456–3467. doi: 10.1128/mcb.10.7.3456. [DOI] [PMC free article] [PubMed] [Google Scholar]
  37. Letovsky J., Dynan W. S. Measurement of the binding of transcription factor Sp1 to a single GC box recognition sequence. Nucleic Acids Res. 1989 Apr 11;17(7):2639–2653. doi: 10.1093/nar/17.7.2639. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Liao X. B., Clemens K. R., Tennant L., Wright P. E., Gottesfeld J. M. Specific interaction of the first three zinc fingers of TFIIIA with the internal control region of the Xenopus 5 S RNA gene. J Mol Biol. 1992 Feb 20;223(4):857–871. doi: 10.1016/0022-2836(92)90248-i. [DOI] [PubMed] [Google Scholar]
  39. Lipkin S. M., När A. M., Kalla K. A., Sack R. A., Rosenfeld M. G. Identification of a novel zinc finger protein binding a conserved element critical for Pit-1-dependent growth hormone gene expression. Genes Dev. 1993 Sep;7(9):1674–1687. doi: 10.1101/gad.7.9.1674. [DOI] [PubMed] [Google Scholar]
  40. Madden S. L., Cook D. M., Morris J. F., Gashler A., Sukhatme V. P., Rauscher F. J., 3rd Transcriptional repression mediated by the WT1 Wilms tumor gene product. Science. 1991 Sep 27;253(5027):1550–1553. doi: 10.1126/science.1654597. [DOI] [PubMed] [Google Scholar]
  41. Maekawa T., Sakura H., Sudo T., Ishii S. Putative metal finger structure of the human immunodeficiency virus type 1 enhancer binding protein HIV-EP1. J Biol Chem. 1989 Sep 5;264(25):14591–14593. [PubMed] [Google Scholar]
  42. Miller I. J., Bieker J. J. A novel, erythroid cell-specific murine transcription factor that binds to the CACCC element and is related to the Krüppel family of nuclear proteins. Mol Cell Biol. 1993 May;13(5):2776–2786. doi: 10.1128/mcb.13.5.2776. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. 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]
  44. Mitchelmore C., Traboni C., Cortese R. Isolation of two cDNAs encoding zinc finger proteins which bind to the alpha 1-antitrypsin promoter and to the major histocompatibility complex class I enhancer. Nucleic Acids Res. 1991 Jan 11;19(1):141–147. doi: 10.1093/nar/19.1.141. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Moberg K. H., Logan T. J., Tyndall W. A., Hall D. J. Three distinct elements within the murine c-myc promoter are required for transcription. Oncogene. 1992 Mar;7(3):411–421. [PubMed] [Google Scholar]
  46. Morishita K., Parker D. S., Mucenski M. L., Jenkins N. A., Copeland N. G., Ihle J. N. Retroviral activation of a novel gene encoding a zinc finger protein in IL-3-dependent myeloid leukemia cell lines. Cell. 1988 Sep 9;54(6):831–840. doi: 10.1016/s0092-8674(88)91175-0. [DOI] [PubMed] [Google Scholar]
  47. Moses K., Ellis M. C., Rubin G. M. The glass gene encodes a zinc-finger protein required by Drosophila photoreceptor cells. Nature. 1989 Aug 17;340(6234):531–536. doi: 10.1038/340531a0. [DOI] [PubMed] [Google Scholar]
  48. Moses K., Rubin G. M. Glass encodes a site-specific DNA-binding protein that is regulated in response to positional signals in the developing Drosophila eye. Genes Dev. 1991 Apr;5(4):583–593. doi: 10.1101/gad.5.4.583. [DOI] [PubMed] [Google Scholar]
  49. Nagai K., Nakaseko Y., Nasmyth K., Rhodes D. Zinc-finger motifs expressed in E. coli and folded in vitro direct specific binding to DNA. Nature. 1988 Mar 17;332(6161):284–286. doi: 10.1038/332284a0. [DOI] [PubMed] [Google Scholar]
  50. Nakamura T., Donovan D. M., Hamada K., Sax C. M., Norman B., Flanagan J. R., Ozato K., Westphal H., Piatigorsky J. Regulation of the mouse alpha A-crystallin gene: isolation of a cDNA encoding a protein that binds to a cis sequence motif shared with the major histocompatibility complex class I gene and other genes. Mol Cell Biol. 1990 Jul;10(7):3700–3708. doi: 10.1128/mcb.10.7.3700. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. 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]
  52. 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]
  53. Natesan S., Gilman M. Z. DNA bending and orientation-dependent function of YY1 in the c-fos promoter. Genes Dev. 1993 Dec;7(12B):2497–2509. doi: 10.1101/gad.7.12b.2497. [DOI] [PubMed] [Google Scholar]
  54. Nehlin J. O., Carlberg M., Ronne H. Control of yeast GAL genes by MIG1 repressor: a transcriptional cascade in the glucose response. EMBO J. 1991 Nov;10(11):3373–3377. doi: 10.1002/j.1460-2075.1991.tb04901.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Nehlin J. O., Ronne H. Yeast MIG1 repressor is related to the mammalian early growth response and Wilms' tumour finger proteins. EMBO J. 1990 Sep;9(9):2891–2898. doi: 10.1002/j.1460-2075.1990.tb07479.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Neuhaus D., Nakaseko Y., Schwabe J. W., Klug A. Solution structures of two zinc-finger domains from SWI5 obtained using two-dimensional 1H nuclear magnetic resonance spectroscopy. A zinc-finger structure with a third strand of beta-sheet. J Mol Biol. 1992 Nov 20;228(2):637–651. doi: 10.1016/0022-2836(92)90846-c. [DOI] [PubMed] [Google Scholar]
  57. Omichinski J. G., Clore G. M., Appella E., Sakaguchi K., Gronenborn A. M. High-resolution three-dimensional structure of a single zinc finger from a human enhancer binding protein in solution. Biochemistry. 1990 Oct 9;29(40):9324–9334. doi: 10.1021/bi00492a004. [DOI] [PubMed] [Google Scholar]
  58. Omichinski J. G., Clore G. M., Robien M., Sakaguchi K., Appella E., Gronenborn A. M. High-resolution solution structure of the double Cys2His2 zinc finger from the human enhancer binding protein MBP-1. Biochemistry. 1992 Apr 28;31(16):3907–3917. doi: 10.1021/bi00131a004. [DOI] [PubMed] [Google Scholar]
  59. Parkhurst S. M., Harrison D. A., Remington M. P., Spana C., Kelley R. L., Coyne R. S., Corces V. G. The Drosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable element, encodes a putative DNA-binding protein. Genes Dev. 1988 Oct;2(10):1205–1215. doi: 10.1101/gad.2.10.1205. [DOI] [PubMed] [Google Scholar]
  60. 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]
  61. 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]
  62. Payre F., Vincent A. Genomic targets of the serendipity beta and delta zinc finger proteins and their respective DNA recognition sites. EMBO J. 1991 Sep;10(9):2533–2541. doi: 10.1002/j.1460-2075.1991.tb07793.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Pelletier J., Bruening W., Kashtan C. E., Mauer S. M., Manivel J. C., Striegel J. E., Houghton D. C., Junien C., Habib R., Fouser L. Germline mutations in the Wilms' tumor suppressor gene are associated with abnormal urogenital development in Denys-Drash syndrome. Cell. 1991 Oct 18;67(2):437–447. doi: 10.1016/0092-8674(91)90194-4. [DOI] [PubMed] [Google Scholar]
  64. Perkins A. S., Fishel R., Jenkins N. A., Copeland N. G. Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein. Mol Cell Biol. 1991 May;11(5):2665–2674. doi: 10.1128/mcb.11.5.2665. [DOI] [PMC free article] [PubMed] [Google Scholar]
  65. Pyrc J. J., Moberg K. H., Hall D. J. Isolation of a novel cDNA encoding a zinc-finger protein that binds to two sites within the c-myc promoter. Biochemistry. 1992 Apr 28;31(16):4102–4110. doi: 10.1021/bi00131a029. [DOI] [PubMed] [Google Scholar]
  66. Párraga G., Horvath S., Hood L., Young E. T., Klevit R. E. Spectroscopic studies of wild-type and mutant "zinc finger" peptides: determinants of domain folding and structure. Proc Natl Acad Sci U S A. 1990 Jan;87(1):137–141. doi: 10.1073/pnas.87.1.137. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. Rauscher F. J., 3rd, Morris J. F., Tournay O. E., Cook D. M., Curran T. Binding of the Wilms' tumor locus zinc finger protein to the EGR-1 consensus sequence. Science. 1990 Nov 30;250(4985):1259–1262. doi: 10.1126/science.2244209. [DOI] [PubMed] [Google Scholar]
  68. Ron D., Brasier A. R., Habener J. F. Angiotensinogen gene-inducible enhancer-binding protein 1, a member of a new family of large nuclear proteins that recognize nuclear factor kappa B-binding sites through a zinc finger motif. Mol Cell Biol. 1991 May;11(5):2887–2895. doi: 10.1128/mcb.11.5.2887. [DOI] [PMC free article] [PubMed] [Google Scholar]
  69. Rosenfeld R., Margalit H. Zinc fingers: conserved properties that can distinguish between spurious and actual DNA-binding motifs. J Biomol Struct Dyn. 1993 Dec;11(3):557–570. doi: 10.1080/07391102.1993.10508015. [DOI] [PubMed] [Google Scholar]
  70. Rustgi A. K., Van 't Veer L. J., Bernards R. Two genes encode factors with NF-kappa B- and H2TF1-like DNA-binding properties. Proc Natl Acad Sci U S A. 1990 Nov;87(22):8707–8710. doi: 10.1073/pnas.87.22.8707. [DOI] [PMC free article] [PubMed] [Google Scholar]
  71. Schuh R., Aicher W., Gaul U., Côté S., Preiss A., Maier D., Seifert E., Nauber U., Schröder C., Kemler R. A conserved family of nuclear proteins containing structural elements of the finger protein encoded by Krüppel, a Drosophila segmentation gene. Cell. 1986 Dec 26;47(6):1025–1032. doi: 10.1016/0092-8674(86)90817-2. [DOI] [PubMed] [Google Scholar]
  72. Schultz S. C., Shields G. C., Steitz T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science. 1991 Aug 30;253(5023):1001–1007. doi: 10.1126/science.1653449. [DOI] [PubMed] [Google Scholar]
  73. 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]
  74. Sham M. H., Vesque C., Nonchev S., Marshall H., Frain M., Gupta R. D., Whiting J., Wilkinson D., Charnay P., Krumlauf R. The zinc finger gene Krox20 regulates HoxB2 (Hox2.8) during hindbrain segmentation. Cell. 1993 Jan 29;72(2):183–196. doi: 10.1016/0092-8674(93)90659-e. [DOI] [PubMed] [Google Scholar]
  75. Shea M. J., King D. L., Conboy M. J., Mariani B. D., Kafatos F. C. Proteins that bind to Drosophila chorion cis-regulatory elements: a new C2H2 zinc finger protein and a C2C2 steroid receptor-like component. Genes Dev. 1990 Jul;4(7):1128–1140. doi: 10.1101/gad.4.7.1128. [DOI] [PubMed] [Google Scholar]
  76. Shi Y., Seto E., Chang L. S., Shenk T. Transcriptional repression by YY1, a human GLI-Krüppel-related protein, and relief of repression by adenovirus E1A protein. Cell. 1991 Oct 18;67(2):377–388. doi: 10.1016/0092-8674(91)90189-6. [DOI] [PubMed] [Google Scholar]
  77. Spana C., Corces V. G. DNA bending is a determinant of binding specificity for a Drosophila zinc finger protein. Genes Dev. 1990 Sep;4(9):1505–1515. doi: 10.1101/gad.4.9.1505. [DOI] [PubMed] [Google Scholar]
  78. Stanojević D., Hoey T., Levine M. Sequence-specific DNA-binding activities of the gap proteins encoded by hunchback and Krüppel in Drosophila. Nature. 1989 Sep 28;341(6240):331–335. doi: 10.1038/341331a0. [DOI] [PubMed] [Google Scholar]
  79. 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]
  80. Takatsuji H., Mori M., Benfey P. N., Ren L., Chua N. H. Characterization of a zinc finger DNA-binding protein expressed specifically in Petunia petals and seedlings. EMBO J. 1992 Jan;11(1):241–249. doi: 10.1002/j.1460-2075.1992.tb05047.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  81. Tebb G., Moll T., Dowzer C., Nasmyth K. SWI5 instability may be necessary but is not sufficient for asymmetric HO expression in yeast. Genes Dev. 1993 Mar;7(3):517–528. doi: 10.1101/gad.7.3.517. [DOI] [PubMed] [Google Scholar]
  82. Thukral S. K., Eisen A., Young E. T. Two monomers of yeast transcription factor ADR1 bind a palindromic sequence symmetrically to activate ADH2 expression. Mol Cell Biol. 1991 Mar;11(3):1566–1577. doi: 10.1128/mcb.11.3.1566. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Treisman J., Desplan C. The products of the Drosophila gap genes hunchback and Krüppel bind to the hunchback promoters. Nature. 1989 Sep 28;341(6240):335–337. doi: 10.1038/341335a0. [DOI] [PubMed] [Google Scholar]
  84. Vincent A., Colot H. V., Rosbash M. Sequence and structure of the serendipity locus of Drosophila melanogaster. A densely transcribed region including a blastoderm-specific gene. J Mol Biol. 1985 Nov 5;186(1):149–166. doi: 10.1016/0022-2836(85)90265-7. [DOI] [PubMed] [Google Scholar]
  85. Wu L. C., Mak C. H., Dear N., Boehm T., Foroni L., Rabbitts T. H. Molecular cloning of a zinc finger protein which binds to the heptamer of the signal sequence for V(D)J recombination. Nucleic Acids Res. 1993 Nov 11;21(22):5067–5073. doi: 10.1093/nar/21.22.5067. [DOI] [PMC free article] [PubMed] [Google Scholar]
  86. Zarkower D., Hodgkin J. Molecular analysis of the C. elegans sex-determining gene tra-1: a gene encoding two zinc finger proteins. Cell. 1992 Jul 24;70(2):237–249. doi: 10.1016/0092-8674(92)90099-x. [DOI] [PubMed] [Google Scholar]
  87. Zarkower D., Hodgkin J. Zinc fingers in sex determination: only one of the two C. elegans Tra-1 proteins binds DNA in vitro. Nucleic Acids Res. 1993 Aug 11;21(16):3691–3698. doi: 10.1093/nar/21.16.3691. [DOI] [PMC free article] [PubMed] [Google Scholar]
  88. Zhu H., Nguyen V. T., Brown A. B., Pourhosseini A., Garcia A. V., van Bilsen M., Chien K. R. A novel, tissue-restricted zinc finger protein (HF-1b) binds to the cardiac regulatory element (HF-1b/MEF-2) in the rat myosin light-chain 2 gene. Mol Cell Biol. 1993 Jul;13(7):4432–4444. doi: 10.1128/mcb.13.7.4432. [DOI] [PMC free article] [PubMed] [Google Scholar]
  89. Zuo P., Stanojević D., Colgan J., Han K., Levine M., Manley J. L. Activation and repression of transcription by the gap proteins hunchback and Krüppel in cultured Drosophila cells. Genes Dev. 1991 Feb;5(2):254–264. doi: 10.1101/gad.5.2.254. [DOI] [PubMed] [Google Scholar]
  90. van 't Veer L. J., Lutz P. M., Isselbacher K. J., Bernards R. Structure and expression of major histocompatibility complex-binding protein 2, a 275-kDa zinc finger protein that binds to an enhancer of major histocompatibility complex class I genes. Proc Natl Acad Sci U S A. 1992 Oct 1;89(19):8971–8975. doi: 10.1073/pnas.89.19.8971. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES