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. 1991 Dec 1;88(23):10450–10454. doi: 10.1073/pnas.88.23.10450

A triplex DNA-binding protein from human cells: purification and characterization.

R Kiyama 1, R D Camerini-Otero 1
PMCID: PMC52946  PMID: 1961709

Abstract

A protein that binds to an oligonucleotide triplex, (dT)34.(dA)34.(dT)34 (TAT triplex), was purified from HeLa cells by a combination of conventional column chromatography and triplex DNA affinity chromatography. The protein has an apparent molecular mass of 55 kDa on sodium dodecyl sulfate/polyacrylamide gels. Although the protein has an affinity for AT duplex and TAT triplex, a higher affinity for TAT triplex was demonstrated by comparing the elution profiles from an AT duplex and a TAT triplex affinity column. The protein has a moderate affinity for poly(dA-dG).poly(dT-dC) and a very low affinity for single-strand (dA)34 or (dT)34 and various sources of duplex DNA including poly(dA-dT).poly(dA-dT). The possible biological function of this triplex DNA-binding protein is discussed.

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Selected References

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

  1. Adachi Y., Käs E., Laemmli U. K. Preferential, cooperative binding of DNA topoisomerase II to scaffold-associated regions. EMBO J. 1989 Dec 20;8(13):3997–4006. doi: 10.1002/j.1460-2075.1989.tb08582.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  3. Beasty A. M., Behe M. J. An oligopurine sequence bias occurs in eukaryotic viruses. Nucleic Acids Res. 1988 Feb 25;16(4):1517–1528. doi: 10.1093/nar/16.4.1517. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Behe M. J. The DNA sequence of the human beta-globin region is strongly biased in favor of long strings of contiguous purine or pyrimidine residues. Biochemistry. 1987 Dec 1;26(24):7870–7875. doi: 10.1021/bi00398a050. [DOI] [PubMed] [Google Scholar]
  5. Churchill M. E., Suzuki M. 'SPKK' motifs prefer to bind to DNA at A/T-rich sites. EMBO J. 1989 Dec 20;8(13):4189–4195. doi: 10.1002/j.1460-2075.1989.tb08604.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Cooney M., Czernuszewicz G., Postel E. H., Flint S. J., Hogan M. E. Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro. Science. 1988 Jul 22;241(4864):456–459. doi: 10.1126/science.3293213. [DOI] [PubMed] [Google Scholar]
  7. Dignam J. D., Lebovitz R. M., Roeder R. G. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983 Mar 11;11(5):1475–1489. doi: 10.1093/nar/11.5.1475. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fox K. R. Long (dA)n.(dT)n tracts can form intramolecular triplexes under superhelical stress. Nucleic Acids Res. 1990 Sep 25;18(18):5387–5391. doi: 10.1093/nar/18.18.5387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Garreau H., Williams J. G. Two nuclear DNA binding proteins of Dictyostelium discoideum with a high affinity for poly(dA)-poly(dT). Nucleic Acids Res. 1983 Dec 10;11(23):8473–8484. doi: 10.1093/nar/11.23.8473. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gasser S. M., Laemmli U. K. Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell. 1986 Aug 15;46(4):521–530. doi: 10.1016/0092-8674(86)90877-9. [DOI] [PubMed] [Google Scholar]
  11. Hentschel C. C. Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease. Nature. 1982 Feb 25;295(5851):714–716. doi: 10.1038/295714a0. [DOI] [PubMed] [Google Scholar]
  12. Hsieh P., Camerini-Otero C. S., Camerini-Otero R. D. Pairing of homologous DNA sequences by proteins: evidence for three-stranded DNA. Genes Dev. 1990 Nov;4(11):1951–1963. doi: 10.1101/gad.4.11.1951. [DOI] [PubMed] [Google Scholar]
  13. Kohwi Y., Kohwi-Shigematsu T. Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc Natl Acad Sci U S A. 1988 Jun;85(11):3781–3785. doi: 10.1073/pnas.85.11.3781. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Käs E., Izaurralde E., Laemmli U. K. Specific inhibition of DNA binding to nuclear scaffolds and histone H1 by distamycin. The role of oligo(dA).oligo(dT) tracts. J Mol Biol. 1989 Dec 5;210(3):587–599. doi: 10.1016/0022-2836(89)90134-4. [DOI] [PubMed] [Google Scholar]
  15. Lee J. S., Burkholder G. D., Latimer L. J., Haug B. L., Braun R. P. A monoclonal antibody to triplex DNA binds to eucaryotic chromosomes. Nucleic Acids Res. 1987 Feb 11;15(3):1047–1061. doi: 10.1093/nar/15.3.1047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Levinger L., Varshavsky A. Protein D1 preferentially binds A + T-rich DNA in vitro and is a component of Drosophila melanogaster nucleosomes containing A + T-rich satellite DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(23):7152–7156. doi: 10.1073/pnas.79.23.7152. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Maher L. J., 3rd, Wold B., Dervan P. B. Inhibition of DNA binding proteins by oligonucleotide-directed triple helix formation. Science. 1989 Aug 18;245(4919):725–730. doi: 10.1126/science.2549631. [DOI] [PubMed] [Google Scholar]
  18. Mirkin S. M., Lyamichev V. I., Drushlyak K. N., Dobrynin V. N., Filippov S. A., Frank-Kamenetskii M. D. DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature. 1987 Dec 3;330(6147):495–497. doi: 10.1038/330495a0. [DOI] [PubMed] [Google Scholar]
  19. Morgan A. R., Wells R. D. Specificity of the three-stranded complex formation between double-stranded DNA and single-stranded RNA containing repeating nucleotide sequences. J Mol Biol. 1968 Oct 14;37(1):63–80. doi: 10.1016/0022-2836(68)90073-9. [DOI] [PubMed] [Google Scholar]
  20. Moser H. E., Dervan P. B. Sequence-specific cleavage of double helical DNA by triple helix formation. Science. 1987 Oct 30;238(4827):645–650. doi: 10.1126/science.3118463. [DOI] [PubMed] [Google Scholar]
  21. Nickol J. M., Felsenfeld G. DNA conformation at the 5' end of the chicken adult beta-globin gene. Cell. 1983 Dec;35(2 Pt 1):467–477. doi: 10.1016/0092-8674(83)90180-0. [DOI] [PubMed] [Google Scholar]
  22. Pilch D. S., Levenson C., Shafer R. H. Structural analysis of the (dA)10.2(dT)10 triple helix. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1942–1946. doi: 10.1073/pnas.87.5.1942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Reeves R., Nissen M. S. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem. 1990 May 25;265(15):8573–8582. [PubMed] [Google Scholar]
  24. Rhodes D. Nucleosome cores reconstituted from poly (dA-dT) and the octamer of histones. Nucleic Acids Res. 1979;6(5):1805–1816. doi: 10.1093/nar/6.5.1805. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Simpson R. T., Künzler P. Cromatin and core particles formed from the inner histones and synthetic polydeoxyribonucleotides of defined sequence. Nucleic Acids Res. 1979 Apr;6(4):1387–1415. doi: 10.1093/nar/6.4.1387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Solomon M. J., Strauss F., Varshavsky A. A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1276–1280. doi: 10.1073/pnas.83.5.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  28. Wells R. D., Collier D. A., Hanvey J. C., Shimizu M., Wohlrab F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988 Nov;2(14):2939–2949. [PubMed] [Google Scholar]
  29. Winter E., Varshavsky A. A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. EMBO J. 1989 Jun;8(6):1867–1877. doi: 10.1002/j.1460-2075.1989.tb03583.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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