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.
Full text
PDFImages in this article
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]