Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1992 Dec 25;20(24):6631–6635. doi: 10.1093/nar/20.24.6631

A single-stranded DNA binding protein from mouse tumor cells specifically recognizes the C-rich strand of the (AGG:CCT)n repeats that can alter DNA conformation.

T Muraiso 1, S Nomoto 1, H Yamazaki 1, Y Mishima 1, R Kominami 1
PMCID: PMC334580  PMID: 1480484

Abstract

A protein that binds to a synthetic oligonucleotide of (CCT)12 has been purified from Ehrlich ascites tumor cells by a (CCT)12 affinity chromatography. The protein (p70) has an apparent molecular mass of 70 kDa, as assayed by Southwestern analysis. A competition experiment revealed that p70 binds to (CCT)12, (CCCT)8 and (CCTCCCT)6, but not to (CTT)12, (CT)16 and (CCTGCCT)6, suggesting that p70 has a sequence-specificity. The complementary (AGG)12 and the double stranded DNA did not show the binding. It is also confirmed by S1 nuclease analysis that the (AGG:CCT)12 duplex takes a single-stranded conformation in the absence of the protein. This raises a possibility that the duplex forms two single-stranded loops in chromosomes, the C-rich strand being bound to p70. Structural analysis of the resulting (AGG)12 strand by non-denaturing polyacrylamide gel electrophoresis demonstrated the presence of slower and faster migrated conformers in a neutral pH buffer containing 50 mM NaCl at 5 degrees C. The ratio was dependent on the DNA concentration. Both conformers disappeared in the absence of NaCl. This suggests that (AGG)12 can form intra- and inter-molecular complexes by non-Watson-Crick, guanine:guanine base-pairing. The possible biological function of the (AGG:CCT)n duplex and the p70 is discussed.

Full text

PDF
6634

Images in this article

6633Image
on p.6633
6633Image
on p.6633
6634Image
on p.6634
6634Image
on p.6634
6634Image
on p.6634

Selected References

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

  1. Beckman J. S., Weber J. L. Survey of human and rat microsatellites. Genomics. 1992 Apr;12(4):627–631. doi: 10.1016/0888-7543(92)90285-z. [DOI] [PubMed] [Google Scholar]
  2. Bennett K. L., Hill R. E., Pietras D. F., Woodworth-Gutai M., Kane-Haas C., Houston J. M., Heath J. K., Hastie N. D. Most highly repeated dispersed DNA families in the mouse genome. Mol Cell Biol. 1984 Aug;4(8):1561–1571. doi: 10.1128/mcb.4.8.1561. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bernués J., Beltrán R., Casasnovas J. M., Azorín F. Structural polymorphism of homopurine--homopyrimidine sequences: the secondary DNA structure adopted by a d(GA.CT)22 sequence in the presence of zinc ions. EMBO J. 1989 Jul;8(7):2087–2094. doi: 10.1002/j.1460-2075.1989.tb03617.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Blackburn E. H. Structure and function of telomeres. Nature. 1991 Apr 18;350(6319):569–573. doi: 10.1038/350569a0. [DOI] [PubMed] [Google Scholar]
  5. 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]
  6. Duval-Valentin G., Thuong N. T., Hélène C. Specific inhibition of transcription by triple helix-forming oligonucleotides. Proc Natl Acad Sci U S A. 1992 Jan 15;89(2):504–508. doi: 10.1073/pnas.89.2.504. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Emery H. S., Weiner A. M. An irregular satellite sequence is found at the termini of the linear extrachromosomal rDNA in Dictyostelium discoideum. Cell. 1981 Nov;26(3 Pt 1):411–419. doi: 10.1016/0092-8674(81)90210-5. [DOI] [PubMed] [Google Scholar]
  8. Grady D. L., Ratliff R. L., Robinson D. L., McCanlies E. C., Meyne J., Moyzis R. K. Highly conserved repetitive DNA sequences are present at human centromeres. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1695–1699. doi: 10.1073/pnas.89.5.1695. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Henderson E., Hardin C. C., Walk S. K., Tinoco I., Jr, Blackburn E. H. Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell. 1987 Dec 24;51(6):899–908. doi: 10.1016/0092-8674(87)90577-0. [DOI] [PubMed] [Google Scholar]
  10. Hoffman-Liebermann B., Liebermann D., Troutt A., Kedes L. H., Cohen S. N. Human homologs of TU transposon sequences: polypurine/polypyrimidine sequence elements that can alter DNA conformation in vitro and in vivo. Mol Cell Biol. 1986 Nov;6(11):3632–3642. doi: 10.1128/mcb.6.11.3632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Kadonaga J. T., Tjian R. Affinity purification of sequence-specific DNA binding proteins. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5889–5893. doi: 10.1073/pnas.83.16.5889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kiyama R., Camerini-Otero R. D. A triplex DNA-binding protein from human cells: purification and characterization. Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10450–10454. doi: 10.1073/pnas.88.23.10450. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kohwi-Shigematsu T., Kohwi Y. Poly(dG)-poly(dC) sequences, under torsional stress, induce an altered DNA conformation upon neighboring DNA sequences. Cell. 1985 Nov;43(1):199–206. doi: 10.1016/0092-8674(85)90024-8. [DOI] [PubMed] [Google Scholar]
  14. Kolluri R., Torrey T. A., Kinniburgh A. J. A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif. Nucleic Acids Res. 1992 Jan 11;20(1):111–116. doi: 10.1093/nar/20.1.111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  16. Lyamichev V. I., Mirkin S. M., Danilevskaya O. N., Voloshin O. N., Balatskaya S. V., Dobrynin V. N., Filippov S. A., Frank-Kamenetskii M. D. An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH. Nature. 1989 Jun 22;339(6226):634–637. doi: 10.1038/339634a0. [DOI] [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. Miskimins W. K., Roberts M. P., McClelland A., Ruddle F. H. Use of a protein-blotting procedure and a specific DNA probe to identify nuclear proteins that recognize the promoter region of the transferrin receptor gene. Proc Natl Acad Sci U S A. 1985 Oct;82(20):6741–6744. doi: 10.1073/pnas.82.20.6741. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Mitani K., Takahashi Y., Kominami R. A GGCAGG motif in minisatellites affecting their germline instability. J Biol Chem. 1990 Sep 5;265(25):15203–15210. [PubMed] [Google Scholar]
  20. Postel E. H., Flint S. J., Kessler D. J., Hogan M. E. Evidence that a triplex-forming oligodeoxyribonucleotide binds to the c-myc promoter in HeLa cells, thereby reducing c-myc mRNA levels. Proc Natl Acad Sci U S A. 1991 Sep 15;88(18):8227–8231. doi: 10.1073/pnas.88.18.8227. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Schmidt A. M., Herterich S. U., Krauss G. A single-stranded DNA binding protein from S. cerevisiae specifically recognizes the T-rich strand of the core sequence of ARS elements and discriminates against mutant sequences. EMBO J. 1991 Apr;10(4):981–985. doi: 10.1002/j.1460-2075.1991.tb08032.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Sen D., Gilbert W. Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis. Nature. 1988 Jul 28;334(6180):364–366. doi: 10.1038/334364a0. [DOI] [PubMed] [Google Scholar]
  24. Smith P. K., Krohn R. I., Hermanson G. T., Mallia A. K., Gartner F. H., Provenzano M. D., Fujimoto E. K., Goeke N. M., Olson B. J., Klenk D. C. Measurement of protein using bicinchoninic acid. Anal Biochem. 1985 Oct;150(1):76–85. doi: 10.1016/0003-2697(85)90442-7. [DOI] [PubMed] [Google Scholar]
  25. Sundquist W. I., Klug A. Telomeric DNA dimerizes by formation of guanine tetrads between hairpin loops. Nature. 1989 Dec 14;342(6251):825–829. doi: 10.1038/342825a0. [DOI] [PubMed] [Google Scholar]
  26. Williamson J. R., Raghuraman M. K., Cech T. R. Monovalent cation-induced structure of telomeric DNA: the G-quartet model. Cell. 1989 Dec 1;59(5):871–880. doi: 10.1016/0092-8674(89)90610-7. [DOI] [PubMed] [Google Scholar]
  27. Yamazaki H., Nomoto S., Mishima Y., Kominami R. A 35-kDa protein binding to a cytosine-rich strand of hypervariable minisatellite DNA. J Biol Chem. 1992 Jun 15;267(17):12311–12316. [PubMed] [Google Scholar]
  28. Yee H. A., Wong A. K., van de Sande J. H., Rattner J. B. Identification of novel single-stranded d(TC)n binding proteins in several mammalian species. Nucleic Acids Res. 1991 Feb 25;19(4):949–953. doi: 10.1093/nar/19.4.949. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES