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. 1988 Sep;85(17):6292–6296. doi: 10.1073/pnas.85.17.6292

Intramolecular DNA triplexes in supercoiled plasmids.

J C Hanvey 1, M Shimizu 1, R D Wells 1
PMCID: PMC281955  PMID: 3413097

Abstract

A series of inserts with oligopurine.oligopyrimidine mirror repeat sequences was investigated at the base pair level with specific chemical probes (OsO4 and diethylpyrocarbonate) to evaluate the in vitro existence of intramolecular triplexes. Two parent inserts in recombinant plasmids with (GAA)9 and (AG)12 sequences and three mutant inserts (containing transitions or transversions) revealed that base pair changes at one location affected the chemical reactivity 13 base pairs away. The specificity and nature of these reactions, as well as the thermal stability of the complexes, provide direct evidence for the existence of a triplex with a portion of the pyrimidine-rich strand folded back and Hoogsteen-paired in the major groove of the Watson-Crick duplex. The biological implications of this unorthodox DNA structure are discussed.

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Selected References

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  1. 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]
  2. 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]
  3. Chamberlin M. J. Comparative properties of DNA, RNA, and hybrid homopolymer pairs. Fed Proc. 1965 Nov-Dec;24(6):1446–1457. [PubMed] [Google Scholar]
  4. Christophe D., Cabrer B., Bacolla A., Targovnik H., Pohl V., Vassart G. An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. Nucleic Acids Res. 1985 Jul 25;13(14):5127–5144. doi: 10.1093/nar/13.14.5127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Collier D. A., Griffin J. A., Wells R. D. Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region. J Biol Chem. 1988 May 25;263(15):7397–7405. [PubMed] [Google Scholar]
  6. Dybvig K., Clark C. D., Aliperti G., Schlesinger M. J. A chicken repetitive DNA sequence that is highly sensitive to single-strand specific endonucleases. Nucleic Acids Res. 1983 Dec 10;11(23):8495–8508. doi: 10.1093/nar/11.23.8495. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Evans T., Efstratiadis A. Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex. J Biol Chem. 1986 Nov 5;261(31):14771–14780. [PubMed] [Google Scholar]
  8. Evans T., Schon E., Gora-Maslak G., Patterson J., Efstratiadis A. S1-hypersensitive sites in eukaryotic promoter regions. Nucleic Acids Res. 1984 Nov 12;12(21):8043–8058. doi: 10.1093/nar/12.21.8043. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Fowler R. F., Skinner D. M. Eukaryotic DNA diverges at a long and complex pyrimidine.purine tract that can adopt altered conformations. J Biol Chem. 1986 Jul 5;261(19):8994–9001. [PubMed] [Google Scholar]
  10. Galazka G., Palecek E., Wells R. D., Klysik J. Site-specific OsO4 modification of the B-Z junctions formed at the (dA-dC)32 region in supercoiled DNA. J Biol Chem. 1986 May 25;261(15):7093–7098. [PubMed] [Google Scholar]
  11. Hanvey J. C., Klysik J., Wells R. D. Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine.oligopyrimidine inserts in plasmids. J Biol Chem. 1988 May 25;263(15):7386–7396. [PubMed] [Google Scholar]
  12. 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]
  13. Herr W. Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. Proc Natl Acad Sci U S A. 1985 Dec;82(23):8009–8013. doi: 10.1073/pnas.82.23.8009. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Htun H., Lund E., Dahlberg J. E. Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavage site within the conserved 3' flanking region. Proc Natl Acad Sci U S A. 1984 Dec;81(23):7288–7292. doi: 10.1073/pnas.81.23.7288. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. INMAN R. B. TRANSITIONS OF DNA HOMOPOLYMERS. J Mol Biol. 1964 Sep;9:624–637. doi: 10.1016/s0022-2836(64)80171-6. [DOI] [PubMed] [Google Scholar]
  16. Jaworski A., Hsieh W. T., Blaho J. A., Larson J. E., Wells R. D. Left-handed DNA in vivo. Science. 1987 Nov 6;238(4828):773–777. doi: 10.1126/science.3313728. [DOI] [PubMed] [Google Scholar]
  17. Johnston B. H., Rich A. Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell. 1985 Oct;42(3):713–724. doi: 10.1016/0092-8674(85)90268-5. [DOI] [PubMed] [Google Scholar]
  18. Kilpatrick M. W., Torri A., Kang D. S., Engler J. A., Wells R. D. Unusual DNA structures in the adenovirus genome. J Biol Chem. 1986 Aug 25;261(24):11350–11354. [PubMed] [Google Scholar]
  19. 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]
  20. Lilley D. M., Palecek E. The supercoil-stabilised cruciform of ColE1 is hyper-reactive to osmium tetroxide. EMBO J. 1984 May;3(5):1187–1192. doi: 10.1002/j.1460-2075.1984.tb01949.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lyamichev V. I., Mirkin S. M., Frank-Kamenetskii M. D. Structures of homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1986 Feb;3(4):667–669. doi: 10.1080/07391102.1986.10508454. [DOI] [PubMed] [Google Scholar]
  22. Mace H. A., Pelham H. R., Travers A. A. Association of an S1 nuclease-sensitive structure with short direct repeats 5' of Drosophila heat shock genes. Nature. 1983 Aug 11;304(5926):555–557. doi: 10.1038/304555a0. [DOI] [PubMed] [Google Scholar]
  23. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  24. McKeon C., Schmidt A., de Crombrugghe B. A sequence conserved in both the chicken and mouse alpha 2(I) collagen promoter contains sites sensitive to S1 nuclease. J Biol Chem. 1984 May 25;259(10):6636–6640. [PubMed] [Google Scholar]
  25. McLean M. J., Blaho J. A., Kilpatrick M. W., Wells R. D. Consecutive A X T pairs can adopt a left-handed DNA structure. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5884–5888. doi: 10.1073/pnas.83.16.5884. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. McLean M. J., Lee J. W., Wells R. D. Characteristics of Z-DNA helices formed by imperfect (purine-pyrimidine) sequences in plasmids. J Biol Chem. 1988 May 25;263(15):7378–7385. [PubMed] [Google Scholar]
  27. McLean M. J., Wells R. D. The role of DNA sequence in the formation of Z-DNA versus cruciforms in plasmids. J Biol Chem. 1988 May 25;263(15):7370–7377. [PubMed] [Google Scholar]
  28. 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]
  29. 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]
  30. 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]
  31. Pulleyblank D. E., Haniford D. B., Morgan A. R. A structural basis for S1 nuclease sensitivity of double-stranded DNA. Cell. 1985 Aug;42(1):271–280. doi: 10.1016/s0092-8674(85)80122-7. [DOI] [PubMed] [Google Scholar]
  32. Schon E., Evans T., Welsh J., Efstratiadis A. Conformation of promoter DNA: fine mapping of S1-hypersensitive sites. Cell. 1983 Dec;35(3 Pt 2):837–848. doi: 10.1016/0092-8674(83)90116-2. [DOI] [PubMed] [Google Scholar]
  33. Shen C. K. Superhelicity induces hypersensitivity of a human polypyrimidine . polypurine DNA sequence in the human alpha 2-alpha 1 globin intergenic region to S1 nuclease digestion--high resolution mapping of the clustered cleavage sites. Nucleic Acids Res. 1983 Nov 25;11(22):7899–7910. doi: 10.1093/nar/11.22.7899. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Voloshin O. N., Mirkin S. M., Lyamichev V. I., Belotserkovskii B. P., Frank-Kamenetskii M. D. Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA. Nature. 1988 Jun 2;333(6172):475–476. doi: 10.1038/333475a0. [DOI] [PubMed] [Google Scholar]
  35. Wells R. D., Larson J. E. Buoyant density studies on natural and synthetic deoxyribonucleic acids in neutral and alkaline solutions. J Biol Chem. 1972 Jun 10;247(11):3405–3409. [PubMed] [Google Scholar]
  36. Wohlrab F., McLean M. J., Wells R. D. The segment inversion site of herpes simplex virus type 1 adopts a novel DNA structure. J Biol Chem. 1987 May 5;262(13):6407–6416. [PubMed] [Google Scholar]

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