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Protonated DNA Structures

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 4))

Abstract

Unusual structures induced by DNA supercoiling attract a good deal of attention these days. The studies of the cruciform and the Z form were extensively reviewed in the first two volumes of this series (Soumpasis and Jovin 1987; Nordheim 1987; Lilley et al. 1987; Holloman 1988). In addition to these well-characterized structures, a new class of DNA structures have recently been discovered. These structures are stabilized not only by negative supercoiling but also by acid pH. They are inherent in sequences with considerable asymmetry in distribution of purines and pyrimidines between the complementary strands (such as homopurine-homopyrimidine) and include non-Watson-Crick base pairing. Pulleyblank (1988) reviewed the early development in the field. However, since then a considerable progress has been achieved, which is reviewed in this chapter.

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References

  • Budarf M, Blackburn E (1987) S1-nuclease sensitivity of a double-stranded telomeric DNA sequence. Nucleic Acids Res 15: 6273–6292

    Article  PubMed  CAS  Google Scholar 

  • Cantor CR, Efstratiadis A (1984) Possible structures of homopurine-homopyrimidine S1-hypersensitive sites. Nucleic Acids Res 12: 8059–8072

    Article  PubMed  CAS  Google Scholar 

  • Cantor CR, Schimmel PR (1980) Biophysical chemistry. Freeman, San Francisco Evans T, Efstratiadis A (1986) Sequence-dependent S1 nuclease hypersensitivity of a heteronomous DNA duplex. J Biol Chem 261: 14771–14780

    Google Scholar 

  • Furlong JC, Lilley DMJ (1986) Highly selective chemical modification of cruciform loops by diethyl pyrocarbonate. Nucleic Acids Res 14: 3995–4007

    Article  PubMed  CAS  Google Scholar 

  • Gray DM, Ratliff RL, Antac VP, Gray CW (1987) CD spectroscopy of acid-induced structures of polydeoxyribonucleotides: importance of C·C+ base pairs. In: Sarma RH, Sarma MH (eds) Structure & expression, vol. 2: DNA and its drug complexes. Adenine Press, New York, pp 147–166

    Google Scholar 

  • Hanvey JC, Klysik J, Wells RD (1988a) Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine-oligopyrimidine inserts in plasmids. J Biol Chem 263: 7386–7396

    PubMed  CAS  Google Scholar 

  • Hanvey JC, Shimizu M, Wells RD (1988b) Intramolecular DNA triplexes in supercoiled plasmids. Proc Natl Acad Sci USA 85: 6292–6296

    Article  PubMed  CAS  Google Scholar 

  • Hentschel CC (1982) Homocopolymer sequences in the spacer of sea urchin histone genes repeat are sensitive to S1 nuclease. Nature 295: 714–717

    Article  PubMed  CAS  Google Scholar 

  • Herr W (1985) Diethyl pyrocarbonate: a chemical probe for secondary structure in negatively supercoiled DNA. Proc Natl Acad Sci USA 82: 8009–8013

    Article  PubMed  CAS  Google Scholar 

  • Holloman WK (1988) Homologous pairing promoted by Ustilago Rec 1 protein. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology 2. Springer, Berlin Heidelberg, pp 198–205

    Google Scholar 

  • Howard FB, Frazier J, Lipsett MN, Miles HT (1964) Infrared demonstration of two- and three-strand helix formation between poly C and guanosine mononucleotides and oligonucleotides. Biochem Biophys Res Commun 17: 93–102

    Article  CAS  Google Scholar 

  • Htun H, Dahlberg JE (1988) Single strands, triple strands, and kinks in H-DNA. Science 241: 1791–1796

    Article  PubMed  CAS  Google Scholar 

  • Htun H, Lund E, Dahlberg JE (1984) Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavege site within the conserved 3’ flanking region. Proc Natl Acad Sci USA 81: 7288–7292

    Article  PubMed  CAS  Google Scholar 

  • Johnston BH (1988a) Chemical probing of the B-Z transition in negatively supercoiled DNA. J Biomol Struct Dyn 6: 153–166

    PubMed  CAS  Google Scholar 

  • Johnston BH (1988b) The S1-sensitive form of d(C-T)n d(A-G)n: chemical evidence for a three-stranded structure in plasmids. Science 241: 1800–1804

    Article  PubMed  CAS  Google Scholar 

  • Johnston BH, Rich A (1985) Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution. Cell 42: 713–724

    Article  PubMed  CAS  Google Scholar 

  • Kohwi Y, Kohwi-Shigimatsu T (1988) Magnesium ion-dependent triple-helix structure formed by homopurine-homopyrimidine sequences in supercoiled plasmid DNA. Proc Natl Acad Sci USA 85: 3781–3785

    Article  PubMed  CAS  Google Scholar 

  • Larsen A, Weintraub H (1982) An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell 29: 609–622

    Article  PubMed  CAS  Google Scholar 

  • Lee JS, Johnson DA, Morgan AR (1979) Complexes formed by (pyrimidine)n (purine)n DNAs on lowering the pH are three-stranded. Nucleic Acids Res 6: 3073–3091

    Article  PubMed  CAS  Google Scholar 

  • Lee JS, Woodsworth ML, Latimer LJP, Morgan AR (1984) Poly(pyrimidine) poly(purine) synthetic DNAs containing 5-methylcytosine form stable triplexes at neutral pH. Nucleic Acids Res 12: 6603–6614

    Article  PubMed  CAS  Google Scholar 

  • Lilley DMJ, Palecek E (1984) The supercoil-stabilized cruciform of ColE1 is hyper-reactive to osmium tetroxide. EMBO J 3: 1187–1192

    PubMed  CAS  Google Scholar 

  • Lilley DMJ, Sullivan KM, Murchie AIH (1987) The extrusion of cruciform structures in supercoiled DNA — Kinetics and Mechanisms. In: Eckstein E, Lilley DMJ (eds) Nucleic acids and molecular biology 1. Springer, Berlin Heidelberg, pp 126–137

    Google Scholar 

  • Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD (1985) A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn 3: 327–338

    PubMed  CAS  Google Scholar 

  • Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD (1986) Structures of homopurine-homopyrimidine tracts in superhelical DNA. J Biomol Struct Dyn 3: 667–669

    PubMed  CAS  Google Scholar 

  • Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD (1987) Structure of (dG)n (dC)n under superhelical stress and acid pH. J Biomol Struct Dyn 5: 275–282

    PubMed  CAS  Google Scholar 

  • Lyamichev VI, Mirkin SM, Frank-Kamenetskii MD, Cantor CR (1988) A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNAs. Nucleic Acids Res 16: 2165–2178

    Article  PubMed  CAS  Google Scholar 

  • Lyamichev VI, Mirkin SM, Danilevkaya ON, Voloshin ON, Balatskaya SV, Dobrynin VN, Filippov SA, Frank-Kamenetskii MD (1989) An unusual structure detected in a telomeric sequence under superhelical stress and low pH. Nature 339: 634–637

    Article  PubMed  CAS  Google Scholar 

  • Mirkin SM, Lyamichev VI, Drushlyak KN, Dobrynin VN, Filippov SA, Frank-Kamenetskii MD (1987) DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature 330: 495–498

    Article  PubMed  CAS  Google Scholar 

  • Nickol JM, Felsenfeld G (1983) DNA conformation at the 5’ end of chicken adult β-globin gene. Cell 35: 467–477

    Article  PubMed  CAS  Google Scholar 

  • Nordheim A (1987) Z-DNA: Exploring the biological significance. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology 1. Springer, Berlin Heidelberg, pp 112–125

    Google Scholar 

  • Pulleyblank DE (1988) Non-commensurate polypurine/polypyrimidine DNA structures. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology 2. Springer, Berlin Heidelberg, pp 31–48

    Google Scholar 

  • Pulleyblank DE, Haniford DB, Morgan AR (1985) A structural basis for S1 nuclease sensitivity of double-stranded DNA. Cell 42: 271–280

    Article  PubMed  CAS  Google Scholar 

  • Scholten PM, Nordheim A (1986) Diethyl pyrocarbonate: a chemical probe for DNA cruciforms. Nucleic Acids Res 14: 3981–3993

    Article  PubMed  CAS  Google Scholar 

  • Schon E, Evans T, Welsh J, Efstratiadis A (1983) Conformation of promoter DNA: fine mapping of S1-hypersensitive sites. Cell 35: 837–848

    Article  PubMed  CAS  Google Scholar 

  • Soumpasis DM, Jovin ThM (1987) Energetics of the B-Z DNA transition. In: Eckstein F, Lilley DMJ (eds) Nucleic acids and molecular biology 1. Springer, Berlin Heidelberg, pp 86–111

    Google Scholar 

  • Vojtiskova M, Mirkin S, Lyamichev V, Voloshin O, Frank-Kamenetskii M, Palecek E (1988) Chemical probing of the homopurine-homopyrimidine tract in supercoiled DNA et singlenucleotide resolution. FEBS Lett 234: 295–299

    Article  PubMed  CAS  Google Scholar 

  • Voloshin ON, Mirkin SM, Lyamichev VI, Belotserkovskii BP, Frank-Kamenetskii MD (1988) Chemical probing of homopurine-homopyrimidine mirror repeats in supercoiled DNA. Nature 333: 475–476

    Article  PubMed  CAS  Google Scholar 

  • Weiner AM (1988) Eukaryotic nuclear telomers: molecular fossils of the RNP world? Cell 52: 155–158

    Article  PubMed  CAS  Google Scholar 

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© 1990 Springer-Verlag Berlin Heidelberg

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Frank-Kamenetskii, M.D. (1990). Protonated DNA Structures. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology 4. Nucleic Acids and Molecular Biology, vol 4. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-84150-7_1

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  • DOI: https://doi.org/10.1007/978-3-642-84150-7_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-84152-1

  • Online ISBN: 978-3-642-84150-7

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