Skip to main content
SpringerLink
Log in

Structural Organization of DNA

  • Chapter
Apoptotic Chromatin Changes

  • 960 Accesses

Summary

This chapter summarizes (a) the building blocks of nucleotides and in this context discusses separately the nucleic acid bases, the sugar and phosphate components, (b) the bond types in nucleotides, (c) the metabolism of nucleotides, (d) the lower levels of DNA structure (primary, secondary, tertiary, nucleosomal), (e) supranucleosomal organization of eukaryotic DNA, (f) chromosomes of animal cells, and (g) the temporal and spatial order of gene replication.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  • Abdel-Monem, M., Lauppe, H.F., Kartenbeck, J., Durwald, H., and Hoffmann-Berling, H. (1977). Enzymatic unwinding of DNA. III. Mode of action of Escherichia coli DNA unwinding enzyme. J Mol Biol 110, 667–685.

    Article  PubMed  CAS  Google Scholar 

  • Abney, J.R., Cutler, B., Fillbach, M.L., Axelrod, D. and Scalettar, B.A. (1997). Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J Cell Sci. 137, 1459–1468.

    CAS  Google Scholar 

  • Adachi, Y., Luke, M. and Laemmli, U.K. (1991). Chromosome assembly in vitro: topoisomerase II is required for condensation. Cell 64, 137–148.

    Article  PubMed  CAS  Google Scholar 

  • Altona, C. and Sundaralingam, M. (1972). Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept pseudorotation. J Amer Chem Soc. 94, 8205–8212.

    Article  CAS  Google Scholar 

  • Altona, C. (1975). Backbone conformation of several dinucleoside monophosphates in solution deduced from Fourier transform NMR spectroscopy at 270 MHz. In Structure and Conformation of Nucleic Acids and Protein-nucleic Acid Interactions. M. Sundaralingam and S.T. Rao, eds. Univ.Park Press, London.

    Google Scholar 

  • Amadi, F., Giacomoni, D. and Zito-Bignami, R. (1969). Ont he duplication of ribosomal RNA cistrons in Chinese hamster ovary cells. Eur J Biochem. 11, 419–423.

    Article  Google Scholar 

  • Arnott, S. and Hukins, W.L. (1972). The dimensions and shapes of the furanose rings in nucleic acids. Biochem J. 130, 453–65.

    PubMed  CAS  Google Scholar 

  • Arnott, S., Hutchinson, F., Spencer, M., Wilkins, M.H., Fuller, W. and Langridge, R. (1966). X-ray diffraction studies of double helical ribonucleic acid. Nature. 211, 227–232.

    Article  PubMed  CAS  Google Scholar 

  • Balaz, J. and Schildkraut, C.L. (1971). DNA replication in synchronized cultured mammalian cells. II. Replication of ribosomal cistrons in thymidine-synchronized HeLa cells. J Mol Biol. 57, 153–158.

    Article  Google Scholar 

  • Baldi, M.I., Benedetti, P., Mattoccia, E. and Tocchini-Valentini, G.P. In vitro catenation and decatenation of DNA and a novel eucaryotic ATP-dependent topoisomerase. Cell. 20, 461–467.

    Google Scholar 

  • Bànfalvi, G. (1984). Demonstration of topoisomers using Solomon’s knot DNA. Biochem Educ. 12, 155–156.

    Article  Google Scholar 

  • Bànfalvi, G. (1986a). Structural organization of DNA. Biochem Educ. 14, 50–59.

    Article  Google Scholar 

  • Bànfalvi, G. (1986b). Transistion from right handed to left handed DNA. Biochem Educ. 14, 7–10.

    Article  Google Scholar 

  • Bànfalvi, G. (1991). Evolution of osmolyte systems. Biochem Educ. 19, 136–139.

    Article  Google Scholar 

  • Bánfalvi, G. (1994). The metabolic clockwork. Biochem Educ. 22, 137–139.

    Article  Google Scholar 

  • Bánfalvi, G. (2006a). Why ribose was selected as the excusive sugar component of nucleic acids. DNA Cell Biol. 25, 189–196.

    Article  Google Scholar 

  • Bánfalvi, G. (2006b). Structure of interphase chromosomes in the nuclei of Drosophila cells. DNA Cell Biol. 25, 547–53.

    Article  Google Scholar 

  • Bánfalvi, G. (2006c). Linear connection of condensing chromosomes in nuclei of synchronized CHO cells. DNA Cell Biol. 25, 541–545.

    Article  Google Scholar 

  • Bánfalvi, G. (2008). Chromatin fiber structure and plectonemic model of chromosome condensation in Drosophila cells. DNA Cell Biol. 27, 65–70.

    Article  PubMed  CAS  Google Scholar 

  • Bánfalvi, G. and Antoni, F. DNA diagnostics. Orvosi Hetilap 131, 953–964 (in Hungarian).

    Google Scholar 

  • Bánfalvi, G. and Fieldhouse, J. (1988). Heliwire DNA model to visualize syn and anti folding of tetraplex structures. Biochem Educ. 16, 80–82.

    Article  Google Scholar 

  • Bánfalvi, G., Chou, W.M., Mikhailova, M. and Poirier, A.L. (1997a) Relationship of repair and replicative DNA synthesis to cell cycle in Chinese hamster Ovary (CHO-K1) cells. DNA Cell Biol. 16, 1155–1160.

    Google Scholar 

  • Bánfalvi, G., Gacsi, M., Nagy, G., Kiss, B.Z. and Basnakian, A.G. (2005). Cadmium induced apoptotic changes in chromatin structure and subphases of nuclear growth during the cell cycle in CHO cells. Apoptosis 10, 631–642.

    Article  PubMed  CAS  Google Scholar 

  • Bánfalvi, G., Mikhailova, M., Poirier, L.A. and Chou, M.W. (1997b). Multiple subphases of DNA replication in CHO cells. DNA Cell Biol. 16, 1493–1498.

    Google Scholar 

  • Banfalavi, G. and Sarkar, N. (1983). Analysis of the 5’-termini of nascent DNA chains synthesized in permeable cells of Bacillus subtilis. J Mol Biol. 163, 147–169.

    Article  Google Scholar 

  • Bánfalvi, G., Trencsenyi G., Ujvarosi, K., Nagy, G., Ombodi, T., Bedei, M., Somogyi, C. and Basnakian, A. (2007). Supranucleosomal organization of chromatin fibers in nuclei of Drosophila S2 cells. DNA Cell Biol. 26, 55–62.

    Article  PubMed  CAS  Google Scholar 

  • Bánfalvi, G., Wiegant, J., Sarkar, N. and Van Duijn, P. (1989). Immunofluoresent visualization of DNA replication sites within nuclei of Chinese hamster ovary cells. Histochemistry. 93, 81–86.

    Article  PubMed  Google Scholar 

  • Bauer, W.R. (1978). Structure and reactions of closed duplex DNA. Annu Rev Biophys Bioeng. 7, 287–313. Review.

    Article  PubMed  CAS  Google Scholar 

  • Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen, J.C., Koster, A.J. and Woodcock, C.L. (1998). Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci USA. 95, 14173–14178.

    Article  PubMed  CAS  Google Scholar 

  • Behe, M. and Felsenfeld, G. (1981). Effects of methylation on a synthetic polynucleotide: the B–Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci USA. 78, 1619–1623.

    Article  PubMed  CAS  Google Scholar 

  • Belmont, A.S. (2006). Mitotic chromosome structure and condensation. Curr Opin Cell Biol. 18, 6632–6638.

    Article  CAS  Google Scholar 

  • Berezney, R., Mortillaro, M.J., Ma, H., Wei, X. and Samarabandu, J. (1995). The nuclear matrix: A structural milieu for genomic function. Int J Cytol. 162A, 1–65.

    CAS  Google Scholar 

  • Bergerat, A., De Massy, B., Gadelle, D., Varoutas, P.C., Nicolas, A. and Forterre, P. (1997). An atypical topoisomerase II from Archaea with implications for meiotic recombination. Nature. 386, 414–417.

    Article  PubMed  CAS  Google Scholar 

  • Bickmore, W.A. and Teague, P. (2002). Influences of chromosome size, gene density and nuclear position on the frequency of constitutional translocations in the human population. Chromosome Res. 10, 707–715.

    Article  PubMed  CAS  Google Scholar 

  • Bolli, M., Micura, R. and Eschenmoser, A. (1977). Pyranosyl-RNA chiroselective self-assembly of base sequences by ligativa oligomerization of tetranucleotide-2′, 3′-cyclophosphates (with a comentary concerning origin of biomolecular homochirality) Chem Biol. 4, 309–320.

    Article  Google Scholar 

  • Bonnefoy, E. (1997). The ribosomal S16 protein of Escherichia coli displaying a DNA-nicking activity binds to cruciform DNA. Eur J Biochem. 247, 852–859.

    Article  PubMed  CAS  Google Scholar 

  • Bordas, J., Perez-Grau, L., Koch, M.H.J., Vega, M.C. and Nave, C. (1986). The superstructure of chromatin and its condensation mechanism. I. Synchrotron radiation X-ray scattering results. Eur Biophys J Biophys Lett. 13, 175–185.

    CAS  Google Scholar 

  • Brem, R.B., Yvert, G., Clinton, R. and Kruglyak, L. (2002). Genetic dissection of transcriptional regulation in budding yeast. Science 296, 752–755.

    Article  PubMed  CAS  Google Scholar 

  • Bridger, J.M. and Bickmore, W.A. (1998). Putting the genome on the map. Trends Genet. 14, 403–410.

    Article  PubMed  CAS  Google Scholar 

  • Britten, R.J. and Davidson, E.H. (1969). Gene regulation for higher cells: A theory. Science 165, 349–357.

    Article  PubMed  CAS  Google Scholar 

  • Brown, D. and Simoni, R.D. (1988). Mevalonate deprivation leads to aneuploidy in Chinese hamster ovary cells. J Biol Chem. 263, 13497–13499.

    PubMed  CAS  Google Scholar 

  • Brown, P.O. and Cozzarelli, N.R. (1979). A sign inversion mechanism for enzymatic supercoiling of DNA. Science. 206, 1081–1083.

    Article  PubMed  CAS  Google Scholar 

  • Brown, P.O., Peebles, C.L. and Cozzarelli, N.R. (1979). A topoisomerase from Escherichia coli related to DNA gyrase. Proc Natl Acad Sci U S A. 76, 6110–6114.

    Article  PubMed  CAS  Google Scholar 

  • Buhler, C., Gadelle, D., Forterre, P., Wang, J.C. and Bergerat, A. (1998). Reconstitution of DNA topoisomerase VI of the thermophilic archaeon Sulfolobus shibatae from subunits separately overexpressed in Escherichia coli. Nucleic Acids Res. 26, 5157–5162.

    Article  PubMed  CAS  Google Scholar 

  • Cairns, J. (1963a). The bacterial chromosome and its manner of replication as seen by autoradiography. J Mol Biol. 6, 208–213.

    CAS  Google Scholar 

  • Cairns, J. (1963b). The chromosome of Escherichia coli. Cold Spring Harbor Symp Quant Biol. 28, 43–46.

    Google Scholar 

  • Cairns, J. (1966). Autoradiography of HeLa cell DNA. J Mol Biol 15, 372–373.

    PubMed  CAS  Google Scholar 

  • Calladine, C.R. (1982). Mechanism of sequence-dependent stacking of bases in B-DNA. J Mol Biol 161, 343–352.

    Article  PubMed  CAS  Google Scholar 

  • Carr, A.M. (1995). DNA structure checkpoints in fission yeast. Semin Cell Biol. 6, 65–72,

    Article  PubMed  CAS  Google Scholar 

  • Castano, I.B., Brzoska, P.M., Sadoff, B.U., Chen, H.Y. and Christman, M.F. (1996) Mitotic chromosome condensation in the rDNA requires TRF4 and DNA topoisomerase I in Saccharomyces cerevisiae. Genes Dev. 10, 2564–2576.

    Article  PubMed  CAS  Google Scholar 

  • Champoux, J.J. (1978). Mechanism of the reaction catalysed by the DNA untwisting enzyme: attachment of the enzyme to 3$′$-terminus of the nicked DNA. J Mol Biol. 118, 441–446.

    Article  PubMed  CAS  Google Scholar 

  • Champoux, J.J. (2001). DNA topoisomerases: Structure, function and mechanism. Annu Rev Biochem. 70, 369–413.

    Article  PubMed  CAS  Google Scholar 

  • Cheung, V.G., Conlin, L.K., Weber, T.M., Arcaro, M., Jen, K.Y., Morley, M. and Spielman, R.S. (2003). Natural variation in human gene expression assessed in lymphoblastoid cells. Nat Genet. 33, 422–425.

    Article  PubMed  CAS  Google Scholar 

  • Clark, M.A., Baumann, L., Thao, M.L., Moran, N.A. and Baumann, P. (2001). Degenerative minimalism in the genome of a psyllid endosymbiont. J Bacteriol. 183, 1853–1861.

    Article  PubMed  CAS  Google Scholar 

  • Conner, B.N., Takano, T., Tanaka, S., Itakura, K., and Dickerson, R.E. (1982). The molecular structure of d(ICpCpGpG), a fragment of right-handed double helical A-DNA. Nature. 295, 294–299.

    Article  PubMed  CAS  Google Scholar 

  • Committee on Rat Nomenclature, Cochairmen Gill T.J. III, Nomura T. 1992. Definition, Committee on Standardized Genetic Nomenclature for Mice. 1963. A revision of the standardized genetic nomenclature for mice. J. Hered. 54, 159–162.

    Google Scholar 

  • Committee on Standardized Genetic Nomenclature for Mice. 1973. Guidelines for nomenclature of genetically determined biochemical variants in the house mouse, Mus musculusBiochem. Genet. 9, 369–374.

    Google Scholar 

  • Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F.: Rules and guidelines for gene nomenclature, pp. 1–7. In: Genetic Variants and Strains of the Laboratory Mouse, Green, M.C. (ed.), First Edition, Gustav Fischer Verlag, Stuttgart, 1981.

    Google Scholar 

  • Committee on Standardized Genetic Nomenclature for Mice, Chair: Lyon, M.F.: Rules and guidelines for gene nomenclature, pp. 1–11. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon, M.F., A.G. Searle (eds.), Second Edition, Oxford University Press, Oxford, 1989.

    Google Scholar 

  • Committee on Standardized Genetic Nomenclature for Mice, Chairperson: Davisson, M.T. Rules and guidelines for gene nomenclature, pp. 1–16. In: Genetic Variants and Strains of the Laboratory Mouse, Lyon, M.F., Rastan, S., Brown, S.D.M. (eds.), Third Edition, Volume 1, Oxford University Press, Oxford, 1996.

    Google Scholar 

  • Cozzarelli, N.R. (1980). DNA gyrase and the supercoiling of DNA. Science. 207, 953–960.

    Article  PubMed  CAS  Google Scholar 

  • Crick, F.H.C. (1976). Linking numbers and nucleosomes. Proc Natl Acad Sci USA. 73, 2639–2643.

    Article  PubMed  CAS  Google Scholar 

  • Dale, R.M.K., Livingston, D.C. and Ward, D.C. (1973). The synthesis and enzymatic polymerization of nucleotides containing mercury: potential tools for nucleic acid sequencing and structure analysis. Proc Nat Acad Sci USA. 70, 2238–2242.

    Article  PubMed  CAS  Google Scholar 

  • Danielson, P. (2002). The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. Curr Drug Metab. 3, 561–597.

    Article  PubMed  CAS  Google Scholar 

  • Davies, B.D. (1978). Conformations of nucleosides and nucleotides. Prog NMR Spectrosc. 12, 135–225.

    Article  CAS  Google Scholar 

  • Denisov, A.Y., Noronha, A.M., Wilds, C.J., Trempe, J.F., Pon, R.T., Gehring, K., and Damha, M.J. (2001). Solution stucture o fan arabinonucleic acid (ANA)/RNA duplex in a chimeric hairpin: comparison with 2’-fluoro-ANA/RNA and DNA/RNA hybrids. Nucleic Acids Res. 29, 4284–4293.

    Article  PubMed  CAS  Google Scholar 

  • Dickerson, R.E. (1983). Base sequence and helix structure variation in B- and A-DNA. J Mol Biol 166, 419–441.

    Article  PubMed  CAS  Google Scholar 

  • Dickerson, R.E., Drew, H.R., Conner, B.N., Wing, R.M., Fratini, A.V., Kopka, M.L. (1982). The anatomy of A-, B-, and Z-DNA. Science 216, 475–485.

    Article  PubMed  CAS  Google Scholar 

  • Dickerson, R.E. (1983a). The DNA hekix and how it is read. Sci Amer 249, 94–111.

    Article  CAS  Google Scholar 

  • Downes, C.S., Clarke, D.J., Mullinger, A.M., Gimenez-Abian, J.F., Creighton, A.M. and Johnson, R.T. (1994). A topoisomerase II-dependent G2 cycle checkpoint in mammalian cells. Nature 372, 467–470.

    Article  PubMed  CAS  Google Scholar 

  • Dresser, M.E. and Giroux, C.N. (1988). Meiotic chromosome behavior in spread preparations of yeast. J Cell Biol. 106, 567–573.

    Article  PubMed  CAS  Google Scholar 

  • Dunn, L.C., Gruneberg, H. and Snell, G.D. (1940). Report of the committee on mouse genetics nomenclature. J Hered. 31, 505–506.

    Google Scholar 

  • Epner, E., Rifkind, R.A. and Marks, P.A. (1981). Replication of α and β globin DNA sequences occurs during early S phase in murine erythroleukemia cells. Proc Natl Acad Sci USA. 78, 3058–3062.

    Article  PubMed  CAS  Google Scholar 

  • Eschenmoser A., and Dobler, M. (1992). Warum Pentose - und nicht Hexose- Nucleinsauren TeilI. Einleitung und Problemstellung, Korformationanalyse für Oligonucleotid Ketten aus 2′3′-Dideoxygluvopyranosyl- Barsteinen (‘Homo-DNA’) sowie Betrachtungenzur Konformation von A- und B-DNA. Helv Chim Acta 75, 218–259.

    Google Scholar 

  • Eschenmoser in Proc. Robert A. Welch Found. (1993). Conf. Chem. Res. 37, (Robert A. Welch Foundation, Houston, TX) pp. 201.

    Google Scholar 

  • Eschenmoser, A. (1994). The TNA-family of nucleic acid systems: Properties and prospects. Orig Life Evol Biosph. 2004. 34, 277–306.

    Article  Google Scholar 

  • Fenech, M. (2002). Chromosomal biomarkers of genomic instability relevant to cancer. Drug Discov Today. 7, 1128–1137.

    Article  PubMed  CAS  Google Scholar 

  • Fieldhouse, J. (1981). A Solomon’s knot DNA. Biochem Educ. 9, 88.

    Article  Google Scholar 

  • Finch, J.T. and Klug, A. (1976). Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci U S A. 73, 1897–1901.

    Article  PubMed  CAS  Google Scholar 

  • Fletterick, R.J., Schroer, T. and Matela, R.J. (1985). In Molecular Structure (ed. Staples, J.). Blackwell Scientific Publications, Oxford.

    Google Scholar 

  • Ford, C.E. and Hamerton, J.L. (1956). The chromosomes of man. Nature. 178, 1020–1023.

    Article  PubMed  CAS  Google Scholar 

  • Fujii, S., Wang, A.H., Van Der Marel, G., Van Boom, J.H. and Rich, A. Molecular structure of (m5 dC-dG)3: The role of the methyl group on 5-methyl cytosine in stabilizing Z-DNA. Nucleic Acids Res. 10, 7879–7892.

    Google Scholar 

  • Fukuda, Y., Washio, T. and Tomita, M. (1999). Comparative study of overlapping genes int he genomes og Mycoplasma gentalium and Mycoplasma pneumoniae. Nucleic Acids Res. 27, 1847–1853.

    Article  PubMed  CAS  Google Scholar 

  • Gacsi, M., Nagy, G., Pinter, G., Basnakian, A.G., and Bánfalvi, G. (2005). Condensation of interphase chromatin in nuclei of Chinese hamster ovary (CHO-K1) cells. DNA Cell Biol. 24, 43–53.

    Article  PubMed  CAS  Google Scholar 

  • Gangloff, S., De Massy, B., Arthur, L., Rothstein, R. and Fabre, F. (1999). The essential role of yeast topoisomerase III in meiosis depends on recombination. Embo J. 18, 1701–1711.

    Article  PubMed  CAS  Google Scholar 

  • Garcia, H.G., Grayson, P., Han, L., Inamdar, M., Kondev, J., Nelson, P.C., Phillips, R., Widom, J. and Wiggins, P.A. (2007). Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity. Biopolymers. 85, 115–130.

    Article  PubMed  CAS  Google Scholar 

  • Gellert, M. (1981). DNA topoisomerases. Annu Rev Biochem. 50, 879–910. Review.

    Article  PubMed  CAS  Google Scholar 

  • Gellert, M., Mizuuchi, K., O’Dea, M.H. and Nash, H.A. (1976). DNA gyrase: An enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci U S A. 73, 3872–3876.

    Article  PubMed  CAS  Google Scholar 

  • Gellert, M., Mizuuchi, K., O’Dea, M.H., Ohmori, H., and Tomizawa, J. (1979). DNA gyrase and DNA supercoiling. Cold Spring Harb Symp Quant Biol. 43, 35–40.

    PubMed  CAS  Google Scholar 

  • Gerchman, L.L. and Ludlum, D.B. (1973). The properties of O 6 -methylguanine in templates for RNA polymerase. Biochim Biophys Acta. 308, 310–316.

    PubMed  CAS  Google Scholar 

  • Ghelardini, P., Pedrini, A.M. and Paolozzi, L. (1982). The topoisomerase activity of T4 amG39 mutant is restored in Mu lysogens. FEBS Lett. 137, 49–52.

    Article  PubMed  CAS  Google Scholar 

  • Giacomoni, D. and Finkel, D. (1972). Time of duplication of ribosomal RNA cistrons in a cell line of Potorus tridactilus (Rat kangaroo). J Mol Biol. 70, 725–728.

    Article  PubMed  CAS  Google Scholar 

  • Gilbert, W. (1986). Evolution of antibodies. The road not taken. Nature. 320, 485–486.

    Article  PubMed  CAS  Google Scholar 

  • Gimmler, G.M. and Schweizer, E. (1972). rDNA replication in synchronized cultures of Saccharomyces cerevisiae. Biochem Biophys Res Commun. 46, 143–149.

    Article  PubMed  CAS  Google Scholar 

  • Goto, T. and Wang, J.C. (1982). Yeast DNA topoisomerase II. An ATP-dependent type II topoisomerase that catalyses the catenation, decatenation, unknotting, and relaxation of double-stranded DNA rings. J Biol Chem. 257, 5866–5872.

    PubMed  CAS  Google Scholar 

  • Grechman, S.E. and Ramakrishnan, V. (1987). Chromatin higher-order structure studied by neutron-scattering and scanning transmission electron microscopy. Proc Natl Acad Sci USA. 84, 7802–7806.

    Article  Google Scholar 

  • Grigoryev, S.A. (2004). Keeping fingers crossed: Heterochromatin spreading through interdigitation of nucleosome arrays. FEBS Lett. 254, 4–8.

    Article  CAS  Google Scholar 

  • Groebke, K. (1998). Warum Pentose- und nicht Hexose- Nucleinsauren? Teil V. (Purin-Purin)- Basenpaarung in der homo-DNA-Reiche: Guanin, Isoguanin, 2,6- Diaminopurin und Xanthin. Helv. Chim Acta. 8, 375–491.

    Article  Google Scholar 

  • Guacci, V., Hogan, E. and Koshland, D. Chromosome condensation and sister chromatid pairing in budding yeast. J Cell Biol. 125, 517–530.

    Google Scholar 

  • Guerrier-Takada, C., Gardiner, K., Marsch, T., Pace, N. and Altmann, S. (1983). The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 35, 849–857.

    Article  PubMed  CAS  Google Scholar 

  • Guschlbauer, W. and Janlowski, K. (1980). Nucleoside conformation is determined by the electronegativity of the sugar substituent. Nucl Acids Res. 8, 1421–1433.

    Article  PubMed  CAS  Google Scholar 

  • Guyton, A.C. (1991). Textbook of Medical Physiology. 8th edition. Philadelphia: W.B. Saunders Company.

    Google Scholar 

  • Hackett, J.A., Feldser, D.M. and Greider, C.W. (2001). Telomere dysfunction increases mutation rate and genomic instability. Cell. 106, 275–286.

    Article  PubMed  CAS  Google Scholar 

  • Hall, L.D., Steiner, P.R. and Pedersen, C. (1970). Studies of specifically fluorinated carbohydrates. Part VI. Some pentafuranosyl fluorides. Can J Chem. 48, 1155–1165.

    Article  CAS  Google Scholar 

  • Hand, R. (1978). Eukaryotic DNA: Organization of the genome for replication. Cell. 15, 317–325.

    Google Scholar 

  • Hartl, D.L. (2000). Molecular melodies in high and low C. Nat Rev Genet. 1, 145–149.

    Article  PubMed  CAS  Google Scholar 

  • Hawkinson, S.W., Coulter, C.L. and Greaves, M.L. (1970). The structure of vitamin B$12$. VIII. The crystal structure of vitamin B$12$–5’-phosphate. Proc Roy Soc Ser. A. 318, 143–167.

    Article  CAS  Google Scholar 

  • Holliday, R. (1965). Induced mitotic crossing-over in relation to genetic replication in synchronously dividing cells of ustilago maydis. Genet Res. 10, 104–120.

    Article  PubMed  CAS  Google Scholar 

  • Holmgreen, A. (1989). Thioredoxin and glutaredoxin systems. J Biol Chem. 264, 13963–13966.

    Google Scholar 

  • Horwitz, M.S. (1989). Transcription regulation in vitro by an E. coli promoter containing a DNA cruciform in the ′-35′ region. Nucleic Acids Res. 17, 5537–5545.

    Article  PubMed  CAS  Google Scholar 

  • Housman, D. and Huberman, J.A. (1975). Changes int he rate of DNA replication fork movement during S phase in mammalian cells. J Mol Biol. 94, 173–181.

    Article  PubMed  CAS  Google Scholar 

  • Hozak, P. and Fakan, S. (2006). Functional structure of the cell nucleus. Histochem Cell Biol. 125, 1–2.

    Article  PubMed  CAS  Google Scholar 

  • Hsieh, T. and Brutlag, D. (1980). ATP-dependent DNA topoisonmerase from D. melanogaster reversibly catenates duplex DNA rings. Cell. 21, 115–125.

    Article  PubMed  CAS  Google Scholar 

  • Huberman, J.A. and Riggs, A.D. (1968). Ont he mechanism of DNA replication in mammalian chromosomes. J Mol Biol. 32, 327–341.

    Article  PubMed  CAS  Google Scholar 

  • Hunziker, J. et al. (1993). Warum Pentose- und nicht Hexose- Nucleinsauren? Teil III. Oligo (2′3′-dideoxy-β-D-glucopyranosyl) nucleotide (‘Homo-DNA’) Paarungseigenschaften. Helv Chim Acta. 76, 259–352.

    Article  CAS  Google Scholar 

  • Irimia, M., Rukov, J.L., Penny, D. and Roy, S.W. (2007). Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol. 7, 188.

    Article  PubMed  CAS  Google Scholar 

  • IUPAC-IUB. (1983). Joint Comission on Biochemical Nomenclature. Abbreviations and symbols for the description of conformations of polynucleotide chains. Eur J Biochem. 131, 9–15.

    Google Scholar 

  • Ivell, R. (1998). A question of faith – or the philosophy of RNA controls. J Endocrinol. 159, 197–200.

    Article  PubMed  CAS  Google Scholar 

  • Jefford, C.E. and Irminger-Finger, I. (2006). Mechanisms of chromosome instability in cancers. Crit Rev Oncol Hematol. 59, 1–14.

    Article  PubMed  Google Scholar 

  • Johnson, D. and Morgan, A.R. (1978). Unique structures formed by pyrimidine-purine DNAs which may be four-stranded. Proc Natl Acad Sci U S A. 75, 1637–1641.

    Article  PubMed  CAS  Google Scholar 

  • Joyce, G.F. and Orgel, L.E. (1993). In The RNA World (eds. Rf. Gesteland and J.F. Atkins), pp.1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.

    Google Scholar 

  • Kalckar, H. (1941). The nature of energetic coupling in biological synthesis. Chem Rev. 28, 71–178.

    Google Scholar 

  • Kalckar, H. (1969). Biological Phosphorylations: Development of Concepts. Prentice-Hall, Englewood Cliffs, N.J.

    Google Scholar 

  • Kaufmann, W.K. (1995). Cell cycle checkpoints and DNA repair preserve the stability of the human genome. Cancer Metast Rev. 14, 31–41.

    Article  CAS  Google Scholar 

  • Kierzek, R., He, L. and Turner, D.H. (1982). Association of 2′-5′ oligoribonucleotides. Nucl Acids Res. 20, 1685.

    Article  Google Scholar 

  • Kilpatrick, J.E., Pitzer, K.S. and Pitzer, R. (1947). The thermodynamics and molecular structure of cyclopentane. J Amer Chem Soc. 69, 2483–2488.

    Article  CAS  Google Scholar 

  • Kilpatrick, M.W., Wei, C.F., Gray, H.B. Jr. and Wells, R.D. (1983). BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction. Nucleic Acids Res. 11, 3811–3822.

    Article  PubMed  CAS  Google Scholar 

  • Kim, R.A. and Wang, J.C. (1992). Identification of the yeast TOP3 gene product as a single strand-specific DNA topoisomerase. J Biol Chem. 267, 17178–17185.

    PubMed  CAS  Google Scholar 

  • Klug, A., Rhodes, D., Smith, J., Finch, J.T. and Thomas, J.O. (1980). A low resolution structure for the histone core of the nucleosome. Nature. 287, 509–516.

    Article  PubMed  CAS  Google Scholar 

  • Klysik, J., Stirdivant, S.M., Larson, J.E., Hart, P.A. and Wells, R.D. (1981). Left-handed DNA in restriction fragments and a recombinant plasmid. Nature. 290, 672–677.

    Article  PubMed  CAS  Google Scholar 

  • Kodani, M. (1958). Three chromosome numbers in whites and Japanese. Science. 127, 1339–1340.

    Article  PubMed  CAS  Google Scholar 

  • Koepsel, R.R. and Khan, S.A. (1987). Static and initiator protein-enhanced bending of DNA at a replication origin. Science. 233, 1316–1318

    Article  Google Scholar 

  • Kolata, G. (1983). Z-DNA moves toward “real biology”. Science. 222, 495–496.

    Article  PubMed  CAS  Google Scholar 

  • Kruger, K., Grabowski, P.J., Zaug, A.J., Sands, J., Gottschling, D.E. and Cech, T.R. (1982). Self-splicing RNA: autoexcision and autocyclization of the ribosomal RNA intervening sequence of Tetrahymena. Cell. 31, 147–157.

    Article  PubMed  CAS  Google Scholar 

  • Kubista, M., Hagmar, P., Nielsen, P.E. and Nordén, B. (1990). Reinterpretation of linear dichroism of chromatin supports a perpendicular linker orientation in the folded state. J Biomol Struct Dyn. 8, 37–54

    PubMed  CAS  Google Scholar 

  • Lam, S.L., Ip, L.N., Cui, X. and Ho, C.N. (2002). Random coil proton chemical shifts of deoxyribonucleic acids. J Biomol NMR. 24, 329–337.

    Article  PubMed  CAS  Google Scholar 

  • Langer, P.R., Waldrop, A.A. and Ward, D.C. (1981). Enzymatic synthesis of biotin-labeled polynucleotides: Novel nucleic acid affinity probes. Proc Nat Acad Sci USA. 78, 6633–6637.

    Article  PubMed  CAS  Google Scholar 

  • Larralde, R., Robertson, M.P. and Miller, S. (1995). Rates of decomposition of ribose and other sugars: Implications for chemical evolution. Proc Natl Acad Sci USA. 92, 8158–8160.

    Article  PubMed  CAS  Google Scholar 

  • Lavoie, B.D., Tuffo, K.M., Oh, S., Koshland, D. and Holm, C. (2000). Mitotic chromosome condensation requires Brn1p, the yeast homologue of Barren. Mol Biol Cell. 11, 1293–1304.

    PubMed  CAS  Google Scholar 

  • Lawrence, J.B., Singer, R.H. and Mcneil, J.A. (1990). Interphase and metaphase resolution of different distances within the human dystrophin gene. Science. 249, 928–932.

    Article  PubMed  CAS  Google Scholar 

  • Lemke, J., Claussen, J., Michel, S., Chuboda, I., Muhling, P., Sperling, K., Rubtsov, N., Grummt, U.W., Ullmann, P. and Kromeyer-Hauschild, K., et al. (2002). The DNA basedstructure of human chromosome 5 in interphase. Am J Hum Genet. 71, 1051–1059.

    Article  PubMed  CAS  Google Scholar 

  • Levan G., Hedrich, H.J., Remmers, E.F., Serikawa, T. and Yoshida, M.C. (1995). Standardized rat genetic nomenclature. Mamm Genome. 6, 447–448.

    Article  PubMed  CAS  Google Scholar 

  • Levitt, M. and Warshel, A. (1978). Extreme conformational flexibility of the furanose ring in DNA and RNA. J Amer Chem Soc. 100, 2607–2613.

    Article  CAS  Google Scholar 

  • Li, G., Sudlow, G. and Belmont, A.S. (1998). Interphase cell cycle dynamics of a late- replicating, heterochromatic homogeneously staining region: precise choreography of condensation/decondensation and nuclear positioning. J Cell Biol. 140, 975–989.

    Article  PubMed  CAS  Google Scholar 

  • Li, R., Yerganian, G., Duesberg, P., Kraemer, A., Willer, A., Rausch, C. and Hehlmann, R. (1997). Aneuploidy correlated 100% with chemical transformation of Chinese hamster cells. Proc Natl Acad Sci USA. 94, 14506–14511.

    Article  PubMed  CAS  Google Scholar 

  • Linial, M. and Shlomai, J. (1987). Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme. Proc Natl Acad Sci U S A. 84, 8205–8209.

    Article  PubMed  CAS  Google Scholar 

  • Linial, M. and Shlomai, J. (1988). Bent DNA structures associated with several origins of replication are recognized by a unique enzyme from trypanosomatids. Nucleic Acids Res. 16, 6477–6492.

    Article  PubMed  CAS  Google Scholar 

  • Lippmann, F. (1941). Metabolic generation and utilization of phosphate bond energy. Adv Enzymol. 18, 99–162.

    Google Scholar 

  • Lipps, H.J., Nordheim, A., Lafer, E.M., Ammermann, D., Stollar, B.D. and Rich, A. (1983). Antibodies against Z DNA react with the macronucleus but not the micronucleus of the hypotrichous ciliate stylonychia mytilus. Cell. 32, 435–441.

    Article  PubMed  CAS  Google Scholar 

  • Liu, L.F., Liu, C-C. and Alberts, M.M. (1979). T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication. Nature. 281, 456–461.

    Google Scholar 

  • Liu, L.F., Liu, C-C. and Alberts, M.M. (1980). Type II DNA topoisomerases: Enzymes that can unknot a topologically knotted DNA molecule via a reversible double-strand break. Cell. 19, 697–707.

    Article  PubMed  CAS  Google Scholar 

  • Liu, L.F. and Wang, J.C. (1978). Micrococcus luteus DNA gyrase: Active components and a model for its supercoiling of DNA. Proc Natl Acad Sci U S A. 75, 2098–102.

    Article  PubMed  CAS  Google Scholar 

  • Luger, K. (2003). Structure and dynamic behavior of nucleosomes. Curr Opin Genet Dev. 13, 127–135.

    Article  PubMed  CAS  Google Scholar 

  • Lyon, M.F. (2003). The Lyon and the LINE hypothesis. Semin Cell Dev Biol. 14, 313–318. Review.

    Article  PubMed  CAS  Google Scholar 

  • Malik, M., Nitiss, K.C., Enriquez-Rios, V. and Nitiss, J.L. (2006). Roles of nonhomologous end-joining pathways in surviving topoisomerase II–mediated DNA damage. Mol Cancer Ther. 5, 1405–1414.

    Article  PubMed  CAS  Google Scholar 

  • Manuelidis, L. (1990). A view of interphase chromosomes. Science. 250, 1533–1540.

    Article  PubMed  CAS  Google Scholar 

  • Massoud S. (2003). Genetic and environmental interactions in psychiatric illnesses [letter]. J Neuropsychiatry Clin Neurosci. 15, 386–387.

    Google Scholar 

  • Milman, G., Chamberlain, M. and Langridge, R. (1967). The structure of a DNA-RNA hybrid. Proc Natl Acad Sci U S A. 57, 1804–1810.

    Article  PubMed  CAS  Google Scholar 

  • Miyano, M., Kawashima, T. and Ohyama, T. (2001). A common feature shared by bent DNA structures locating in the eukaryotic promoter region. Mol Biol Rep. 28, 53–61.

    Article  PubMed  CAS  Google Scholar 

  • Mizuuchi, K., Fisher, L.M., O’Dea, M.H. and Gellert, M. (1980). DNA gyrase action involves the introduction of transient double-strand breaks into DNA. Proc Natl Acad Sci U S A. 77, 1847–1851.

    Article  PubMed  CAS  Google Scholar 

  • Mizuuchi, K., O’Dea, M.H. and Gellert, M. (1978). DNA gyrase: subunit structure and ATPase activity of the purified enzyme. Proc Natl Acad Sci U S A. 75, 5960–5963.

    Article  PubMed  CAS  Google Scholar 

  • Moller, A., Nordheim, A., Nichols, S.R. and Rich, A. (1981). 7-Methylguanine in poly(dG-dC).poly(dG-dC) facilitates z-DNA formation. Proc Natl Acad Sci U S A. 78, 4777–4781.

    Article  PubMed  CAS  Google Scholar 

  • Morrison, A. and Cozzarelli, N.R. (1979). Site-specific cleavage of DNA by E. coli DNA gyrase. Cell. 17, 175–184.

    Article  PubMed  CAS  Google Scholar 

  • Mozziconacci, J., Lavelle, C., Barbi, B., Lesne, A. and Victor, J.-M. (2006). A physical model for the condensation and decondensation of eukaryotic chromosomes. FEBS Letts. 580, 368–372.

    Article  CAS  Google Scholar 

  • Muller, D., Pitsch, S., Kittaka, A., Wagner, E., Wintner, C.E., Eschenmoser, A. and Ohlof, G. (1990). Chemie von α-Aminonitrilen. Aldomerisierung von Glycolaldehid-phosphat zu racemischen Hexose-2,4,6-triphosphat und rac-Ribose-2,4-diphosphat sind die Reaktionshamptprodukte. Helv Chim Acta. 73, 1410–1469.

    Article  Google Scholar 

  • Murray, L.J., Arendal, W.B. 3rd, Richardson, D.C. and Richardson, J.S. (2003). RNA backbone is rotameric. Proc Natl Acad Sci USA. 100, 13904–13909.

    Article  PubMed  CAS  Google Scholar 

  • Nagy, G., Gacsi, M., Rehak, M., Basnakian, A.G., Klaisz, M. and Bánfalvi, G. (2004). Gamma irradiation-induced apoptosis in murine pre-B cells prevents the condensation of fibrillar chromatin in early S phase. Apoptosis. 9, 765–776.

    Article  PubMed  CAS  Google Scholar 

  • Nordheim, A., Pardue, M.L., Lafer, E.M., Möller, A., Stollar, B.D. and Rich, A. (1981). Antibodies to left-handed Z-DNA bind to interband regions of Drosophila polytene chromosomes. Nature. 294, 417–422.

    Article  PubMed  CAS  Google Scholar 

  • O’Brien, E.J. and Macewan, A.W. (1970) Molecular and crystal structure of the polynucleotide complex: Polyinosinic acid plus polydeoxycytidylic acid. J Mol Biol. 48, 243–261.

    Article  PubMed  CAS  Google Scholar 

  • Orgel, L.E. (1968). Evolution of the genetic apparatus. J Mol Biol. 38, 381–393.

    Article  PubMed  CAS  Google Scholar 

  • Ottig, G. et al. (1993). Warum Pentose- und nicht Hexose- Nucleinsauren? Teil IV. ‘Homo-DNA’: 1H, 13C,31P und 15N NMR-spektoskopische Untersuchung von ddGIc (A-A-A-A-A-T-T-T-T-T) in wassriger Lösung. Helv Chim Acta. 76, 2701–2757.

    Article  Google Scholar 

  • Ozaki, H., Nakajima, K., Izumi, C. and Sawai, H. (2000). Convenient synthesis of arabinonucleoside containing oligodeoxyrobonucleotides. Nucleic Acids Symp Ser. 44, 37–38.

    PubMed  Google Scholar 

  • Paulus, H. (2000). Protein splicing and related forms of protein autoprocessing. Annu Rev Biochem. 69, 447–495.

    Article  PubMed  CAS  Google Scholar 

  • Pitsch, S. et al. (1995). Pyranosyl- RNA (‘p-RNA’): Base-Pairing selectivity and potential to replicate. Preliminary communication. Helv Chim Acta. 78, 1621–1636.

    Article  CAS  Google Scholar 

  • Pitzer, K.S. and Donath, E. (1959). Conformations and strain energy of cyclopentane and its derivatives. J Amer Chem Soc. 81, 3213–3218.

    Article  CAS  Google Scholar 

  • Prakash, T.P., Roberts, C. and Switzer, C. (1997). Angew Chem Int Ed Engl. 36, 1522.

    CAS  Google Scholar 

  • Prusiner, P. and Sundaralingam, M. (1972). Stereochemistry of nucleic acids and their substituents. XXV. Crystal and molecular structure of allopurinol, a potent inhibitor of xanthine oxidase. Acta Crystallogr. B28, 2148–2152.

    Google Scholar 

  • Record, M.T. Jr., Mazur, S.J., Melancon, P., Roe, J.H., Shaner, S.L. and Unger, L. (1981). Double helical DNA: Conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 50, 997–1024. Review.

    Article  PubMed  CAS  Google Scholar 

  • Rees, A.R. and Sternberg, M.J.E. (1984). From Cells to Atoms. Blackwell Scientific Publications, Oxford.

    Google Scholar 

  • Rehak, M., Csuka, I., Szepessy, E. and Bánfalvi, G. (2000) Subphases of DNA replication in Drosophila cells. DNA Cell Biol. 19, 607–612.

    Article  PubMed  CAS  Google Scholar 

  • Reichard, P. (1993). The anaerobic ribonucleotide reductase from Escherichia coli. J Biol Chem. 268, 8383–8386.

    PubMed  CAS  Google Scholar 

  • Rich, A. (1983). Right-handed and left-handed DNA: Conformational information in genetic material. Cold Spring Harb Symp Quant Biol. 47, 1–12.

    PubMed  Google Scholar 

  • Rich, A. and Zhang, S. (2003). Timeline: Z-DNA: The long road to biological function. Nat Rev Genet. 4, 566–572.

    Article  PubMed  CAS  Google Scholar 

  • Richmond, T.J., Finch, J.T. and Klug, A. (1983). Studies of nucleosome structure. Cold Spring Harb Symp Quant Biol. 47, 493–501.

    PubMed  Google Scholar 

  • Rogozin, I.B., Spiridonov, A.N., Sorokin, A.V., Wolf, I., Jordan, I.K., Tatusov, R.L. and Koonin, E.V. (2002). Purifying and directional selection in overlapping prokaryotic genes. Trends Genet. 18, 228–232.

    Article  PubMed  CAS  Google Scholar 

  • Ross, M., Shulman, M. and Landy, A. (1982). Biochemical analysis of att-defective mutants of the phage lambda site-specific recombination system. J Mol Biol. 156, 505–522.

    Article  PubMed  CAS  Google Scholar 

  • Rubin, G.M. (2001). The draft sequences: comparing species. Nature. 409, 820–821.

    Article  PubMed  CAS  Google Scholar 

  • Rydberg, B., Holley, W.R, Mian, I.S. and Chatterjee, A. (1998). Chromatin conformation in living cells: Support for a zig-zag model of the 30 nm chromatin fibril. J Mol Biol. 284, 71–84.

    Article  PubMed  CAS  Google Scholar 

  • Ryder, K., Silver, S., Delucia, A.L., Fanning, E. and Tegtmeyer, P. (1986). An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 44, 719–25.

    Article  PubMed  CAS  Google Scholar 

  • Saenger, W. (1984). Principles of Nucleic Acid Structure. (ed. C.R. Cantor), pp. 17–21. Springer Verlag, New York.

    Google Scholar 

  • Sasisekharan, V. and Pattabiraman, N. (1978). Structure of DNA predicted from stereochemistry of nucleoside derivatives. Nature 275, 159–162.

    Article  PubMed  CAS  Google Scholar 

  • Sawai, H., Seki, J., and Ozaki, H. (1996). Comparative studies of duplex and triplex formation of 2′,5′ and 3′,5′ linked oligoribonucleotides. J Biomol Struct Dyn. 13, 1043–1051.

    PubMed  CAS  Google Scholar 

  • Schmidt-Nielsen, K. (1997). Animal Physiology. Cambridge University Press, Cambridge, pp. 192–193.

    Google Scholar 

  • Schweyer, S., Hemmerlein, B., Radzun, H.J. and Fayyazi, A. (2004) Continuous recruitment, co-expression of tumour necrosis factor-a and matrix metalloproteinases, and apoptosis of macrophages in gout tophi. Virchows Archiv. 437, 534–539.

    Article  Google Scholar 

  • Selsing, E., Wells, R.D., Early, T.A. and Kearns, D.R. (1978). Two contiguous conformations in a nucleic acid duplex. Nature. 21, 249–250.

    Article  Google Scholar 

  • Seto, H., Otake, N. and Yonehara, H. (1972). The structures of pentopyranine A and C, two cytosine nucleotides with α-α configuration. Tetrahedron Lett. 35, 3991–3994.

    Article  Google Scholar 

  • Sharp, P.A. (1985). On the origin of RNA splicing and introns. Cell. 42, 397–400. Review.

    Article  PubMed  CAS  Google Scholar 

  • Snyder, M., Buchman, A.R. and Davis, R.W. (1986). Bent DNA at a yeast autonomously replicating sequence. Nature. 324, 87–89.

    Article  PubMed  CAS  Google Scholar 

  • Stambrook, P.J. (1974). The temporal relication of ribosomal genes in synchronized Chinese hamster cells. J Mol Biol. 82, 303–313.

    Article  PubMed  CAS  Google Scholar 

  • Stent, G.S. (1958). Mating in the reproduction of bacterial viruses. Adv Virus Res. 5, 95–149.

    Article  PubMed  CAS  Google Scholar 

  • Stryer, L. (1995). Biochemistry (Fourth Edition), pp. 746. Freeman and Company, New York.

    Google Scholar 

  • Stupina, V.A. and Wang, J.C. (2004). Proc Natl Acad Sci USA. 101, 8608–8613.

    Article  PubMed  CAS  Google Scholar 

  • Sugino, A. and Bott, K.F. (1980). Bacillus subtilis deoxyribonucleic acid gyrase. J Bacteriol. 141, 1331–1339.

    PubMed  CAS  Google Scholar 

  • Sun, J., Zhang, Q. and Schlick, T. (2005). Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci U S A. 102, 8180–8185.

    Article  PubMed  CAS  Google Scholar 

  • Sundaralingam, M, (1971). Stereochemistry of Nucleic acids and their constituents. XVIII. Conformational analysis of α-nucleotides by X-ray crystallography. J Amer Soc. 93, 6644–6647.

    Article  CAS  Google Scholar 

  • Suzuki, K., Nakano, H. and Sizuki, S. (1967). Natural occurrence of and enzymatic synthesis of α-nicotamide adenine dinucleotide phosphate. J Biol Chem. 242, 3319–3325.

    PubMed  CAS  Google Scholar 

  • Taljanidisz, J., Pppowski, J. and Sarkar, N. Temporal order of gene replication in Chinese hamster ovary cells. Mol Cell Biol. 9, 2881–2889.

    Google Scholar 

  • Taylor, J.H. (1963). DNA synthesis in relation to chromosome reproduction and reunion of breaks. J Cell Comp Physiol. 62, 73–85.

    Article  CAS  Google Scholar 

  • Thelander, L. and Reichard, P. (1979). Reduction of ribonucleotides. Annu Rev Biochem. 48, 133–158.

    Article  PubMed  CAS  Google Scholar 

  • Thomas, C.A. (1971). The genetic organization of chromosomes. Annu Rev Genet. 5, 237–256.

    Article  PubMed  CAS  Google Scholar 

  • Thorp, H.H. (2000). The importance of being r: Greater oxidation stability of RNA compared with DNA. Chem Biol. 7, 33–36.

    Article  Google Scholar 

  • Tjio, J.H. and Levan, A. (1956). The chromosome number of man. Heraditas 42, 1–6.

    Article  Google Scholar 

  • Tjio, J.H. and Puck, T.T. (1958). The somatic chromosomes of man. Proc Natl Acas Sci USA. 44, 1229–1237.

    Article  CAS  Google Scholar 

  • Uesugi, S., Miki, H., Ikehara, M., Iwahashi, H. and Kyogoku, Y. (1979). A linear relationship between electronegativity of 2′-substituents and conformation of adenosine nucleosides. Tetrahedron Lett. 42, 4073–4076.

    Article  Google Scholar 

  • Usher, D.A. (1972). RNA double helix and the evolution of the $3′,5′-linkage. Nat New Biol. 235, 207–208.

    PubMed  CAS  Google Scholar 

  • Usher, D.A. and McHabe, A.H. (1976). Hydrolytic stability of helical RNA a sensitive advantage for the natural 3′,5′-bond. Proc Natl Acad Sci USA. 73, 1149–1153.

    Article  PubMed  CAS  Google Scholar 

  • Van Holde, K. and Zlatanova, J. (1996). What determines the folding of the chromatin fiber? Proc Natl Acad Sci USA. 93, 10548–10555.

    Article  PubMed  Google Scholar 

  • Walsh, K. and Gualberto, A. (1992). MyoD binds to the guanine tetrad nucleic acid structure. J Biol Chem. 267, 13714–13718.

    PubMed  CAS  Google Scholar 

  • Wang, J.C. Interaction between DNA and an Escherichia coli protein omega. J Mol Biol. 55, 523–533.

    Google Scholar 

  • Wang, J.C. (1980). Superhelical DNA. Trends Biochem Sci. 5, 219–221.

    Article  CAS  Google Scholar 

  • Wang, J.C., Peck, L.J. and Becherer, K. (1983). DNA supercoiling and its effects on DNA structure and function. Cold Spring Harb Symp Quant Biol. 47, 85–91.

    PubMed  Google Scholar 

  • Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., Van Boom, J.H., Van Der Marel, G. and Rich, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 282, 680–686.

    Article  PubMed  CAS  Google Scholar 

  • Watson, J.D. and Crick, F.H.C. (1963). A structure for deoxyribose nucleic acid. Nature. 171, 737–738.

    Article  Google Scholar 

  • Weintraub, H. (1983). A dominant role for DNA secondary structure in forming hypersensitive structures in chromatin. Cell. 32, 1191–1203.

    Article  PubMed  CAS  Google Scholar 

  • Weiss, L. (Ed.). Cell and Tissue Biology: A Textbook of Histology. 6th edition. Baltimore, MD: Urban and Schwarzenberg; 1983.

    Google Scholar 

  • Wells, R.D., Brennan, R., Chapman, K.A., Goodman, T.C., Hart, P.A., Hillen, W., Kellogg, D.R., Kilpatrick, M.W., Klein, R.D., Klysik, J., Lambert, P.F., Larson, J.E., Miglietta, J.J., Neuendorf, S.K., O’Connor, T.R., Singleton, C.K., Stirdivant, S.M., Veneziale, C.M., Wartell, R.M. and Zacharias, W. (1983). Left-handed DNA helices, supercoiling, and the B-Z junction. Cold Spring Harb Symp Quant Biol. 47, 77–84.

    PubMed  Google Scholar 

  • Wells, R.D., Goodman, T.C., Hillen, W., Horn, G.T., Klein, R.D., Larson, J.E., Muller, U.R., Neuendorf, S.K., Panayotatos, N. and Stirdivant, S.M. (1980). DNA structure and gene regulation. Prog Nucleic Acid Res Mol Biol. 24, 167–267.

    Article  PubMed  CAS  Google Scholar 

  • Whitehead, A. and Crawford, D.L. (2005). Variation in tissue-specific gene expression among natural populations. Genome Biol. 6, R13.

    Article  PubMed  Google Scholar 

  • Widom, J. (1998). Structure, dynamics, and function of chromatin in vitro. Annu Rev Biophys Biomol Struct. 27, 285–327.

    Article  PubMed  CAS  Google Scholar 

  • Williams, S.P., Athey, B.D., Muglia, L.J., Schappe, R.S., Gough, A.H. and Langmore, J.P. (1986). Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length. Biophys J. 49, 233–248.

    Article  PubMed  CAS  Google Scholar 

  • Woodcock, C.L., Frado, L.L. and Rattner, J.B. (1984). The higher-order structure of chromatin: Evidence for a helical ribbon arrangement. J Cell Biol. 99, 42–52.

    Article  PubMed  CAS  Google Scholar 

  • Woodcock, C.L., Grigoryev, S.A., Horowitz, R.A. and Whitaker, N. (1993). A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc Natl Acad Sci USA. 90, 9021–9025.

    Article  PubMed  CAS  Google Scholar 

  • Woodcock, C.L. and Horowitz, R.A. (1995). Chromatin organization re-viewed. Trends Cell Biol. 5, 272–277.

    Article  PubMed  CAS  Google Scholar 

  • Worzel, A., Strogatz, A. and Riley, D. (1981). Structure of chromatin and the linking number of DNA. Proc Natl Acad Sci U S A. 78, 1461–1465.

    Article  Google Scholar 

  • Zahn, K. and Blattner, F.R. (1985). Sequence-induced DNA curvature at the bacteriophage lambda origin of replication. Nature. 317, 451–453.

    Article  PubMed  CAS  Google Scholar 

  • Zimmerman, S.B. (1982). The three-dimensional structure of DNA. Ann Rev Biochem. 51, 395–427.

    Google Scholar 

  • Zlatanova, J., Leuba, S.H. and Van Holde, K. (1998). Chromatin fiber structure: Morphology, molecular determinants, structural transitions. Biophys J. 74, 2554–2566.

    Article  PubMed  CAS  Google Scholar 

  • Zubay, G. (1958). A template model for the synthesis of ribonucleic acid from deoxyribonucleic acid. Nature. 182, 1290–1292.

    Article  PubMed  CAS  Google Scholar 

  • Zubay, G. (1998). Orig Life Evol Biosph. 28, 13.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Biology and Ecology, University of Debrecen, Egyetem Square 1, Debrecen 4010, Hungary

    Gáspár Bánfalvi (Prof.)

Authors
  1. Gáspár Bánfalvi
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Bánfalvi, G. (2009). Structural Organization of DNA. In: Apoptotic Chromatin Changes. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-9561-0_2

Download citation

Publish with us

Policies and ethics

Search

Navigation