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Elementary Steps of Base Recognition and Helix-Coil Transitions in Nucleic Acids

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Chemical Relaxation in Molecular Biology

Part of the book series: Molecular Biology Biochemistry and Biophysics ((MOLECULAR,volume 24))

Abstract

Although the general processes involved in storage and transfer of genetic information have been known for quite some time, a great number of questions concerning replication, transcription and translation remain to be answered. In particular, the high accuracy of the information transfer observed in living organisms is very poorly understood. A first step towards an understanding of these processes is the investigation of elementary reactions involved in the transfer. Since the information transfer is not only exceedingly accurate, but also very fast, the corresponding elementary reactions can only be studied with the aid of fast relaxation techniques.

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Abbreviations

ct :

total nucleotide concentration in monomer units

S:

chain growth parameter, i.e. stability constant for the addition of a base pair to a préexistent nucleus

ß:

nucleation parameter, the product 3s being the stability constant for the formation of an isolated base pair

kf:

rate of chain growth = rate of base pair addition to a préexistent nucleus

N:

chain length of oligonucleotides

References

  • APPLEQUIST, J., DAMLE, V.: Thermodynamics of the helix-coil equilibrium in oligoadenylic acid from hypochromicity studies. J. Amer. Chem. Soc. 87, 1450–1458 (1965)

    Article  CAS  Google Scholar 

  • BLOOMFIELD, V.A., CROTHERS, D.M., TINOCO, I., Jr.: Physical Chemistry of Nucleic Acids, pp. 84–102. New York, Evanston, San Francisco, London: Harper & Row: 1974

    Google Scholar 

  • COUTTS, S.M.: Thermodynamics and kinetics of GC base pairing in the isolated extra arm of serine — specific transfer RNA from yeast. Biochem. Biophys. Acta 232, 94–106 (1971)

    PubMed  CAS  Google Scholar 

  • CRAIG, M.E., CROTHERS, D.M., DOTY, P.: Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62, 383–401 (1971)

    Article  PubMed  CAS  Google Scholar 

  • CROTHERS, D.M., SPATZ, H.C.: Theory of friction-limited DNA unwinding. Biopolymers 10, 1949–1972 (1971)

    Article  CAS  Google Scholar 

  • DAVIES, R.J.H.: Kinetics of dissociation of polynucleotide-monomer complexes. J. Mol. Biol. 63, 117–137 (1972)

    Article  PubMed  CAS  Google Scholar 

  • DAVIS, R.C., TINOCO, I., Jr.: Temperature-dependent properties of dinucleoside phosphates. Biopolymers 6, 223–242 (1968)

    Article  PubMed  CAS  Google Scholar 

  • DAVISON, P.F.: The rate of strand separation in alkali-treated DNA. J. Mol. Biol. 22, 97–108 (1966)

    Article  CAS  Google Scholar 

  • DAVISON, P.F.: Viscosity and temperature effects on- the rate of DNA strand separation in alkali. Biopolymers 5, 715–721 (1967)

    Article  PubMed  CAS  Google Scholar 

  • FRANK, H.S., EVANS, M.W.: Free volume and entropy in condensed systems. J. Chem. Phys. 13, 507–532 (1945)

    Article  CAS  Google Scholar 

  • FRANKS, F.: The hydrophobic interaction. In: Water, a Comprehensive Treatise. FRANKS, F. (ed.), pp. 1–94. New York: Plenum 1975

    Google Scholar 

  • GAARZ, U., LÜDEMANN, H.D.: Pressure dependence of the self-asso- ciation of 9-methylpurine in aqueous solution. Ber. Bunsenges. 80, 607–614 (1976)

    CAS  Google Scholar 

  • GARLAND, F., PATEL, R.C.: Relaxation spectra of 6-methylp.urine in aqueous solution. J. Phys. Chem. 78, 848–850 (1974)

    Article  CAS  Google Scholar 

  • GRALLA, J., CROTHERS, D.M.: Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol. 73, 497- 511 (1973)

    Article  Google Scholar 

  • HEARST, J.E., BOTCHAN, M.: Deoxyribonucleic acid renaturation kinetics and hybridization. Probes to the structure of the eukaryotic chromosome. Acc. Chem. Res. 6, 293–298 (1973)

    Article  CAS  Google Scholar 

  • HOFFMAN, G.W.: A nanosecond temperature-jump apparatus. Rev. Sci. Instr. 42, 1643–1647 (1971)

    Article  CAS  Google Scholar 

  • HOFFMAN, G.W., PöRSCHKE, D.: Cooperative nonenzymic base recognition. Kinetics of the binding of a base monomer to a complementary polynucleotide template. Biopolymers 12, 1625–16 38 (1973)

    Article  Google Scholar 

  • HOGGETT, J.G., MAASS, G.: Thermodynamics and kinetics of the formation of a hybrid double helix of oligomers of riboadenylic and deoxyribothymidylic acids of definite chain lengths. Ber. Bunsenges. 75, 45–54 (1971)

    CAS  Google Scholar 

  • KASARDA, D.D.: Dilution volume changes of some purine and pyrimi-dine compounds. Biochem. Biophys. Acta 217, 535–538 (1970)

    PubMed  CAS  Google Scholar 

  • KAUZMANN, W.: Some factors in the interpretation of protein de-naturation. Adv. Prot. Chem. 14, 1–63 (1959)

    Article  CAS  Google Scholar 

  • NEMETHY, G.: Hydrophobe Wechselwirkungen. Angew. Chem. 79, 260- 271 (1967)

    Article  Google Scholar 

  • NEMETHY, G., SCHERAGA, H.A.: The structure of water and hydrophobic bonding in proteins. J. Phys. Chem. 66, 1773–1789 (1962)

    Article  CAS  Google Scholar 

  • PODDER, S.U.: Cooperative non-enzymic base recognition. A kinetic study of interaction between GpGpGpC and GpCpCpC and of self- association of GpGpGpC. Eur. J. Biochem. 22, 467 (1971)

    Article  PubMed  CAS  Google Scholar 

  • PöRSCHKE, D.: Thermodynamik und Kinetik der Helix-Knauel Umwand-lung von Oligonucleotiden. Dissertation Braunschweig (1968)

    Google Scholar 

  • PöRSCHKE, D.: Cooperative nonenzymic base recognition II. Thermodynamics of the helix coil transition of oligoadenylic + oligo- uridylic acids. Biopolymers 10, 1989–2013 (1971)

    Article  Google Scholar 

  • PöRSCHKE, D.: The dynamics of nucleic acid single-strand-confor- mation changes. Oligo- and polyriboadenylic acids. Eur. J. Biochem. 39, 117–126 (1973)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D.: Model calculations on the kinetics of oligonucleotide double helix-coil transitions. Evidence for a fast chain sliding reaction. Biophys. Chem. 2, 83–96 (1974a)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D.: A direct measurement of the unzippering rate of a nucleic acid double helix. Biophys. Chem. 2, 97–101 (1974b)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D.: Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. Biophys. Chem..1, 381–386 (1974c)

    Article  Google Scholar 

  • PöRSCHKE, D.: Cable temperature jump with improved sensitivity and time resolution. Rev. Sci. Instrum. 47, 1363–1365 (1976a)

    Article  Google Scholar 

  • PöRSCHKE, D.: The nature of stacking interactions in polynucleotides. Molecular states in oligo- and polyribocytidylic acids by relaxation analysis. Biochemistry 15, 1495–1499 (1976b)

    Article  Google Scholar 

  • PöRSCHKE, D.: Thermodynamic and kinetic parameters of ion condensation to polynucleotides. Outer sphere complex formed by Mg++ ions. Biophys. Chem. 4, 383–394 (1976c)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D.: Dynamic properties of short helices. Studia biophys. 51, 35–46 (1976d);

    Google Scholar 

  • PöRSCHKE, D., EGGERS, F.: Thermodynamics ahd kinetics of base-stacking interactions. Eur. J. Biochem. 26, 490–498 (1972)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D., EIGEN, M.: Cooperative nonenzymic base recognition III. Kinetics of the helix-coil transition of the oligoribo- uridylic oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. J. Mol. Biol. 62, 361–381 (1971)

    Article  PubMed  Google Scholar 

  • PöRSCHKE, D., HOFFMAN, G.W., SENEAR, A.: Double helical complex formed from a polynucleotide and a complementary monomer. Nature N.B. 242, 45–46 (1973)

    PubMed  Google Scholar 

  • PöRSCHKE, D., UHLENBECK, O.C., MARTIN, F.H.: Thermodynamics and kinetics of the helix coil transition of oligomers containing GC base pairs. Biopolymers 12, 1313–1335 (1973)

    Article  Google Scholar 

  • RECORD, M.T., ZIMM, B.H.: Kinetics of the helix coil transition in DNA. Biopolymers 11, 1435–1484 (1972)

    Article  PubMed  CAS  Google Scholar 

  • RIESNER, D., ROMER, R., in: Physicochemical Properties of Nucleic Acids. DUCHESNE, J. (ed.), Vol. 2, pp. 237–318. London-New York: Academic Press 1973

    Google Scholar 

  • ROSS, P.D., STURTEVANT, J.M.: The kinetics of double helix formation from polyriboadenylic acid and polyribouridylic acid. Proc. Nat. Acad. Sci. (Wash.) 46, 1360–1365 (1960)

    Article  CAS  Google Scholar 

  • SAENGER, W., RIECKE, J., SUCK, D.: A structural model for the polyadenylic acid single helix. J. Mol. Biol. 93, 529–534 (1975)

    Article  PubMed  CAS  Google Scholar 

  • SPATZ, H.C., CROTHERS, D.M.: The rate of DNA unwinding. J. Mol. Biol. 42, 191–219 (1969)

    Article  PubMed  CAS  Google Scholar 

  • TS’O, P.O.P.: Basic Principles in Nucleic Acid Chemistry, Vol. I, pp. 453–584. New York-London: Academic Press 1974

    Google Scholar 

  • UHLENBECK, O.C., BORER, P.N., DENGLER, B., TINOCO, I., Jr.: Stability of RNA hairpin loops: A6-Cm-U6. J. Mol. Biol. 73, 483–496 (1973)

    Article  PubMed  CAS  Google Scholar 

  • WARING, M., BRITTEN, R.J.: Nucleotide sequence repetition: A rapidly reassociating fraction of mouse DNA. Science 154, 791-794 (1966)

    Article  PubMed  CAS  Google Scholar 

  • WETMUR, J.G., DAVIDSON, N.: Kinetics of renaturation of DNA. J. Mol. Biol. 31, 349–370 (1968)

    Article  PubMed  CAS  Google Scholar 

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Authors
  1. D. Pörschke
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Editors and Affiliations

  1. Department of Chemical Immunology, The Weizmann Institute of Science, Rehovot, Israel

    Israel Pecht

  2. Department of Medical Biophysics, Karolinska Institutet, S-10401, Stockholm 60, Sweden

    Rudolf Rigler

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Pörschke, D. (1977). Elementary Steps of Base Recognition and Helix-Coil Transitions in Nucleic Acids. In: Pecht, I., Rigler, R. (eds) Chemical Relaxation in Molecular Biology. Molecular Biology Biochemistry and Biophysics, vol 24. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-81117-3_5

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  • DOI: https://doi.org/10.1007/978-3-642-81117-3_5

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-81119-7

  • Online ISBN: 978-3-642-81117-3

  • eBook Packages: Springer Book Archive

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