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)
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
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)
CRAIG, M.E., CROTHERS, D.M., DOTY, P.: Relaxation kinetics of dimer formation by self complementary oligonucleotides. J. Mol. Biol. 62, 383–401 (1971)
CROTHERS, D.M., SPATZ, H.C.: Theory of friction-limited DNA unwinding. Biopolymers 10, 1949–1972 (1971)
DAVIES, R.J.H.: Kinetics of dissociation of polynucleotide-monomer complexes. J. Mol. Biol. 63, 117–137 (1972)
DAVIS, R.C., TINOCO, I., Jr.: Temperature-dependent properties of dinucleoside phosphates. Biopolymers 6, 223–242 (1968)
DAVISON, P.F.: The rate of strand separation in alkali-treated DNA. J. Mol. Biol. 22, 97–108 (1966)
DAVISON, P.F.: Viscosity and temperature effects on- the rate of DNA strand separation in alkali. Biopolymers 5, 715–721 (1967)
FRANK, H.S., EVANS, M.W.: Free volume and entropy in condensed systems. J. Chem. Phys. 13, 507–532 (1945)
FRANKS, F.: The hydrophobic interaction. In: Water, a Comprehensive Treatise. FRANKS, F. (ed.), pp. 1–94. New York: Plenum 1975
GAARZ, U., LÜDEMANN, H.D.: Pressure dependence of the self-asso- ciation of 9-methylpurine in aqueous solution. Ber. Bunsenges. 80, 607–614 (1976)
GARLAND, F., PATEL, R.C.: Relaxation spectra of 6-methylp.urine in aqueous solution. J. Phys. Chem. 78, 848–850 (1974)
GRALLA, J., CROTHERS, D.M.: Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J. Mol. Biol. 73, 497- 511 (1973)
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)
HOFFMAN, G.W.: A nanosecond temperature-jump apparatus. Rev. Sci. Instr. 42, 1643–1647 (1971)
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)
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)
KASARDA, D.D.: Dilution volume changes of some purine and pyrimi-dine compounds. Biochem. Biophys. Acta 217, 535–538 (1970)
KAUZMANN, W.: Some factors in the interpretation of protein de-naturation. Adv. Prot. Chem. 14, 1–63 (1959)
NEMETHY, G.: Hydrophobe Wechselwirkungen. Angew. Chem. 79, 260- 271 (1967)
NEMETHY, G., SCHERAGA, H.A.: The structure of water and hydrophobic bonding in proteins. J. Phys. Chem. 66, 1773–1789 (1962)
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)
PöRSCHKE, D.: Thermodynamik und Kinetik der Helix-Knauel Umwand-lung von Oligonucleotiden. Dissertation Braunschweig (1968)
PöRSCHKE, D.: Cooperative nonenzymic base recognition II. Thermodynamics of the helix coil transition of oligoadenylic + oligo- uridylic acids. Biopolymers 10, 1989–2013 (1971)
PöRSCHKE, D.: The dynamics of nucleic acid single-strand-confor- mation changes. Oligo- and polyriboadenylic acids. Eur. J. Biochem. 39, 117–126 (1973)
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)
PöRSCHKE, D.: A direct measurement of the unzippering rate of a nucleic acid double helix. Biophys. Chem. 2, 97–101 (1974b)
PöRSCHKE, D.: Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. Biophys. Chem..1, 381–386 (1974c)
PöRSCHKE, D.: Cable temperature jump with improved sensitivity and time resolution. Rev. Sci. Instrum. 47, 1363–1365 (1976a)
PöRSCHKE, D.: The nature of stacking interactions in polynucleotides. Molecular states in oligo- and polyribocytidylic acids by relaxation analysis. Biochemistry 15, 1495–1499 (1976b)
PöRSCHKE, D.: Thermodynamic and kinetic parameters of ion condensation to polynucleotides. Outer sphere complex formed by Mg++ ions. Biophys. Chem. 4, 383–394 (1976c)
PöRSCHKE, D.: Dynamic properties of short helices. Studia biophys. 51, 35–46 (1976d);
PöRSCHKE, D., EGGERS, F.: Thermodynamics ahd kinetics of base-stacking interactions. Eur. J. Biochem. 26, 490–498 (1972)
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)
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)
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)
RECORD, M.T., ZIMM, B.H.: Kinetics of the helix coil transition in DNA. Biopolymers 11, 1435–1484 (1972)
RIESNER, D., ROMER, R., in: Physicochemical Properties of Nucleic Acids. DUCHESNE, J. (ed.), Vol. 2, pp. 237–318. London-New York: Academic Press 1973
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)
SAENGER, W., RIECKE, J., SUCK, D.: A structural model for the polyadenylic acid single helix. J. Mol. Biol. 93, 529–534 (1975)
SPATZ, H.C., CROTHERS, D.M.: The rate of DNA unwinding. J. Mol. Biol. 42, 191–219 (1969)
TS’O, P.O.P.: Basic Principles in Nucleic Acid Chemistry, Vol. I, pp. 453–584. New York-London: Academic Press 1974
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)
WARING, M., BRITTEN, R.J.: Nucleotide sequence repetition: A rapidly reassociating fraction of mouse DNA. Science 154, 791-794 (1966)
WETMUR, J.G., DAVIDSON, N.: Kinetics of renaturation of DNA. J. Mol. Biol. 31, 349–370 (1968)
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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
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