Solvent Effects on the Kinetics and Thermodynamics of Stacking in Poly(cytidylic acid)

Susan M. Freier, K. O. Hill, T. G. Dewey, Douglas H. Turner, Luis A. Marky, Kenneth J. Breslauer

Research output: Contribution to journalArticle

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Abstract

The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix formation is rotationally diffusion controlled. The rate of coil formation in poly(C) has an activation energy of - 11 kcal/mol, presumably reflecting the electronic stacking interactions which stabilize the helix. Viscous cosolvents, glycerol or sucrose, slow down the rate of coil formation; acetonitrile and formamide at 5 mol % increase the rate relative to that in water. The polar cosolvents may specifically attack a cytosine stack. The absorbance vs. temperature profiles for poly(C) are analyzed with the one-dimensional Ising model. When only optical data are used, the cooperativity parameter, σ, and the enthalpy, ∆H, cannot be uniquely determined. A method is proposed that allows determination of σ by combining spectroscopic and calorimetric data. The values of σ derived for poly(C) are between 0.8 and 1.0, and AH is about -9 kcal/mol of stack. An alternative method using integration of the excess heat capacity curve and extrapolation to fully stacked and random coil species yields a ∆H of -7 kcal/mol of stack.

Original languageEnglish (US)
Pages (from-to)1419-1426
Number of pages8
JournalBiochemistry
Volume20
Issue number6
DOIs
StatePublished - Mar 1981

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Cytidine Monophosphate
Thermodynamics
Kinetics
Activation energy
Ising model
Temperature
Cytosine
Extrapolation
Viscosity
Glycerol
Specific heat
Sucrose
Enthalpy
Lasers
Hot Temperature
Water

ASJC Scopus subject areas

  • Biochemistry

Cite this

Freier, S. M., Hill, K. O., Dewey, T. G., Turner, D. H., Marky, L. A., & Breslauer, K. J. (1981). Solvent Effects on the Kinetics and Thermodynamics of Stacking in Poly(cytidylic acid). Biochemistry, 20(6), 1419-1426. https://doi.org/10.1021/bi00509a003

Solvent Effects on the Kinetics and Thermodynamics of Stacking in Poly(cytidylic acid). / Freier, Susan M.; Hill, K. O.; Dewey, T. G.; Turner, Douglas H.; Marky, Luis A.; Breslauer, Kenneth J.

In: Biochemistry, Vol. 20, No. 6, 03.1981, p. 1419-1426.

Research output: Contribution to journalArticle

Freier, SM, Hill, KO, Dewey, TG, Turner, DH, Marky, LA & Breslauer, KJ 1981, 'Solvent Effects on the Kinetics and Thermodynamics of Stacking in Poly(cytidylic acid)', Biochemistry, vol. 20, no. 6, pp. 1419-1426. https://doi.org/10.1021/bi00509a003
Freier, Susan M. ; Hill, K. O. ; Dewey, T. G. ; Turner, Douglas H. ; Marky, Luis A. ; Breslauer, Kenneth J. / Solvent Effects on the Kinetics and Thermodynamics of Stacking in Poly(cytidylic acid). In: Biochemistry. 1981 ; Vol. 20, No. 6. pp. 1419-1426.
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