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Methods for Obtaining Thermodynamic Data on Oligonucleotide Transitions

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Thermodynamic Data for Biochemistry and Biotechnology

Abstract

The goal of this chapter is to present a critical survey of spectroscopic and calorimetric methods for obtaining thermodynamic data on conformational transitions in oligonucleotides. A comprehensive compilation of the large body of published thermodynamic data on oligo- and polynucleotides will not be included here since these results have been tabulated and reviewed elsewhere [1–4]. Instead, selected data will be presented to help illustrate the relative merits of each experimental method described for extracting thermodynamic data from optical and calorimetric studies on oligonucleotides.

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Abbreviations

K:

equilibrium constant

K(Tm):

equilibrium constant at T m

Tm:

melting temperature at α=0.5

ΔHvH :

van’t Hoff enthalpy as derived from temperature dependence of equilibrium constant [kJ (mol of cooperative unit) - 1]

ΔH con.depVH .:

van’ Hoff enthalpy calculated using Eq. (9)

ΔH shapeVH :

van’t Hoff enthalpy calculated using Eq. (5) or (6)

ΔH calVH :

van’t Hoff enthalpy calculated using Eq. (8)

ΔHcal :

calorimetrically obtained molar enthalpy. The numerical value depends on the unit of the mol (strands or base pairs)

ΔH 0cal :

calorimetrically obtained standard molar enthalpy

ΔH:

transition enthalpy per mole of base pair stack

ΔH 0obs :

observed standard transition enthalpy per mol of duplex

ΔH 0pred :

predicted standard transition enthalpy per mol of duplex

ΔH0 :

standard enthalpy change

ΔG0 :

standard Gibbs energy change

ΔS0 :

standard entropy change

CT :

total strand concentration

C iT :

total strand concentration of substance i

C jT :

total strand concentration of substance j

α:

fraction of oligonucleotide strands in the double-stranded state (degree of association)

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Authors
  1. Kenneth J. Breslauer
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Editors and Affiliations

  1. Institut für Biophysik und Physikalische Biochemie, Universität Regensburg, Universitätsstraße 31, 8400, Regensburg, Germany

    Hans-Jürgen Hinz

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Breslauer, K.J. (1986). Methods for Obtaining Thermodynamic Data on Oligonucleotide Transitions. In: Hinz, HJ. (eds) Thermodynamic Data for Biochemistry and Biotechnology. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-71114-5_15

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  • DOI: https://doi.org/10.1007/978-3-642-71114-5_15

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