Analysis of high‐resolution thermal dispersion profiles of DNA: Treatment as a collection of discrete subtransitions

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Abstract
The thermal dissociation of DNA by five distinct local processes as outlined by Azbel [(1980) Biopolymers 19, 61–80] is treated as a collection of two‐state substransitions. With the traditional expression for loop entropy and the assumption of a small, positive loop‐initiation enthalpy, explicit relationships between thermodynamic parameters are derived for all five processes. The effect of each process on subtransitional width, unit enthalpy, and melting temperature is estimated; the latter being in excellent agreement with that predicted by Azbel. Criteria proposed for the deconvolution of the oscillatory high‐resolution melting profiles exhibited by short, homogeneous DNAs [Yen & Blake (1980) Biopolymers 19, 681–700] have been applied to profiles of SV40 fragment [Gabbarro‐Arpa et al. (1979) Nature 280, 515–517] and ϕx174‐RF DNA at two ionic strengths [Vizard et al. (1978) 275, 250–251] and indicate that dissociation of the strands proceeds as a series of local two‐state subtransitions of domains 200–300 base pairs in length. Although the obvious overlap of some subtransitions raises questions about resolution, most sections are very well resolved with the minimum number of subtransitions and yield values for the apparent van't Hoff enthalpy in excellent agreement with those expected by calorimetric measurements. The flexibility of such an approach, where the enthalpy is recognized explicitly as an adjustable parameter, is especially suited for the analysis of profiles from unkown DNA sequences, and for the evaluation of extraordinary variations in free energy, such as that associated with loop formation or that resulting from variations in the linear charge density at low ionic strengths.