Statistical physics of the melting of inhomogeneous DNA

Abstract

We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused on precise sequences and investigated the succession of local openings that lead to their dissociation. For this purpose, we performed Transfer Integral type calculations with two different dynamical models, namely the heterogeneous Dauxois-Peyrard-Bishop model and the model based on finite stacking enthalpies we recently proposed. It appears that, for both models, the essential effect of heterogeneity is to let different portions of the investigated sequences open at slightly different temperatures. Besides this macroscopic effect, the local aperture of each portion indeed turns out to be very similar to that of a homogeneous sequence with the same length. Rounding of each local opening transition is therefore merely a size effect. For the Dauxois-Peyrard-Bishop model, sequences with a few thousands base pairs are still far from the thermodynamic limit, so that it is inappropriate, for this model, to discuss the order of the transition associated with each local opening. In contrast, sequences with several hundreds to a few thousands base pairs are pretty close to the thermodynamic limit for the model we proposed. The temperature interval where power laws holds is consequently broad enough to enable the estimation of critical exponents. On the basis of the few examples we investigated, it seems that, for our model, disorder does not necessarily induce a decrease of the order of the transition.

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Cited by in corpus (13)

• Effect of salt concentration on the stability of heterogeneous DNA
• Thermodynamics of Twisted DNA with Solvent Interaction
• Path Integral Method for DNA Denaturation
• Denaturation Patterns in Heterogeneous DNA
• Stacking Interactions in Denaturation of DNA Fragments
• End-to-end distance and contour length distribution functions of DNA helices
• Dynamical versus statistical mesoscopic models for DNA denaturation
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Phase diagram of mechanically stretched DNA: The salt effect
• Pulling short DNA molecules having defects on different locations
• Renormalisation group determination of the order of the DNA denaturation transition
• Mapping between the order of thermal denaturation and the shape of the critical line of mechanical unzipping in 1-dimensional DNA models
• On the Pseudo-Schrödinger Equation approximation of the Transfer-Integral operator for 1-dimensional DNA models