DNA unzipping phase diagram calculated via replica theory

C. Brian Roland; Kristi Adamson Hatch; Mara Prentiss; Eugene I. Shakhnovich

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DNA unzipping phase diagram calculated via replica theory

C. Brian Roland·Kristi Adamson Hatch·Mara Prentiss·Eugene I. Shakhnovich

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Abstract

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We study a model for a long molecule of dsDNA, and compute the equilibrium phase diagram for the experiment in which the molecule is unzipped under force. We consider a perfect-matching dsDNA model, in which the loops are volume-excluding chains with arbitrary loop exponent c. We include stacking interactions, hydrogen bonds, and main-chain entropy, including sequence heterogeneity at the level of random sequences. We use the replica method to calculate the equilibrium properties of the system. As a function of temperature, we obtain the minimal force at which the molecule separates completely. This critical force curve is a line in the temperature-force phase diagram that marks the regions where the molecule exists primarily as a helix, versus the region where the molecule exists as two separate strands. Near melting, the critical force curve of our random-sequence model is very different from that of the homogeneous version of our model. For both sequence models, the critical force falls to zero at the melting temperature with a power law having exponent alpha. For the homogeneous model, alpha is 1/2 almost exactly, while for the random model, alpha is about 0.9. The shape of the critical force determines how the helix fraction falls to zero at melting, and thus classifies the melting transition as a type of phase transition.

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C. Brian Roland, Kristi Adamson Hatch, Mara Prentiss, Eugene I. Shakhnovich. 2007-03-22. DNA unzipping phase diagram calculated via replica theory. https://arxiv.org/abs/cond-mat/0703588

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