Excluded volume effect in unzipping DNA with a force

Abstract

A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base pairs goes as M approximately (F - Fc)(-2) and diverges at the critical force Fc with an exponent chi = 2. We find that when excluded volume effect is taken into account for the unzipped part of the DNA, the exponent chi = 2 is not changed but the critical force Fc is changed. The force versus temperature phase diagram depends on only two parameters in the model, the persistence length and the denaturation temperature. Furthermore a scaling form of the phase diagram can be found. This scaling form is parameter independent and depends only on the spatial dimension. It applies to all DNA molecules and should provide a useful framework for comparison with experiments.

Effects of the eye phase in DNA unzipping

“…The prediction of unzipping transition based on interacting Gaussian chains [10] raised a lot interest and now results are available from dynamical approach [11], exact solutions of lattice models [12, 13], simple models of quenched-averaged DNA [14, 15], numerical simulations and scaling analysis [16, 17]. Recently for a model of interacting polymers where any monomer of one chain can interact with any monomer of the other chain (we call it model A), the role of an intermediate entropy-stabilized phase was recognized and a force-induced triple point [18] in a force-temperature plane was established.In most of the models studied for dsDNA [12,13,14,15,16,19], a monomer i of one strand can only interact with the i-th monomer of the other strand, which is similar to the models of DNA (we call it model B) proposed earlier by Poland and Scheraga [20]. These models do not take into account the directional nature of the hydrogen bond and underestimate the entropy by restricting the formation of hydrogen bonds.…”

Unzipping DNA by force: thermodynamics and finite size behaviour

“…This curve (for B ′ ) represents the jump from one coexistence region to another with a sudden, detectable change in force (Eqs. (11) and (12)). Point B ′ corresponds to the separation X(s, T ) of Eq.…”

Non-entropic theory of rubber elasticity: Flexible chains grafted on a rigid surface

“…Serious progress in the analysis of statistics of single polymer chains and membranes with excluded-volume interactions was reached by using the renormalization group technique [3,4,5,6]. These methods, however, have been employed for the analysis of the distribution functions only and have not yet been applied to determine the strain energy of a network, despite the importance of the latter problem for applications, see [7,8] and the references therein, as well as recent publications [9,10,11,12].…”