Different pulling modes in DNA overstretching: a theoretical analysis

Elasticity of a DNA chain dotted with bubbles under force

The flexibility and the extension along the direction of the force are shown to be related to the bubble number fluctuation and the average number of bubbles, respectively, when the strands of the DNA are subjected to a force along the same direction, here called a stretching force. The force-temperature phase diagram shows the existence of a tricritical point, where the first-order force-induced zipping transition becomes continuous. On the other hand, when the forces are being applied in opposite directions, here called an unzipping force, the transition remains first order, with the possibility of vanishing of the low-temperature reentrant phase for a semiflexible DNA. Moreover, we found that the bulk elasticity changes only if an external force penetrates the bound phase and affects the bubble states.

Rigidity of melting DNA

The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in the other the double-stranded DNA is taken to have an intrinsic rigidity for bending. In both cases single strands are completely flexible. The change in the elastic constant for the flexible case due to thermally generated bubbles is obtained exactly. For the case of intrinsic rigidity, the elastic constant is found to be proportional to the square root of the bubble number fluctuation.

Coarse-grained simulations of DNA overstretching

We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23 °C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore, the model reproduces the temperature dependence of the overstretching force well. The mechanism of overstretching is always force-induced melting by unpeeling from the free ends. That we never see S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that S-DNA is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.

Dynamical model for the full stretching curve of DNA

We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications, which properly describes the elongation features at low and intermediate forces. The dynamics is developed under a double-well potential with a linear term, which, at high forces, accounts for the narrow transition present in the DNA elongation (overstretching). A quite good agreement between simulation and experiment is obtained.

Stacking interactions in denaturation of DNA fragments

A mesoscopic model for heterogeneous DNA denaturation is developed in the framework of the path integral formalism. The base pair stretchings are treated as one-dimensional, time-dependent paths contributing to the partition function. The size of the paths ensemble, which measures the degree of cooperativity of the system, is computed versus temperature consistently with the model potential physical requirements. It is shown that the ensemble size strongly varies with the molecule backbone stiffness providing a quantitative relation between stacking and features of the melting transition. The latter is an overall smooth crossover which begins from the adenine-thymine-rich portions of the fragment. The harmonic stacking coupling shifts, along the T -axis, the occurrence of the multistep denaturation but it does not change the character of the crossover. The methods to compute the fractions of open base pairs versus temperature are discussed: by averaging the base pair displacements over the path ensemble, we find that such fractions signal the multisteps of the transition in good agreement with the indications provided by the specific heat plots.