Statistical mechanics of DNA rupture: theory and simulations

Appearance of de Gennes length in force-induced transitions

Using Langevin dynamic simulations, a simple coarse-grained model of a DNA protein construct is used to study the DNA rupture and the protein unfolding. We identify three distinct states: (i) zipped DNA and collapsed protein, (ii) unzipped DNA and stretched protein, and (iii) unzipped DNA and collapsed protein. Here, we find a phase diagram that shows these states depending on the size of the DNA handle and the protein. For a less stable protein, unfolding is solely governed by the size of the linker DNA, whereas if the protein's stability increases, complete unfolding becomes impossible because the rupture force for DNA has reached a saturation regime influenced by the de Gennes length. We show that unfolding occurs via a few intermediate states by monitoring the force-extension curve of the entire protein. We extend our study to a heterogeneous protein system, where similar intermediate states in two systems can lead to different protein unfolding paths.

DNA-Based Single-Molecule Electronics: From Concept to Function

Beyond being the repository of genetic information, DNA is playing an increasingly important role as a building block for molecular electronics. Its inherent structural and molecular recognition properties render it a leading candidate for molecular electronics applications. The structural stability, diversity and programmability of DNA provide overwhelming freedom for the design and fabrication of molecular-scale devices. In the past two decades DNA has therefore attracted inordinate amounts of attention in molecular electronics. This review gives a brief survey of recent experimental progress in DNA-based single-molecule electronics with special focus on single-molecule conductance and I–V characteristics of individual DNA molecules. Existing challenges and exciting future opportunities are also discussed.

Opening of DNA chain due to force applied on different locations

We consider a homogeneous DNA molecule and investigate the effect of random force applied on the unzipping profile of the molecule. How the critical force varies as a function of the chain length or number of base pairs is the objective of this study. In general, the ratio of the critical forces that is applied on the middle of the chain to that which is applied on one of the ends is two. Our study shows that this ratio depends on the length of the chain. This means that the force which is applied to a point can be experienced by a section of the chain. Beyond a length, the base pairs have no information about the applied force. In the case when the chain length is shorter than this length, this ratio may vary. Only in the case when the chain length exceeds a critical length, this ratio is found to be two. Based on the de Gennes formulation, we developed a method to calculate these forces at zero temperature. The exact results at zero temperature match numerical calculations.

Rupture of DNA aptamer: New insights from simulations

Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules, e.g., adenosinemonophosphate and adenosinetriphosphate, form additional hydrogen bonds with base-pockets termed as "binding-pockets," which enhance the stability. Using the Langevin dynamics simulations of coarse grained model of DNA followed by atomistic simulations, we investigated the influence of base-pocket and binding-pocket on the stability of DNA aptamer. Striking differences have been reported here for the separation induced by temperature and force, which require further investigation by single molecule experiments.

Periodically driven DNA: Theory and simulation

We propose a generic model of driven DNA under the influence of an oscillatory force of amplitude F and frequency ν and show the existence of a dynamical transition for a chain of finite length. We find that the area of the hysteresis loop, A_{loop}, scales with the same exponents as observed in a recent study based on a much more detailed model. However, towards the true thermodynamic limit, the high-frequency scaling regime extends to lower frequencies for larger chain length L and the system has only one scaling (A_{loop}≈ν^{-1}F^{2}). Expansion of an analytical expression for A_{loop} obtained for the model system in the low-force regime revealed that there is a new scaling exponent associated with force (A_{loop}≈ν^{-1}F^{2.5}), which has been validated by high-precision numerical calculation. By a combination of analytical and numerical arguments, we also deduce that for large but finite L, the exponents are robust and independent of temperature and friction coefficient.

Piezoresistivity in single DNA molecules

Piezoresistivity is a fundamental property of materials that has found many device applications. Here we report piezoresistivity in double helical DNA molecules. By studying the dependence of molecular conductance and piezoresistivity of single DNA molecules with different sequences and lengths, and performing molecular orbital calculations, we show that the piezoresistivity of DNA is caused by force-induced changes in the π-π electronic coupling between neighbouring bases, and in the activation energy of hole hopping. We describe the results in terms of thermal activated hopping model together with the ladder-based mechanical model for DNA proposed by de Gennes.

Effect of mechanical stretching on DNA conductance

Studying the structural and charge transport properties in DNA is important for unraveling molecular scale processes and developing device applications of DNA molecules. Here we study the effect of mechanical stretching-induced structural changes on charge transport in single DNA molecules. The charge transport follows the hopping mechanism for DNA molecules with lengths varying from 6 to 26 base pairs, but the conductance is highly sensitive to mechanical stretching, showing an abrupt decrease at surprisingly short stretching distances and weak dependence on DNA length. We attribute this force-induced conductance decrease to the breaking of hydrogen bonds in the base pairs at the end of the sequence and describe the data with a mechanical model.