Related papers: Pulling short DNA molecules having defects on diff…
We study numerically the mechanical stability and elasticity properties of duplex DNA molecules within the frame of a network model incorporating microscopic degrees of freedom related with the arrangement of the base pairs. We pay special…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
We study DNA denaturation by integrating elasticity -- as described by the Gaussian network model -- with bond binding energies, distinguishing between different base-pair and stacking energies. We use exact calculation, within the model,…
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a…
Protonation of DNA basepairs is a reversible phenomenon which can be controlled by tuning the pH of the system. Under mild acidic conditions, the hydrogen bonding pattern of the DNA basepairs undergoes a change. We study the effect of…
Interest in studying the interaction of small molecules with DNA is caused by the need to develop new, highly effective, and low-toxic drugs for cancer treatment. The strong and highly specific binding of thionine with DNA makes it a…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Dielectric spectroscopy is used to investigate fundamental length scales of 146 bp short-fragment (nucleosomal) dilute Na-DNA solutions. Two relaxation modes are detected: the high- and the low-frequency mode. Dependence of the…
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…
Using Langevin Dynamic simulations, we study effects of the shear force on the rupture of a double stranded DNA molecule. The model studied here contains two single diblock copolymers interacting with each other. The elastic constants of…
We investigate irreversibility and dissipation in single molecules that cooperatively fold/unfold in a two state manner under the action of mechanical force. We apply path thermodynamics to derive analytical expressions for the average…
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…
Although mechanical properties of DNA are well characterized at the kilo base-pair range, a number of recent experiments have suggested that DNA is more flexible at shorter length scales, which correspond to the regime that is crucial for…
At present, there have been suggested two types of physical mechanism that may facilitate preferential pairing between DNA molecules, with identical or similar base pair texts, without separation of base pairs. One solely relies on base…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
DNA cyclization is a powerful technique to gain insight into the nature of DNA bending. The worm-like chain model provides a good description of small to moderate bending fluctuations, but some experiments on strongly-bent shorter molecules…
An analysis of the stability of a duplex containing G.A mispairs or G.A/A.G tandem during DNA melting has revealed that duplex stability depends on both DNA sequences and on the conformations of the G.A mispairs. The thermodynamics of…