相关论文: Defects Can Increase the Melting Temperature of DN…

Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not…

In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…

DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…

We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…

The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…

We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…

We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…

Recent advances in the understanding of the melting behavior of double-stranded DNA with statistical mechanics methods lead to improved estimates of the weight factors for the dissociation events of the chains, in particular for interior…

We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…

Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…

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…

The melting phase diagram of a double-stranded DNA in poor solvent is studied using the pruned and enriched Rosenbluth method on a simple cubic lattice. As the solvent quality is changed from good to poor, there is a non-monotonic change in…

With the help of one-dimensional random Potts-like model we study the origins of fine structure observed on differential melting profiles of double-stranded DNA. We assess the effects of sequence arrangement on DNA melting curves through…

DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…

We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…

The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has…

The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…

Additive manufacturing of a single crystalline metallic column is studied using molecular dynamics simulations. In the model, a melt pool is incrementally added and cooled to a target temperature under isobaric conditions to build a…

We present a method of detecting sequence defects by supercoiling DNA with magnetic tweezers. The method is sensitive to a single mismatched base pair in a DNA sequence of several thousand base pairs. We systematically compare DNA molecules…

We study the effect of crowders on the melting profile of homogeneous and heterogeneous DNA molecules. We find out the melting profile of short DNA molecules and compare our findings with the experiments. We consider some random…