Related papers: Adding a New Dimension to DNA Melting Curves
Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this…
The stability of DNA molecule during the encapsulation process is a topic of intense research. We study the thermal stability of the double-stranded DNA molecule of different lengths in a confined space. Using a statistical model we…
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…
The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main…
DNA-gold nanoparticle assemblies have shown promise as an alternative technology to DNA microarrays for DNA detection and RNA profiling. Understanding the effect of DNA sequences on the melting temperature of the system is central to…
We study the melting of a double stranded DNA in the presence of stretching forces, via 3D Monte-Carlo simulations, exactly solvable models and heuristic arguments. The resulting force-temperature phase diagram is dramatically different for…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
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…
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…
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…
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…
When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively…
Complementary strands in DNA double helix show temporary fluctuational openings which are essential to biological functions such as transcription and replication of the genetic information. Such large amplitude fluctuations, known as the…
The melting curves of short heterogeneous DNA chains in solution are calculated on the basis of statistical thermodynamics and compared to experiments. The computation of the partition function is based on the Peyrard-Bishop hamiltonian,…
We study the effect of the composition of the genetic sequence on the melting temperature of double stranded DNA, using some simple analytically solvable models proposed in the framework of the wetting problem. We review previous work on…
Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates roughly twice its initial contour length at a pulling force about 70 pN. The transition to this highly overstretched form of DNA is very…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the…