相关论文: Helix-coil Transition in Closed Circular DNA

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…

DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…

The helical coil is ubiquitous in biological and natural systems and often it is the basic form that leads to complex structures. This paper considers the question of its dimensionality in biological information as the helical coil goes…

Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…

We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…

The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…

The sequence-dependent elasticity of double-helical DNA on a nm length scale can be captured by the rigid base-pair model, whose strains are the relative position and orientation of adjacent base-pairs. Corresponding elastic potentials have…

The flexibility of short DNA fragments is studied by a Hamiltonian model which treats the inter-strand and intra-strand forces at the level of the base pair. The elastic response of a set of homogeneous helices to externally applied forces…

We find that both continuous and discontinuous hexatic-liquid transitions can happen in the melting of two-dimensional solids of soft-core disks. For three typical model systems, Hertzian, harmonic, and Gaussian-core models, we observe the…

The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair…

We propose a model Hamiltonian for charge transfer along the DNA double helix with temperature driven fluctuations in the base pair positions acting as the rate limiting factor for charge transfer between neighboring base pairs. We compare…

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 used high-resolution quasielastic neutron scattering spectroscopy to study the single-particle dynamics of water molecules on the surface of hydrated DNA samples. Both H2O and D2O hydrated samples were measured. The contribution of…

For a given crystal structure, say body-centred-cubic, the many-body Hamiltonian in which nuclear and electron motions are to be treated from the outset on the same footing, has parameters, for the elements, which can be classified as (i)…

Phase I of hydrogen has several peculiarities. Despite having a close-packed crystal structure, it is less dense than either the low temperature Phase II or the liquid phase. At high pressure, it transforms into either phase III or IV,…

The two-dimensional generalization of the Polyelectolite model of DNA is proposed. It is reduced to the boundary problem for nonlinear completely integrable equation $\sh$-Gordon. In the linearisible version the exact solution is…

The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…

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…

A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…

Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…