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Register a new userStretching DNA: Role of electrostatic interaction
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The effect of electrostatic interactions on the stretching of DNA is investigated using a simple worm like chain model. In the limit of small force there are large conformational fluctuations which are treated using a self-consistent variational approach. For small values of the external force f, we find theoreticlly and by a simple blob picture that the extension scales as fr_D where r_D is the Debye screening length. In the limit of large force the electrostatic effects can be accounted for within the semiflexible chain model of DNA by assuming that only small excursions from rod-like conformations are possible. In this regime the extension approaches the contour length as f^{-1/2} where f is the magnitude of the external force. The theory is used to analyze experiments that have measured the extension of double-stranded DNA subject to tension at various salt concentrations. The theory reproduces nearly quantitatively the elastic response of DNA at small and large values of f and for all concentration of the monovalent counterions. The limitations of the theory are also pointed out.
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The problem of DNA-DNA interaction mediated by divalent counterions is studied using computer simulation. Although divalent counterions cannot condense free DNA molecules in solution, we show that if DNA configurational entropy is restricted, divalent counterions can cause DNA reentrant condensation similar to that caused by tri- or tetra-valent counterions. DNA-DNA interaction is strongly repulsive at small or large counterion concentration and is negligible or slightly attractive for a concentration in between. Implications of our results to experiments of DNA ejection from bacteriophages are discussed. The quantitative result serves to understand electrostatic effects in other experiments involving DNA and divalent counterions.
The complex mechanisms governing charge migration in DNA oligomers reflect the rich structural and electronic properties of the molecule of life. Controlling the mechanical stability of DNA nanowires in charge transport experiments is a requisite for identifying intrinsic issues responsible for long range charge transfers. By merging density-functional-theory-based calculations and model-Hamiltonian approaches, we have studied DNA quantum transport during the stretching-twisting process of poly(GC) DNA oligomers. During the stretching process, local maxima in the charge transfer integral t between two nearest-neighbor GC pairs arise from the competition between stretching and twisting. This is reflected in local maxima for the conductance, which depend very sensitively on the coupling to the electrodes. In the case of DNA-electrode couplings smaller than t, the conductance versus stretching distance saturates to plateau in agreement with recent experimental observations.
This simulation study investigates the dependence of the structure of dry Nafion$^{tinytextregistered}$-like ionomers on the electrostatic interactions between the components of the molecules. In order to speed equilibration, a procedure was adopted which involved detaching the side chains from the backbone and cutting the backbone into segments, and then reassembling the macromolecule by means of a strong imposed attractive force between the cut ends of the backbone, and between the non-ionic ends of the side chains and the midpoints of the backbone segments. Parameters varied in this study include the dielectric constant, the free volume, side-chain length, and strength of head-group interactions. A series of coarse-grained mesoscale simulations shows the morphlogy to depend sensitively on the ratio of the strength of the dipole-dipole interactions between the side-chain acidic end groups to the strength of the other electrostatic components of the Hamiltonian. Examples of the two differing morphologies proposed by Gierke and by Gebel emerge from our simulations.
Double-stranded DNA `overstretches at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNAs biological function and technological application. Overstretching is thought by some to be a force-induced denaturation, and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model we consider the effect upon overstretching of extreme sequence heterogeneity. `Chimeric sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data display two plateaux at forces whose difference varies with pulling rate in a manner that depends qualitatively upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment. Our results suggest that qualitatively different, spatially segregated conformational transitions can occur at a single thermodynamic state within single molecules of DNA.
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule transition, whereas in concentrated solution, DNA molecules exhibit an extended conformation via macroscopic phase segregation. The long axis length of the stretched state in DNA is about 1000 times larger than that of the compact state. Phase segregation at high DNA concentrations occurs at lower PEG concentrations than the compaction at low DNA concentrations. These opposite changes in the conformation of DNA molecule are interpreted in terms of the free energy, including depletion interaction.
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