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Register a new userFacilitated diffusion on confined DNA
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In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.
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The capture and translocation of biomolecules through nanometer-scale pores are processes with a potential large number of applications, and hence they have been intensively studied in the recent years. The aim of this paper is to review existing models of the capture process by a nanopore, together with some recent experimental data of short single- and double-stranded DNA captured by Cytolysin A (ClyA) nanopore. ClyA is a transmembrane protein of bacterial origin which has been recently engineered through site-specific mutations, to allow the translocation of double- and single-stranded DNA. A comparison between theoretical estimations and experiments suggests that for both cases the capture is a reaction-limited process. This is corroborated by the observed salt dependence of the capture rate, which we find to be in quantitative agreement with the theoretical predictions.
We report a theoretical study of DNA flexibility and quantitatively predict the ring closure probability as a function of DNA contour length. Recent experimental studies show that the flexibility of short DNA fragments (as compared to the persistence length of DNA l_P~150 base pairs) cannot be described by the traditional worm-like chain (WLC) model, e.g., the observed ring closure probability is much higher than predicted. To explain these observations, DNA flexibility is investigated with explicit considerations of a new length scale l_D~10 base pairs, over which DNA local bend angles are correlated. In this correlated worm-like chain (C-WLC) model, a finite length correction term is analytically derived and the persistence length is found to be contour length dependent. While our model reduces to the traditional worm-like chain model when treating long DNA at length scales much larger than l_P, it predicts that DNA becomes much more flexible at shorter sizes, which helps explain recent cyclization measurements of short DNA fragments around 100 base pairs.
Single molecule force spectroscopy of DNA strands adsorbed at surfaces is a powerful technique used in air or liquid environments to quantify their mechanical properties. Although the force responses are limited to unfolding events so far, single base detection might be possible in more drastic cleanliness conditions such as ultra high vacuum. Here, we report on high resolution imaging and pulling attempts at low temperature (5K) of a single strand DNA (ssDNA) molecules composed of 20 cytosine bases adsorbed on Au(111) by scanning probe microscopy and numerical calculations. Using electrospray deposition technique, the ssDNA were successfully transferred from solution onto a surface kept in ultra high vacuum. Real space characterizations reveal that the ssDNA have an amorphous structure on gold in agreement with numerical calculations. Subsequent substrate annealing promotes the desorption of solvent molecules, DNA as individual molecules as well as the formation of DNA self assemblies. Furthermore, pulling experiments by force spectroscopy have been conducted to measure the mechanical response of the ssDNA while detaching. A periodic pattern of 0.2 to 0.3nm is observed in the force curve which arises from the stick slip of single nucleotide bases over the gold. Although an intra molecular response is obtained in the force curve, a clear distinction of each nucleotide detachment is not possible due the complex structure of ssDNA adsorbed on gold.
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is investigated, based on the DNA-DNA electrostatic pair potential that takes into account DNA helical symmetry and the amount and distribution of adsorbed counterions. A phase diagram obtained by lattice sum calculations predicts a variety of positionally and azimuthally ordered phases and bundling transitions strongly depending on the counterion adsorption patterns.
In this study, we compare the charge transport properties of multiple (double stranded) dsRNA sequences with corresponding dsDNA sequences. Recent studies have presented a contradictory picture of relative charge transport efficiencies in A-form DNA:RNA hybrids and dsDNA. Using a multiscale modelling framework, we compute conductance of dsDNA and dsRNA using Landauer formalism in coherent limit and Marcus-Hush theory in the incoherent limit. We find that dsDNA conducts better than dsRNA in both the charge transport regimes. Our analysis shows that the structural differences in the twist angle and slide of dsDNA and dsRNA are the main reasons behind the higher conductance of dsDNA in the incoherent hopping regime. In the coherent limit however, for the same base pair length, the conductance of dsRNA is higher than that of dsDNA for the morphologies where dsRNA has smaller end-to-end length relative to that of dsDNA.
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