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Register a new userKinky DNA in solution: Small angle scattering study of a nucleosome positioning sequence
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DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p approx 500,$AA is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element, and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an $AT$-domain.
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Advanced Monte Carlo simulations are used to study the effect of nano-slit confinement on metric and topological properties of model DNA chains. We consider both linear and circularised chains with contour lengths in the 1.2--4.8 $mu$m range and slits widths spanning continuously the 50--1250nm range. The metric scaling predicted by de Gennes blob model is shown to hold for both linear and circularised DNA up to the strongest levels of confinement. More notably, the topological properties of the circularised DNA molecules have two major differences compared to three-dimensional confinement. First, the overall knotting probability is non-monotonic for increasing confinement and can be largely enhanced or suppressed compared to the bulk case by simply varying the slit width. Secondly, the knot population consists of knots that are far simpler than for three-dimensional confinement. The results suggest that nano-slits could be used in nano-fluidic setups to produce DNA rings having simple topologies (including the unknot) or to separate heterogeneous ensembles of DNA rings by knot type.
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 investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.
Semiflexible polymers characterized by the contour length $L$ and persistent length $ell_p$ confined in a spatial region $D$ have been described as a series of ``{em spherical blobs} and ``{em deflecting lines} by de Gennes and Odjik for $ell_p < D$ and $ell_p gg D$ respectively. Recently new intermediate regimes ({em extended de Gennes} and {em Gauss-de Gennes}) have been investigated by Tree {em et al.} [Phys. Rev. Lett. {bf 110}, 208103 (2013)]. In this letter we derive scaling relations to characterize these transitions in terms of universal scaled fluctuations in $d$-dimension as a function of $L,ell_p$, and $D$, and show that the Gauss-de Gennes regime is absent and extended de Gennes regime is vanishingly small for polymers confined in a 2D strip. We validate our claim by extensive Brownian dynamics (BD) simulation which also reveals that the prefactor $A$ used to describe the chain extension in the Odjik limit is independent of physical dimension $d$ and is the same as previously found by Yang {em et al.}[Y. Yang, T. W. Burkhardt, G. Gompper, Phys. Rev. E {bf 76}, 011804 (2007)]. Our studies are relevant for optical maps of DNA stretched inside a nano-strip.
We perform a spatially resolved simulation study of an AND gate based on DNA strand displacement using several lengths of the toehold and the adjacent domains. DNA strands are modelled using a coarse-grained dynamic bonding model {[}C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012){]}. We observe a complex transition path from the initial state to the final state of the AND gate. This path is strongly influenced by non-ideal effects due to transient bubbles revealing undesired toeholds and thermal melting of whole strands. We have also characterized the bound and unbound kinetics of single strands, and in particular the kinetics of the total AND operation and the three distinct distinct DNA transitions that it is based on. We observe a exponential kinetic dependence on the toehold length of the competitive displacement operation, but that the gate operation time is only weakly dependent on both the toehold and adjacent domain length. Our gate displays excellent logical fidelity in three input states, and quite poor fidelity in the fourth input state. This illustrates how non-ideality can have very selective effects on fidelity. Simulations and detailed analysis such as those presented here provide molecular insights into strand displacement computation, that can be also be expected in chemical implementations.
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