Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userOvertwisting induces polygonal shapes in bent DNA
59
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
By combining analytical results and simulations of various coarse-grained models we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross interaction term discussed in the recent DNA literature, induces minimal energy shapes with a periodic alternance of parts with high and low curvature resembling rounded polygons. We briefly discuss the possible experimental relevance of these findings. We finally show that the twist and bending energies of minicircles are governed by renormalized stiffness constants, not the bare ones. This has important consequences for the analysis of experiments involving circular DNA meant to determine DNA elastic constants.
rate research
Read More
In recent years there have been a number of proposals to utilize the specificity of DNA based interactions for potential applications in nanoscience. One interesting direction is the self-assembly of micro- and nanoparticle clusters using DNA scaffolds. In this letter we consider a DNA scaffold method to self-assemble clusters of colored particles. Stable clusters of microspheres have recently been produced by an entirely different method. Our DNA based approach self-assembles clusters with additional degrees of freedom associated with particle permutation. We demonstrate that in the non-equilibrium regime of irreversible binding the self-assembly process is experimentally feasible. These color degrees of freedom may allow for more diverse intercluster interactions essential for hierarchical self-assembly of larger structures.
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear bodies exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To shed light on this, we perform large-scale Brownian dynamics simulations of a chromatin fiber interacting with an ensemble of (multivalent) DNA-binding proteins; these proteins switch between two states -- active (binding) and inactive (non-binding). This system provides a model for any DNA-binding protein that can be modified post-translationally to change its affinity for DNA (e.g., like the phosphorylation of a transcription factor). Due to this out-of-equilibrium process, proteins spontaneously assemble into clusters of self-limiting size, as individual proteins in a cluster exchange with the soluble pool with kinetics like those seen in photo-bleaching experiments. This behavior contrasts sharply with that exhibited by equilibrium, or non-switching, proteins that exist only in the binding state; when these bind to DNA non-specifically, they form clusters that grow indefinitely in size. Our results point to post-translational modification of chromatin-bridging proteins as a generic mechanism driving the self-assembly of highly dynamic, non-equilibrium, protein clusters with the properties of nuclear bodies. Such active modification also reshapes intra-chromatin contacts to give networks resembling those seen in topologically-associating domains, as switching markedly favors local (short-range) contacts over distant ones.
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors and nanoparticle based drug delivery platforms. In Chapter I we introduce the system, which generically consists of colloidal particles functionalized with specially designed DNA markers. The sequence of bases on the DNA markers determines the particle type. Due to the hybridization between complementary single-stranded DNA, specific, type-dependent interactions can be introduced between particles by choosing the appropriate DNA marker sequences. In Chapter II we develop a statistical mechanical description of the aggregation and melting behavior of particles with DNA-mediated interactions. In Chapter III a model is proposed to describe the dynamical departure and diffusion of particles which form reversible key-lock connections. In Chapter IV we propose a method to self-assemble nanoparticle clusters using DNA scaffolds. A natural extension is discussed in Chapter V, the programmable self-assembly of nanoparticle clusters where the desired cluster geometry is encoded using DNA-mediated interactions. In Chapter VI we consider a nanoparticle based drug delivery platform for targeted, cell specific chemotherapy. In Chapter VII we present prospects for future research: the connection between DNA-mediated colloidal crystallization and jamming, and the inverse problem in self-assembly.
DNA is an ideal candidate to organize matter on the nanoscale, primarily due to the specificity and complexity of DNA based interactions. Recent advances in this direction include the self-assembly of colloidal crystals using DNA grafted particles. In this article we theoretically study the self-assembly of DNA-caged particles. These nanoblocks combine DNA grafted particles with more complicated purely DNA based constructs. Geometrically the nanoblock is a sphere (DNA grafted particle) inscribed inside a polyhedron (DNA cage). The faces of the DNA cage are open, and the edges are made from double stranded DNA. The cage vertices are modified DNA junctions. We calculate the equilibriuim yield of self-assembled, tetrahedrally caged particles, and discuss their stability with respect to alternative structures. The experimental feasability of the method is discussed. To conclude we indicate the usefulness of DNA-caged particles as nanoblocks in a hierarchical self-assembly strategy.
Employing recent advances in response theory and nonequilibrium ensemble reweighting, we study the dynamic and static correlations that give rise to an electric field-dependent ionic conductivity in electrolyte solutions. We consider solutions modeled with both implicit and explicit solvents, with different dielectric properties, and at multiple concentrations. Implicit solvent models at low concentrations and small dielectric constants exhibit strongly field-dependent conductivities. We compared these results to the Onsager-Wilson theory of the Wien effect, which provides a qualitatively consistent prediction at low concentrations and high static dielectric constants, but is inconsistent away from these regimes. The origin of the discrepancy is found to be increased ion correlations under these conditions. Explicit solvent effects act to suppress nonlinear responses, yielding a weakly field-dependent conductivity over the range of physically realizable field strengths. By decomposing the relevant time correlation functions, we find that the insensitivity of the conductivity to the field results from the persistent frictional forces on the ions from the solvent. Our findings illustrate the utility of nonequilibrium response theory in rationalizing nonlinear transport behavior.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
