The self-assembly of DNA Holliday junctions studied with a minimal model

In this paper, we explore the feasibility of using coarse-grained models to simulate the self-assembly of DNA nanostructures. We introduce a simple model of DNA where each nucleotide is represented by two interaction sites corresponding to the phosphate-sugar backbone and the base. Using this model, we are able to simulate the self-assembly of both DNA duplexes and Holliday junctions from single-stranded DNA. We find that assembly is most successful in the temperature window below the melting temperatures of the target structure and above the melting temperature of misbonded aggregates. Furthermore, in the case of the Holliday junction, we show how a hierarchical assembly mechanism reduces the possibility of becoming trapped in misbonded configurations. The model is also able to reproduce the relative melting temperatures of different structures accurately, and allows strand displacement to occur.Comment: 13 pages, 14 figure

Mesoscopic order and the dimentionality of long-range resonance energy transfer in supramolecular semiconductors

We present time-resolved photoluminescence measurements on two series of oligo-p-phenylenevinylene materials that self-assemble into supramolecular nanostructures with thermotropic reversibility in dodecane. One set of derivatives form chiral, helical stacks while the second set form less organised, frustrated stacks. Here we study the effects of supramolecular organisation on the resonance energy transfer rates. We measure these rates in nanoassemblies formed with mixed blends of oligomers and compare them with the rates predicted by Foerster theory. Our results and analysis show that control of supramolecular order in the nanometre lengthscale has a dominant effect on the efficiency and dimentionality of resonance energy transfer.Comment: 17 Pages, 5 Figures, Submitted to J. Chem. Phy

Control of silver-polymer aggregation mechanism by primary particle spatial correlations in dynamic fractal-like geometry

Silver nanocrystals have been prepared by reacting silver nitrate with ascorbic acid in aqueous solution containing a low concentration of a commercial polynaphtalene sulphonate polymer (Daxad 19). Various crystalline morphologies have been obtained simply by tuning the reaction temperature. We have investigated the nanoparticle formation mechanism at three different temperatures by in situ and time resolved Small Angle X ray Scattering measurements. By modeling the scattering intensity with interacting spherical particles in a fractal-like polymer-Ag matrix, we found signatures of nucleation, growth and assembly of primary particles of about 15-20 nm. We observed how the time evolution of both spatial correlations between primary particles and the dynamic fractal geometry of the polymer-Ag matrix could influence and determine both the aggregation mechanism and the morphology of forming nanostructures in solution

Coarse Graining RNA Nanostructures for Molecular Dynamics Simulations

A series of coarse-grained models have been developed for the study of the molecular dynamics of RNA nanostructures. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Such a treatment allows us to reach, for the systems of thousands of nucleotides, a time scale of microseconds (i.e. by three orders of magnitude longer than in the full atomistic modelling) and thus to enable simulations of large RNA polymers in the context of bionanotechnology. We find that the 3-beads-per-nucleotide models, described by a set of just a few universal parameters, are able to describe different RNA conformations and are comparable in structural precision to the models where detailed values of the backbone P-C4' dihedrals taken from a reference structure are included. These findings are discussed in the context of the RNA conformation classes

A general method for the synthesis of nanostructured large-surface-area materials through the self-assembly of functionalized nanoparticles

A general synthetic method for the preparation of nanostructured materials with large surface area was developed by using nanoparticle building blocks. The preparation route involves the self-assembly of functionalized nanoparticles in a liquid-crystal phase. These nanoparticles are functionalized by using difunctional amino acid species to provide suitable interactions with the template. Optimum interactions for self-assembly of the nanoparticles in the liquid-crystal phase were achieved with one -NH2 group anchored to the nanoparticle surface per 25 Å2. To maximize the surface area of these materials, the wall thicknesses are adjusted so that they are composed of a monolayer of nanoparticles. To form such materials, numerous parameters have to be controlled such as the relative volume fraction of the nanoparticles and the template and size matching between the hydrophilic component of the copolymer and nanoparticles. The surface functionalization renders our synthetic route independent of the nanoparticles and allows us to prepare a variety of nanostructured composite materials that consist of a juxtaposition of different discrete oxide nanoparticles. Examples of such materials include CeO2, ZrO2, and CeO2–Al(OH)3 composites