Molecular Dynamics Simulation of Supercoiled DNA Rings

DNA supercoiling is a widespread phenomenon in biology. Here we introduce a coarse-grained DNA model and study supercoiled DNA rings via a rigid body molecular dynamics simulation. Our model allows us to investigate these structures in more detail than previously. The simulations are performed on rings of one to six kilobase pairs length and are compared to available experimental data and former simulation studies. The current study provides new additional information about some of the geometrical parameters of the supercoiled DNA rings. It also shows how enforcing a supercoiled DNA ring to two-dimensional space changes its geometrical parameters. Finally, our molecular dynamics method allows us to observe some dynamical effects like the creation and movement of supercoiled branches

Variation of Protein Corona Composition of Gold Nanoparticles Following Plasmonic Heating

It is well recognized that the primary interaction of most biological environments with nanoparticles (NPs) is strongly influenced by a long-lived (“hard”) protein corona that surrounds the NP and remains strongly adsorbed to its surface. The amount and composition of associated proteins in the corona adsorbed onto the NPs is related to several important factors, including the physicochemical properties of the NPs and the composition of the protein solution. Here, for the first time, it is shown that plasmonic heat induction (by laser activation) leads to significant changes in the composition of the hard protein corona adsorbed on low aspect ratio gold nanorods. Using mass spectrometry, several proteins in the corona were identified whose concentrations change most substantially as a result of photoinduced (plasmonic) heating versus simple thermal heating. Molecular modeling suggests that the origin of these changes in protein adsorption may be the result of protein conformational changes in response to much higher local temperatures that occur near the gold nanorods during photoinduced, plasmonic heating. These results may define new applications in vivo for NPs with hyperthermia capability and better define the likely interactions of cells with NPs after plasmonic heating. Potential changes in the protein corona following hyperthermia treatment may influence the final biological fate of plasmonic NPs in clinical applications and help elucidate safety considerations for hyperthermia applications

Bimodal Phonon Scattering in Graphene Grain Boundaries

Graphene has served as the model 2D system for over a decade, and the effects of grain boundaries (GBs) on its electrical and mechanical properties are very well investigated. However, no direct measurement of the correlation between thermal transport and graphene GBs has been reported. Here, we report a simultaneous comparison of thermal transport in supported single crystalline graphene to thermal transport across an individual graphene GB. Our experiments show that thermal conductance (per unit area) through an isolated GB can be up to an order of magnitude lower than the theoretically anticipated values. Our measurements are supported by Boltzmann transport modeling which uncovers a new bimodal phonon scattering phenomenon initiated by the GB structure. In this novel scattering mechanism, boundary roughness scattering dominates the phonon transport in low-mismatch GBs, while for higher mismatch angles there is an additional resistance caused by the formation of a disordered region at the GB. Nonequilibrium molecular dynamics simulations verify that the amount of disorder in the GB region is the determining factor in impeding thermal transport across GBs

Modeling and Analysis of Intercalant Effects on Circular DNA Conformation

The large-scale conformation of DNA molecules plays a critical role in many basic elements of cellular functionality and viability. By targeting the structural properties of DNA, many cancer drugs, such as anthracyclines, effectively inhibit tumor growth but can also produce dangerous side effects. To enhance the development of innovative medications, rapid screening of structural changes to DNA can provide important insight into their mechanism of interaction. In this study, we report changes to circular DNA conformation from intercalation with ethidium bromide using all-atom molecular dynamics simulations and characterized experimentally by translocation through a silicon nitride solid-state nanopore. Our measurements reveal three distinct current blockade levels and a 6-fold increase in translocation times for ethidium bromide-treated circular DNA as compared to untreated circular DNA. We attribute these increases to changes in the supercoiled configuration hypothesized to be branched or looped structures formed in the circular DNA molecule. Further evidence of the conformational changes is demonstrated by qualitative atomic force microscopy analysis. These results expand the current methodology for predicting and characterizing DNA tertiary structure and advance nanopore technology as a platform for deciphering structural changes of other important biomolecules