Stuffing a virus with DNA: dissecting viral genome packaging

Simulation study on the critical adsorption and diffusion of polymer chains on heterogeneous surfaces with random adsorption sites

The critical adsorption and diffusion of a linear polymer chain on a heterogeneous surface with randomly distributed adsorption sites are studied using dynamic Monte Carlo simulations. Results show that the critical fraction of the adsorption sites at which critical adsorption takes place decreases exponentially with the increasing polymer-surface attraction strength and, at the same time, decreases with the increasing intra-polymer attraction strength. For adsorbed polymers with large intra-polymer attraction strength, we also find an adsorption-induced structural transition from a three-dimensional compact globule to a two-dimensional compacted pancake with an increasing fraction of adsorption sites. Anomalous sub-diffusion is observed for the adsorbed polymer diffusion on heterogeneous surfaces, in contrast to the normal diffusion on a homogeneous surface. The polymer on heterogeneous surfaces shows larger fluctuation in the total surface attraction energy and a longer waiting time.

Inconsistency of Diffusion and Relaxation of Ring Polymers Adsorbed on Rough Surfaces

We explore the diffusion and relaxation dynamics of a single ring polymer strongly adsorbed on rough surfaces with different roughnesses by means of molecular dynamics simulations. Our simulations demonstrate that on rough surfaces the intrachain topological constraint deriving from the closed architecture induces the inconsistency of diffusion and relaxation of ring polymers. When the lateral chain size is larger than the obstacle distance (2R_g∥,r > d), the ring closure induces the polymers to anchor on a single obstacle and dramatically reduces their diffusivity, where R_g∥,r and d are the lateral components of the mean-square radius of gyration and the obstacle distance, respectively. However, the single obstacle anchoring has no effect on the relaxation of ring polymers, which implies a deviation between the diffusion and the relaxation. With the lateral chain size beyond twice of the obstacle distance (R_g∥,r > d), the ring polymers are totally confined in the array of obstacles and can only diffuse through hopping over the obstacles, resulting in an exponential reduction of their diffusion coefficient. However, the relaxation of ring polymers mainly depends on their rotating reptation and satisfies the reptation-like dynamics, which means that the diffusion and the relaxation are nearly irrelevant. This inconsistency between the diffusion and relaxation is a unique property of adsorbed ring polymers, which would be meaningful to understand the physical nature of polymers with ring closure and significant to develop the corresponding applications.

Effects of surface roughness on the self-diffusion dynamics of a single polymer

We employ molecular dynamics simulations to simulate the diffusion dynamics of a single polymer adsorbed on surfaces with different roughnesses, which are characterized by the separation distance between obstacles and the height of obstacles. Our simulations demonstrate that for strong adsorption and when the confinement of obstacles is strong enough for all chains, the scaling exponent α of the diffusion coefficient on the chain length exhibits three cases with increase of the height of obstacles: a Rouse plateau with α ≈ -1 (the lateral motion of the polymer chains is free), a reptationlike plateau with α ≈ -1.5 (the polymer chains can hardly stride over the obstacles in the perpendicular direction) and a transition from the Rouse plateau to the reptationlike plateau with -1.5 < α < -1 (the obstacles hinder the lateral motion of the polymer chains). However, with increase of the separation distance between obstacles, the confinement from the obstacles exhibits a decrease (more lateral motions of the polymer chains are allowed), which results in a higher plateau (no longer separate reptationlike dynamics). Our results clarify the effects of surface roughness on the diffusion mechanism of polymer chains strongly adsorbed on solid surfaces in dilute solutions and the resulting transition mechanism from the Rouse scaling to the reptationlike scaling, which is significant for the understanding of the physical nature and the development of the corresponding applications.

Dynamics of adsorbed polymers on attractive homogeneous surfaces

Dynamic behaviors of polymer chains adsorbed on an attractive, homogeneous surface are studied by using dynamic Monte Carlo simulations. The translational diffusion coefficient D_xy parallel to the surface decreases as the intra-polymer attraction strength E_PP or the polymer-surface attraction strength E_PS increases. The rotational relaxation time τ_R increases with E_PS, but the dependence of τ_R on E_PP is dependent on the adsorption state of the polymer. We find that τ_R decreases with increasing E_PP for a partially adsorbed polymer but it increases with E_PP for a fully adsorbed polymer. Scaling relations D_xy ~ N^−α and τ_R ~ N^β are found for long polymers. The scaling exponent α is independent of E_PS for long polymers but increases with E_PP from α = 1.06 at E_PP = 0. While β ≈ 2.7 is also roughly independent of E_PS for the adsorbed polymer at E_PP = 0, but β increases with E_PS at E_PP > 0. Moreover, we find that β always decreases with increasing E_PP. Our results reveal different effects of the attractive surface on the diffusion and rotation of adsorbed polymers.

Dynamics of a polymer adsorbed to an attractive homogeneous flat surface

Polymer conformation and statistical sizes change with the surface contact number during the adsorption.

Critical adsorption of a flexible polymer confined between two parallel interacting surfaces

Critical adsorption of a lattice self-avoiding bond fluctuation polymer chain confined between two parallel impenetrable surfaces is studied using the Monte Carlo method. The dependence of the mean contact number <M> on the temperature T and on the chain length N is simulated for a polymer-surface interaction E=-1. A critical adsorption of the polymer is found at T(c)=1.65 for large surface separation distance D>N(ν)b, whereas no critical adsorption is observed for small distance D<N(ν)b, where ν ≈ 0.58 is the Flory exponent and b is the mean bond length. The critical adsorption point T(c)=1.65 is the same as that of a grafted polymer. Normal diffusion is observed for the confined polymer; however, the diffusion rate is dependent on the temperature and surface separation distance.

Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel

Currently, no theory is available to describe the conformation of DNA confined in a channel when the nanochannel diameter is around the persistence length. Back-folded hairpins in the undulating wormlike chain conformation result in the formation of loops, which reduces the stretch of the molecule in the longitudinal direction of the channel. A cooperativity model is used to quantify the frequency and size of the loop domains. The predictions agree with results from the Monte Carlo simulation.

Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins

Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states.

Formation of DNA toroids inside confined droplets adsorbed on mica surfaces

We report observations of in vitro DNA compaction into toroids in the absence of any condensing agent. The DNA toroid formation is induced by geometry confinement from microdroplets on mica surfaces. With AFM imaging we show that the confined DNA molecules may take the form of random coils or semiordered folded loops with large microdroplets, while they readily take the form of compact and ordered toroids when the microdroplet sizes are small enough. To better understand these phenomena, we carried out coarse-grained Brownian dynamics simulation, obtaining results that were in good agreement with the experimental observations. The simulation reveals that the toroid formation is sensitive to not only the microdroplet size, but also the DNA stiffness.

Conformation and dynamics of DNA confined in slitlike nanofluidic channels

Using laser fluorescence microscopy, we study the shape and dynamics of individual DNA molecules in slitlike nanochannels confined to a fraction of their bulk radius of gyration. With a confinement size spanning 2 orders of magnitude, we observe a transition from the de Gennes regime to the Odijk regime in the scaling of both the radius of gyration and the relaxation time. The radius of gyration and the relaxation time follow the predicted scaling in the de Gennes regime, while, unexpectedly, the relaxation time shows a sharp decrease in the Odijk regime. The radius of gyration remains constant in the Odijk regime. Additionally, we report the first measurements of the effect of confinement on the shape anisotropy.

Self-assembly approaches to nanomaterial encapsulation in viral protein cages

A perspective on abiotic material encapsulation inside virus capsids is provided. The emphasis is on the physical principles of virus assembly relevant to packaging, strategies for encapsulation and capsid modification, and on emerging applications.