Conformational and Dynamic Properties of Short DNA Minicircles in Aqueous Solution from Atomistic Molecular Dynamics Simulations

A computer simulation study of a chiral active ring polymer

We investigate a ring polymer under the influence of chiral active Brownian forces in two dimensions using coarse-grained computer simulations. We observe a non-monotonic behavior of the radius of gyration of an active Brownian ring as a function of active force. However, the shrinkage of the ring in the intermediate strength of active forces becomes more pronounced in the presence of chiral active forces, and the shrinkage is monotonic at a given activity level as a function of the angular frequency controlling the direction of the active force. The distribution of radius of gyration, inter-monomer distance, and radial distribution suggest that the monomers come close to each other, eventually leading to the shrinkage of the ring. Moreover, the bond-correlation suggests that the chirality introduces a local folding of the monomers. Furthermore, using the diameter correlation function, we show that the ring performs tank-treading motion with a frequency following power-law relation with active force with exponent 3/2. The mean squared displacement of the monomers further assists the tank-treading dynamics by exhibiting oscillatory behavior.

Excluded volume effects on tangentially driven active ring polymers

The conformational and dynamical properties of active ring polymers are studied by numerical simulations. The two-dimensionally confined polymer is modeled as a closed bead-spring chain, driven by tangential forces, put in contact with a heat bath described by the Brownian multiparticle collision dynamics. Both phantom polymers and chains comprising excluded volume interactions are considered for different bending rigidities. The size and shape are found to be dependent on persistence length, driving force, and bead mutual exclusion. The lack of excluded volume interactions is responsible for a shrinkage of active rings when increasing driving force in the flexible limit, while the presence induces a moderate swelling of chains. The internal dynamics of flexible phantom active rings shows activity-enhanced diffusive behavior at large activity values while, in the case of self-avoiding active chains, it is characterized by active ballistic motion not depending on stiffness. The long-time dynamics of active rings is marked by rotational motion whose period scales as the inverse of the applied tangential force, irrespective of persistence length and beads' self-exclusion.

Structure and dynamics of double-stranded DNA rotaxanes

A DNA rotaxane, with its unique mechanically interlocked architecture consisting of a circular DNA molecule threaded onto a linear DNA axle, holds promise as a fundamental component for nanoscale functional devices. Nevertheless, its structural and dynamic behaviors, essential for advancing molecular machinery, remain largely unexplored. Using extensive all-atom molecular dynamics simulations, we investigated the behaviors of double-stranded DNA (dsDNA) rotaxanes, concentrating on the effects of shape distortion induced by torsional stress in small circular dsDNA containing 70-90 base pairs. We analyzed structural characteristics, including shape, intermolecular distances, and tilt angles, while also exploring dynamic properties such as translational diffusion and toroidal rotation. Our results indicate that shape distortion brings the circular and linear dsDNA components into closer proximity and causes a slight increase in translational diffusion yet a minor decrease in toroidal rotation. Nevertheless, there is no apparent evidence of coupling between translation and rotation. Overall, the insights from this study indicate that such shape distortion does not significantly alter their structure and dynamics. This finding provides flexibility for the design of DNA rotaxanes in nanoscale applications.

Cluster Formation in Solutions of Polyelectrolyte Rings

We use molecular dynamics simulations to explore concentrated solutions of semiflexible polyelectrolyte ring polymers, akin to the DNA mini-circles, with counterions of different valences. We find that the assembly of rings into nanoscopic cylindrical stacks is a generic feature of the systems, but the morphology and dynamics of such a cluster can be steered by the counterion conditions. In general, a small addition of trivalent ions can stabilize the emergence of clusters due to the counterion condensation, which mitigates the repulsion between the like-charged rings. Stoichiometric addition of trivalent ions can even lead to phase separation of the polyelectrolyte ring phase due to the ion-bridging effects promoting otherwise entropically driven clustering. On the other hand, monovalent counterions cause the formation of stacks to be re-entrant with density. The clusters are stable within a certain window of concentration, while above the window the polyelectrolytes undergo an osmotic collapse, disfavoring ordering. The cluster phase exhibits characteristic cluster glass dynamics with arrest of collective degrees of freedom but not the self-ones. On the other hand, the collapsed phase shows arrest on both the collective and single level, suggesting an incipient glass-to-glass transition, from a cluster glass of ring clusters to a simple glass of rings.

Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency

A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.

How DNA affects the hyperthermophilic protein Ape10b2 for oligomerization: an investigation using multiple short molecular dynamics simulations

Alba2 is a hyperthermophilic DNA-binding protein, and DNA plays a crucial role in the Alba2 oligomerization process. It is a pity that there is limited research in terms of how DNA affects the conformational change of Alba2 in oligomerization. Herein, we complement the crystal structure of the Ape10b2 (belongs to Alba2)-dsDNA complex (PDB ID: 3U6Y) and employ multiple short molecular dynamics (MSMD) simulations to illuminate the influence of DNA on Ape10b2 at four temperatures (300, 343, 363, and 373 K). Our results indicate that DNA could cause the conformational changes of two important regions (loop1 and loop5), which may be beneficial for protein oligomerization. The results of hydrogen bond analysis show that the increasing number of hydrogen bonds between two monomers of Ape10b2 may also be a favorable factor for oligomerization. In addition, Ape10b2 can stabilize DNA by electrostatic interactions with an increase in temperature, and five residues (Arg40, Arg42, Asn43, Asn45, and Arg46) play a stabilizing role during protein binding to DNA. Our findings could help in understanding the favorable factors leading to protein oligomerization, which contributes to enzyme engineering research from an industrial perspective.