Structural ensemble and dynamics of toroidal-like DNA shapes in bacteriophage ϕ29 exit cavity

Two-phase dynamics of DNA supercoiling based on DNA polymer physics

DNA supercoils are generated in genome regulation processes such as transcription and replication and provide mechanical feedback to such processes. Under tension, a DNA supercoil can present a coexistence state of plectonemic and stretched phases. Experiments have revealed the dynamic behaviors of plectonemes, e.g., diffusion, nucleation, and hopping. To represent these dynamics with conformational changes, we demonstrated first the fast dynamics on the DNA to reach torque equilibrium within the plectonemic and stretched phases, and then identified the two-phase boundaries as collective slow variables to describe the essential dynamics. According to the timescale separation demonstrated here, we developed a two-phase model on the dynamics of DNA supercoiling, which can capture physiologically relevant events across timescales of several orders of magnitudes. In this model, we systematically characterized the slow dynamics between the two phases and compared the numerical results with those from the DNA polymer physics-based worm-like chain model. The supercoiling dynamics, including the nucleation, diffusion, and hopping of plectonemes, have been well represented and reproduced, using the two-phase dynamic model, at trivial computational costs. Our current developments, therefore, can be implemented to explore multiscale physical mechanisms of the DNA supercoiling-dependent physiological processes.

Simulation of DNA Supercoil Relaxation

Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics. Here we employ our discrete wormlike chain model to bypass experimental limitations and simulate the dynamic response of supercoiled DNA to a single strand nick. From our simulations, we make three major observations. First, extension is a poor dynamic measure of supercoil relaxation; in fact, the linking number relaxes so fast that it cannot have much impact on extension. Second, the rate of linking number relaxation depends upon its initial partitioning into twist and writhe as determined by tension. Third, the extensional response strongly depends upon the initial position of plectonemes.

Phage-like packing structures with mean field sequence dependence

Packing of double-stranded DNA in phages must overcome both electrostatic repulsions and the problem of persistence length. We consider coarse-grained models with the ability to kink and with randomly generated disorder. We show that the introduction of kinking into configurations of the DNA polymer packaged within spherical confinement results in significant reductions of the overall energies and pressures. We use a kink model which has the ability to deform every 24 bp, close to the average length predicted from phage sequence. The introduction of such persistence length defects even with highly random packing models increases the local nematic ordering of the packed DNA polymer segments. Such local ordering allowed by kinking not only reduces the total bending energy of confined DNA due to nonlinear elasticity but also reduces the electrostatic component of the energy and pressure. We show that a broad ensemble of polymer configurations is consistent with the structural data. © 2016 Wiley Periodicals, Inc.

Free-energy landscape and characteristic forces for the initiation of DNA unzipping

DNA unzipping, the separation of its double helix into single strands, is crucial in modulating a host of genetic processes. Although the large-scale separation of double-stranded DNA has been studied with a variety of theoretical and experimental techniques, the minute details of the very first steps of unzipping are still unclear. Here, we use atomistic molecular-dynamics simulations, coarse-grained simulations, and a statistical-mechanical model to study the initiation of DNA unzipping by an external force. Calculation of the potential of mean force profiles for the initial separation of the first few terminal basepairs in a DNA oligomer revealed that forces ranging between 130 and 230 pN are needed to disrupt the first basepair, and these values are an order of magnitude larger than those needed to disrupt basepairs in partially unzipped DNA. The force peak has an echo of ∼50 pN at the distance that unzips the second basepair. We show that the high peak needed to initiate unzipping derives from a free-energy basin that is distinct from the basins of subsequent basepairs because of entropic contributions, and we highlight the microscopic origin of the peak. To our knowledge, our results suggest a new window of exploration for single-molecule experiments.

Confined polyelectrolytes: The complexity of a simple system

The interaction between polyelectrolytes and counterions in confined situations and the mutual relationship between chain conformation and ion condensation is an important issue in several areas. In the biological field, it assumes particular relevance in the understanding of the packaging of nucleic acids, which is crucial in the design of gene delivery systems. In this work, a simple coarse-grained model is used to assess the cooperativity between conformational change and ion condensation in spherically confined backbones, with capsides permeable to the counterions. It is seen that the variation on the degree of condensation depends on counterion valence. For monovalent counterions, the degree of condensation passes through a minimum before increasing as the confining space diminishes. In contrast, for trivalent ions, the overall tendency is to decrease the degree of condensation as the confinement space also decreases. Most of the particles reside close to the spherical wall, even for systems in which the density is higher closer to the cavity center. This effect is more pronounced, when monovalent counterions are present. Additionally, there are clear variations in the charge along the concentric layers that cannot be totally ascribed to polyelectrolyte behavior, as shown by decoupling the chain into monomers. If both chain and counterions are confined, the formation of a counterion rich region immediately before the wall is observed. Spool and doughnut-like structures are formed for stiff chains, within a nontrivial evolution with increasing confinement.

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

We consider the consequences of assuming that DNA inside of phages can be approximated as a strongly nonlinear persistence length polymer. Recent cryo-EM experiments find a hole in the density map of P-SSP7 phage, located in the DNA segment filling the portal channel of the phage. We use experimentally derived structural constraints with coarse-grained simulation techniques to consider contrasting model interpretations of reconstructed density in the portal channel. The coarse-grained DNA models used are designed to capture the effects of torsional strain and electrostatic environment. Our simulation results are consistent with the interpretation that the vacancy or hole in the experimental density map is due to DNA strain leading to strand separation. We further demonstrate that a moderate negative twisting strain is able to account for the strand separation. This effect of nonlinear persistence length may be important in other aspects of phage DNA packing.

DNA buckling in bacteriophage cavities as a mechanism to aid virus assembly

While relatively simple biologically, bacteriophages are sophisticated biochemical machines that execute a precise sequence of events during virus assembly, DNA packaging, and ejection. These stages of the viral life cycle require intricate coordination of viral components whose structures are being revealed by single molecule experiments and high resolution (cryo-electron microscopy) reconstructions. For example, during packaging, bacteriophages employ some of the strongest known molecular motors to package DNA against increasing pressure within the viral capsid shell. Located upstream of the motor is an elaborate portal system through which DNA is threaded. A high resolution reconstruction of the portal system for bacteriophage ϕ29 reveals that DNA buckles inside a small cavity under large compressive forces. In this study, we demonstrate that DNA can also buckle in other bacteriophages including T7 and P22. Using a computational rod model for DNA, we demonstrate that a DNA buckle can initiate and grow within the small confines of a cavity under biologically-attainable force levels. The forces of DNA-cavity contact and DNA-DNA electrostatic repulsion ultimately limit cavity filling. Despite conforming to very different cavity geometries, the buckled DNA within T7 and P22 exhibits near equal volumetric energy density (∼1kT/nm(3)) and energetic cost of packaging (∼22kT). We hypothesize that a DNA buckle creates large forces on the cavity interior to signal the conformational changes to end packaging. In addition, a DNA buckle may help retain the genome prior to tail assembly through significantly increased contact area with the portal.

Role of microscopic flexibility in tightly curved DNA

The genetic material in living cells is organized into complex structures in which DNA is subjected to substantial contortions. Here we investigate the difference in structure, dynamics, and flexibility between two topological states of a short (107 base pair) DNA sequence in a linear form and a covalently closed, tightly curved circular DNA form. By employing a combination of all-atom molecular dynamics (MD) simulations and elastic rod modeling of DNA, which allows capturing microscopic details while monitoring the global dynamics, we demonstrate that in the highly curved regime the microscopic flexibility of the DNA drastically increases due to the local mobility of the duplex. By analyzing vibrational entropy and Lipari–Szabo NMR order parameters from the simulation data, we propose a novel model for the thermodynamic stability of high-curvature DNA states based on vibrational untightening of the duplex. This novel view of DNA bending provides a fundamental explanation that bridges the gap between classical models of DNA and experimental studies on DNA cyclization, which so far have been in substantial disagreement.