Single DNA molecule jamming and history-dependent dynamics during motor-driven viral packaging

Addressing Buffer, Size, and Clogging Challenges in LAMP-Coupled Solid-State Nanopores for Point-of-Care Testing

Loop-mediated isothermal amplification (LAMP) is a promising method for point-of-care nucleic acid testing due to its simplicity, rapidity, and high sensitivity. Coupling LAMP with solid-state nanopores enables label-free, single-molecule sensing, enhancing diagnostic accuracy. However, conventional LAMP-coupled nanopore protocols require high-salt buffers (>1 M) to improve signal strength and translocation frequency, complicating workflows and increasing contamination risks. In native LAMP buffers (50 mM KCl), electroosmotic flow (EOF) hinders amplicon transport in sub-10 nm pores, while large amplicons increase the risk of clogging. These challenges limit event rates, data throughput, and device reliability. To address these limitations, we developed a glass nanopore device optimized for direct sensing of amplicons in native buffers, featuring integrated declogging capabilities. Our results revealed that 200 nm pores provided the best balance between minimizing EOF interference and maintaining strong signal strength, achieving the highest event rates. Smaller pores (<100 nm) had low event rates due to EOF effects, while larger pores (>1 μm) showed weakened signal strength. We discovered that clogging in low-salt conditions differs from high-salt environments, with physical vibration effectively resolving clogging in low-salt settings. This led to the integration of an automated vibration motor, extending nanopore lifespan and ensuring continuous data acquisition. Our clog-free, native-buffer sensing platform demonstrated a sensitivity of 0.12 parasite/μL using Plasmodium vivax (P. vivax) as a model organism, exceeding the threshold for detecting asymptomatic infections. These advancements highlight the potential of our nanopore device for rapid, reliable, and user-friendly diagnostics for point-of-care testing.

Optical Tweezers to Study Viruses

A virus is a complex molecular machine that propagates by channeling its genetic information from cell to cell. Unlike macroscopic engines, it operates in a nanoscopic world under continuous thermal agitation. Viruses have developed efficient passive and active strategies to pack and release nucleic acids. Some aspects of the dynamic behavior of viruses and their substrates can be studied using structural and biochemical techniques. By the turn of the millennium, physical techniques have been applied to dynamic studies of viruses in which their intrinsic mechanical activity can be measured directly. Optical tweezers are a technology that can be used to measure the force, torque, and strain produced by molecular motors, as a function of time and at the single-molecule level. Thanks to this technique, some bacteriophages are now known to be powerful nanomachines; they exert force in the piconewton range and their motors work in a highly coordinated fashion for packaging the viral nucleic acid genome. Nucleic acids, whose elasticity and condensation behavior are inherently coupled to the viral packaging mechanisms, virion assembly, and virion-cell interactions are also amenable to examination with optical tweezers. In this chapter, we provide a comprehensive analysis of this laser-based tool, its combination with imaging methods, and its application to the study of viruses and viral molecules.

Knot formation of dsDNA pushed inside a nanochannel

Recent experiments demonstrated that knots in single molecule dsDNA can be formed by compression in a nanochannel. In this manuscript, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment in silico, where an equilibrated coarse-grained double-stranded DNA confined in a square channel is pushed by a piston. The probability of forming knots is a non-monotonic function of the persistence length and can be enhanced significantly by increasing the piston speed. Under compression knots are abundant and delocalized due to a backfolding mechanism from which chain-spanning loops emerge, while knots are less frequent and only weakly localized in equilibrium. Our in silico study thus provides insights into the formation, origin and control of DNA knots in nanopores.

Ion-dependent DNA configuration in bacteriophage capsids

Bacteriophages densely pack their long double-stranded DNA genome inside a protein capsid. The conformation of the viral genome inside the capsid is consistent with a hexagonal liquid crystalline structure. Experiments have confirmed that the details of the hexagonal packing depend on the electrochemistry of the capsid and its environment. In this work, we propose a biophysical model that quantifies the relationship between DNA configurations inside bacteriophage capsids and the types and concentrations of ions present in a biological system. We introduce an expression for the free energy that combines the electrostatic energy with contributions from bending of individual segments of DNA and Lennard-Jones-type interactions between these segments. The equilibrium points of this energy solve a partial differential equation that defines the distributions of DNA and the ions inside the capsid. We develop a computational approach that allows us to simulate much larger systems than what is possible using the existing molecular-level methods. In particular, we are able to estimate bending and repulsion between the DNA segments as well as the full electrochemistry of the solution, both inside and outside of the capsid. The numerical results show good agreement with existing experiments and with molecular dynamics simulations for small capsids.

Physics of viral dynamics

Viral capsids are often regarded as inert structural units, but in actuality they display fascinating dynamics during different stages of their life cycle. With the advent of single-particle approaches and high-resolution techniques, it is now possible to scrutinize viral dynamics during and after their assembly and during the subsequent development pathway into infectious viruses. In this Review, the focus is on the dynamical properties of viruses, the different physical virology techniques that are being used to study them, and the physical concepts that have been developed to describe viral dynamics.

History-dependent nonequilibrium conformations of a highly confined polymer globule in a sphere

Chromatin undergoes condensation-decondensation processes repeatedly during its cell lifetime. The spatial organization of chromatin in nucleus resembles the fractal globule, of which structure significantly differs from an equilibrium polymer globule. There have been efforts to develop a polymer globule model to describe the fractal globulelike structure of tightly packed chromatin in nucleus. However, the transition pathway of a polymer toward a globular state has been often ignored. Because biological systems are intrinsically in nonequilibrium states, the transition pathway that the chromatin would take before reaching the densely packaged globule should be of importance. In this study, by employing a simple polymer model and Langevin dynamics simulations, we investigate the conformational transition of a single polymer from a swollen coil to a compact globule. We aim to elucidate the effect of transition pathways on the final globular structure. We show that a fast collapse induces a nonequilibrium structure even without a specific intramolecular interaction and that its relaxation toward an equilibrium globule is extremely slow. Due to a strong confinement, the fractal globule never relaxes into an equilibrium state during our simulations such that the globular structure becomes dependent on the transition pathway.

Pressurized DNA state inside herpes capsids-A novel antiviral target

Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, "turns off" capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target-suppressing pressure-driven viral genome ejection-that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.

Loop-Mediated Isothermal Amplification-Coupled Glass Nanopore Counting Toward Sensitive and Specific Nucleic Acid Testing

Solid-state nanopores have shown great promise and achieved tremendous success in label-free single-molecule analysis. However, there are three common challenges in solid-state nanopore sensors, including the nanopore size variations from batch to batch that makes the interpretation of the sensing results difficult, the incorporation of sensor specificity, and the impractical analysis time at low analyte concentration due to diffusion-limited mass transport. Here, we demonstrate a novel loop-mediated isothermal amplification (LAMP)-coupled glass nanopore counting strategy that could effectively address these challenges. By using the glass nanopore in the counting mode (versus the sizing mode), the device fabrication challenge is considerably eased since it allows a certain degree of pore size variations and no surface functionalization is needed. The specific molecule replication effectively breaks the diffusion-limited mass transport thanks to the exponential growth of the target molecules. We show the LAMP-coupled glass nanopore counting has the potential to be used in a qualitative test as well as in a quantitative nucleic acid test. This approach lends itself to most amplification strategies as long as the target template is specifically replicated in numbers. The highly sensitive and specific sensing strategy would open a new avenue for solid-state nanopore sensors toward a new form of compact, rapid, low-cost nucleic acid testing at the point of care.

Functional Dissection of a Viral DNA Packaging Machine's Walker B Motif

Many viruses employ ATP-powered motors for genome packaging. We combined genetic, biochemical, and single-molecule techniques to confirm the predicted Walker-B ATP-binding motif in the phage λ motor and to investigate the roles of the conserved residues. Most changes of the conserved hydrophobic residues resulted in >107-fold decrease in phage yield, but we identified nine mutants with partial activity. Several were cold-sensitive, suggesting that mobility of the residues is important. Single-molecule measurements showed that the partially active A175L exhibits a small reduction in motor velocity and increase in slipping, consistent with a slowed ATP binding transition, whereas G176S exhibits decreased slipping, consistent with an accelerated transition. All changes to the conserved D178, predicted to coordinate Mg2+•ATP, were lethal except conservative change D178E. Biochemical interrogation of the inactive D178N protein found no folding or assembly defects and near-normal endonuclease activity, but a ∼200-fold reduction in steady-state ATPase activity, a lag in the single-turnover ATPase time course, and no DNA packaging, consistent with a critical role in ATP-coupled DNA translocation. Molecular dynamics simulations of related enzymes suggest that the aspartate plays an important role in enhancing the catalytic activity of the motor by bridging the Walker motifs and precisely contributing its charged group to help polarize the bound nucleotide. Supporting this prediction, single-molecule measurements revealed that change D178E reduces motor velocity without increasing slipping, consistent with a slowed hydrolysis step. Our studies thus illuminate the mechanistic roles of Walker-B residues in ATP binding, hydrolysis, and DNA translocation by this powerful motor.

Effects of spherical confinement and backbone stiffness on flexible polymer jamming

We use molecular simulations to study jamming of a crumpled bead-spring model polymer in a finite container and compare to jamming of repulsive spheres. After proper constraint counting, the onset of rigidity is seen to occur isostatically as in the case of repulsive spheres. Despite this commonality, the presence of the curved container wall and polymer backbone bonds introduce new mechanical properties. Notably, these include additional bands in the vibrational density of states that reflect the material structure as well as oscillations in local contact number and density near the wall but with lower amplitude for polymers. Polymers have fewer boundary contacts, and this low-density surface layer strongly reduces the global bulk modulus. We further show that bulk-modulus dependence on backbone stiffness can be described by a model of stiffnesses in series and discuss potential experimental and biological applications.

The breakdown of the local thermal equilibrium approximation for a polymer chain during packaging

The conformational relaxation of a polymer chain often slows down in various biological and engineering processes. The polymer, then, may stay in nonequilibrium states throughout the process such that one may not invoke the local thermal equilibrium (LTE) approximation, which has been usually employed to describe the kinetics of various processes. In this work, motivated by recent single-molecule experiments on DNA packaging into a viral capsid, we investigate how the nonequilibrium conformations and the LTE approximation would affect the packaging of a polymer chain into small confinement. We employ a simple but generic coarse-grained model and Langevin dynamics simulations to investigate the packaging kinetics. The polymer segments (both inside and outside the confinement) stay away from equilibrium under strong external force. We devise a simulation scheme to invoke the LTE approximation during packaging and find that the relaxation of nonequilibrium conformations plays a critical role in regulating the packaging rate.

Slow and steady wins the race: physical limits on the rate of viral DNA packaging

During the assembly of dsDNA viruses such as the tailed bacteriophages and herpesviruses, the viral chromosome is compacted to near crystalline density inside a preformed head shell. DNA translocation is driven by powerful ring ATPase motors that couple ATP binding, hydrolysis, and release to force generation and movement. Studies of the motor of the bacteriophage phi29 have revealed a complex mechanochemistry behind this process that slows as the head fills. Recent studies of the physical behavior of packaging DNA suggest that surprisingly long-time scales of relaxation of DNA inside the head and jamming phenomena during packaging create the physical need for regulation of the rate of packaging. Studies of DNA packaging in viral systems have, therefore, revealed fundamental insight into the complex behavior of DNA and the need for biological systems to accommodate these physical constraints.

Nucleotide-dependent DNA gripping and an end-clamp mechanism regulate the bacteriophage T4 viral packaging motor

ATP-powered viral packaging motors are among the most powerful biomotors known. Motor subunits arranged in a ring repeatedly grip and translocate the DNA to package viral genomes into capsids. Here, we use single DNA manipulation and rapid solution exchange to quantify how nucleotide binding regulates interactions between the bacteriophage T4 motor and DNA substrate. With no nucleotides, there is virtually no gripping and rapid slipping occurs with only minimal friction resisting. In contrast, binding of an ATP analog engages nearly continuous gripping. Occasional slips occur due to dissociation of the analog from a gripping motor subunit, or force-induced rupture of grip, but multiple other analog-bound subunits exert high friction that limits slipping. ADP induces comparably infrequent gripping and variable friction. Independent of nucleotides, slipping arrests when the end of the DNA is about to exit the capsid. This end-clamp mechanism increases the efficiency of packaging by making it essentially irreversible.

Packaging of viral DNA depends on strong molecular motors that are powered by ATP hydrolysis. Here, the authors develop a single-molecule assay to monitor how nucleotide binding regulates motor-DNA interactions and reveal a generic mechanism that prevents exit of the whole DNA from the viral capsid during packaging.

8-Bit Adder and Subtractor with Domain Label Based on DNA Strand Displacement

DNA strand displacement, which plays a fundamental role in DNA computing, has been widely applied to many biological computing problems, including biological logic circuits. However, there are many biological cascade logic circuits with domain labels based on DNA strand displacement that have not yet been designed. Thus, in this paper, cascade 8-bit adder/subtractor with a domain label is designed based on DNA strand displacement; domain t and domain f represent signal 1 and signal 0, respectively, instead of domain t and domain f are applied to representing signal 1 and signal 0 respectively instead of high concentration and low concentration high concentration and low concentration. Basic logic gates, an amplification gate, a fan-out gate and a reporter gate are correspondingly reconstructed as domain label gates. The simulation results of Visual DSD show the feasibility and accuracy of the logic calculation model of the adder/subtractor designed in this paper. It is a useful exploration that may expand the application of the molecular logic circuit.

The mobility of packaged phage genome controls ejection dynamics

The cell decision between lytic and lysogenic infection is strongly influenced by dynamics of DNA injection into a cell from a phage population, as phages compete for limited resources and progeny. However, what controls the timing of viral DNA ejection events was not understood. This in vitro study reveals that DNA ejection dynamics for phages can be synchronized (occurring within seconds) or desynchronized (displaying minutes-long delays in initiation) based on mobility of encapsidated DNA, which in turn is regulated by environmental factors, such as temperature and extra-cellular ionic conditions. This mechano-regulation of ejection dynamics is suggested to influence viral replication where the cell’s decision between lytic and latent infection is associated with synchronized or desynchronized delayed ejection events from phage population adsorbed to a cell. Our findings are of significant importance for understanding regulatory mechanisms of latency in phage and Herpesviruses, where encapsidated DNA undergoes a similar mechanical transition.

Viruses are tiny ‘parasites’ that smuggle their genetic material inside a cell and then hijack its resources for their own benefit. A viral infection can either be lytic or latent. In a lytic cycle, viruses make their host produce many copies of themselves, ultimately killing the cell. In contrast, during a latent infection, the viruses go ‘dormant’: for instance, some of them can insert their genetic material into the DNA of their host, which then gets passed on as the cell divides.

Certain viruses are capable of both lytic and latent infections. One example is the lambda phage, which targets Escherichia coli bacteria. In the first stage of infection, the genetic material ‘shoots out’ of the virus and gets injected inside the bacterium. The dynamics of the ejection process determine the type of infection that will follow. If multiple phages release their genomes quickly and within seconds of each other into the same cell, the bacterium tends to incorporate the viral DNA into its own genome, leading to a latent cycle. If the infections take place more slowly and not all at the same time, the cell is more likely to go through a lytic phase. However, the mechanism behind the different injection behaviors is still unknown; in particular, it is unclear which factors control the specificities of the ejection process in the first place.

Here, Alex Evilevitch demonstrates that the mechanical state of the phage DNA just before ejection dictates how the genetic material will then be injected in the bacteria. The experiments measured the stiffness of the DNA and the amount of heat given off during infection. Like fluid toothpaste, if the DNA is more liquid and flexible, it gets ejected quickly and simultaneously from several phages. Then, the genetic information of these viruses can be incorporated in the genome of the bacteria. On the other hand, if the DNA is more solid, it is likely to ‘stick’ and take time before it can be squeezed out: the injections become unsynchronised, which leads to a lytic phase.

Evilevitch then shows that the environment can influence the properties of the phages’ genome. A little more heat, or certain chemicals, can make the DNA more fluid inside the viruses, and change the way it can be injected inside the bacteria.

Many viruses that cause diseases in humans – from cold sores to glandular fever – can switch between the lytic and latent cycles. For the first time, these results show that the mechanical properties of the DNA inside a virus influence the ‘decision’ between the two types of infection. This knowledge could help us prevent infections from becoming lytic and ultimately allow us to control the spread of disease.

Flow-induced polymer separation through a nanopore: effects of solvent quality

Using a hybrid simulation method that combines a lattice-Boltzmann approach for the flow and a molecular dynamics model for the polymer, we investigated the effect of solvent quality on the flow-induced polymer translocation through a nanopore. We demonstrate the nontrivial dependence of the translocation dynamics of polymers on the solvent quality, i.e., the enhancement in the polymer insolubility increases the critical velocity flux and shortens the translocation time. Accordingly, we propose a new strategy to separate polymers with different solubilities via their translocations in the nanopore by adjusting the velocity flux of the flow, which appears to be promising for the design of micro-scaled polymer separation devices.

Compaction of quasi-one-dimensional elastoplastic materials

Insight into crumpling or compaction of one-dimensional objects is important for understanding biopolymer packaging and designing innovative technological devices. By compacting various types of wires in rigid confinements and characterizing the morphology of the resulting crumpled structures, here, we report how friction, plasticity and torsion enhance disorder, leading to a transition from coiled to folded morphologies. In the latter case, where folding dominates the crumpling process, we find that reducing the relative wire thickness counter-intuitively causes the maximum packing density to decrease. The segment size distribution gradually becomes more asymmetric during compaction, reflecting an increase of spatial correlations. We introduce a self-avoiding random walk model and verify that the cumulative injected wire length follows a universal dependence on segment size, allowing for the prediction of the efficiency of compaction as a function of material properties, container size and injection force.

Principles underlying crumpling of one-dimensional objects may be relevant to both biomolecular processes and to design of mechanical devices. By compacting various wires under rigid confinement and modelling observed geometric features, the authors show how friction, plasticity and torsion enhance disorder and lead to a transition from coiled to folded geometries.

A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions

Genome packing in viruses and prokaryotes relies on positively charged ions to reduce electrostatic repulsions, and induce attractions that can facilitate DNA condensation. Here we present molecular dynamics simulations spanning several microseconds of dsDNA packing inside nanometer-sized viral capsids. We use a detailed molecular model of DNA that accounts for molecular structure, basepairing, and explicit counterions. The size and shape of the capsids studied here are based on the 30-nanometer-diameter gene transfer agents of bacterium Rhodobacter capsulatus that transfer random 4.5-kbp (1.5 μm) DNA segments between bacterial cells. Multivalent cations such as spermidine and magnesium induce attraction between packaged DNA sites that can lead to DNA condensation. At high concentrations of spermidine, this condensation significantly increases the shear stresses on the packaged DNA while also reducing the pressure inside the capsid. These effects result in an increase in the packing velocity and the total amount of DNA that can be packaged inside the nanometer-sized capsids. In the simulation results presented here, high concentrations of spermidine³⁺ did not produce the premature stalling observed in experiments. However, a small increase in the heterogeneity of packing velocities was observed in the systems with magnesium and spermidine ions compared to the system with only salt. The results presented here indicate that the effect of multivalent cations and of spermidine, in particular, on the dynamics of DNA packing, increases with decreasing packing velocities.

Scaling, crumpled wires, and genome packing in virions

The packing of a genome in virions is a topic of intense current interest in biology and biological physics. The area is dominated by allometric scaling relations that connect, e.g., the length of the encapsulated genome and the size of the corresponding virion capsid. Here we report scaling laws obtained from extensive experiments of packing of a macroscopic wire within rigid three-dimensional spherical and nonspherical cavities that can shed light on the details of the genome packing in virions. We show that these results obtained with crumpled wires are comparable to those from a large compilation of biological data from several classes of virions.

Translocation dynamics of knotted polymers under a constant or periodic external field

We perform Brownian dynamics simulations to examine how knots alter the dynamics of polymers moving through nanopores under an external field. In the first part of this paper, we study the situation when the field is constant. Here, knots halt translocation above a critical force with jamming occurring at smaller forces for twist topologies compared to non-twist topologies. Slightly below the jamming transition, the polymer's transit times exhibit large fluctuations. This phenomenon is an example of the knot's molecular individualism since the conformation of the knot plays a large role in the chain's subsequent dynamics. In the second part of the paper, we study the motion of the chain when one cycles the field on and off. If the off time is comparable to the knot's relaxation time, one can adjust the swelling of the knot at the pore and hence design strategies to ratchet the polymer in a controllable fashion. We examine how the off time affects the ratcheting dynamics. We also examine how this strategy alters the fluctuations in the polymer's transit time. We find that cycling the force field can reduce fluctuations near the knot's jamming transition, but can enhance the fluctuations at very high forces since knots get trapped in metastable states during the relaxation process. The latter effect appears to be more prominent for non-torus topologies than torus ones. We conclude by discussing the feasibility of this approach to control polymer motion in biotechnology applications such as sequencing.