Single-molecule studies of DNA mechanics

A mutant complement factor H (W1183R) enhances proteolytic cleavage of von Willebrand factor by ADAMTS-13 under shear

BACKGROUND

A loss-of-functional mutation (W1183R) in human complement factor H (CFH) is associated with complement-associated hemolytic uremic syndrome; mice carrying a similar mutation (W1206R) in CFH also develop thrombotic microangiopathy but its plasma von Willebrand factor (VWF) multimer sizes were dramatically reduced. The mechanism underlying such a dramatic change in plasma VWF multimer distribution in these mice is not fully understood.

OBJECTIVES

To determine the VWF and CFH interaction and how CFH proteins affect VWF multimer distribution.

METHODS

We employed recombinant protein expression, purification, and various biochemical and biophysical tools.

RESULTS

Purified recombinant W1183R-CFH but not wild-type (WT) CFH protein enhanced the proteolytic cleavage of both peptidyl and multimeric VWF substrates by recombinant ADAMTS-13 in a concentration-dependent manner. Microscale thermophoresis assay demonstrated that both W1183R-CFH and WT-CFH proteins bound various VWF fragments (eg, AIM-A1, A1-A2-A3, D'D3, D'D3-A1, and D'D3-A1-A2) with high affinities. Optical tweezer experiments further showed a concentration-dependent alteration in the contour length (Lc) and the persistent length (Lp) following pulling VWF-A2 domain in the presence of W1183R-CFH or WT-CFH protein. AlphaFold experiments revealed conformational changes in the VWF-A2, particularly the central region where the cleavage bond resides following addition of W1183R-CFH or WT-CFH protein.

CONCLUSION

These results demonstrate for the first time that W1183R-CFH but not WT-CFH protein enhances the proteolytic cleavage of VWF by ADAMTS-13 under shear. This may be achieved by mechanic-induced conformational changes of the central A2 domain, leading to an enhanced cleavage of Tyr1605-Met1606 bond by ADAMTS-13 under pathophysiological conditions.

ATP hydrolysis-driven structural transitions within the S. cerevisiae Rad51 and Dmc1 nucleoprotein filaments

Homologous recombination (HR) is essential for the maintenance of genome stability and for generating genetic diversity during meiosis. The eukaryotic protein Rad51 is member of the Rad51/RecA family of DNA recombinases and is responsible for guiding the DNA pairing reactions that take place in HR during mitosis. Dmc1 is a meiosis-specific paralog of Rad51 and is responsible for the DNA pairing reactions that take place in HR during meiosis. Rad51 and Dmc1 are both ATP-dependent DNA-binding proteins and both form extended helical filaments on ssDNA which are key intermediates in HR. The stability of these nucleoprotein filaments is highly regulated and is also tightly coupled to nucleotide binding and hydrolysis. ATP binding promotes filament assembly whereas the hydrolysis of ATP to ADP reduces filament stability to promote filament disassembly. Here, we present CryoEM structures of the Saccharomyces cerevisiae recombinases Rad51 and Dmc1 in the ADP-bound states and provide a detailed structural comparison to the ATP-bound filaments. Our findings yield insights into the structural transitions that take place during the hydrolysis of ATP to ADP and suggest a new model for how these structural changes may be linked to nucleoprotein filament disassembly.

Subwavelength-scale off-axis optical nanomanipulation within Gaussian-beam traps

It is generally recognized that there is only a single optical potential-well near the focus in optical traps with a focused Gaussian beam. In this work, we show that this classic Gaussian-beam optical trap has additional optical potential-wells for optical manipulation at the subwavelength scale in the off-focus transverse plane. The additional optical potential-wells are formed by the synergy of both the gradient trapping force and the transverse scattering force, though in previous studies the scattering force usually has adverse effect such as reducing trapping stability. These potential-wells work for not only the metallic particles, but also the high refractive-index dielectric particles. By engineering the contribution of the gradient force and scattering force through the particle size, the particle material and the position of the manipulation transverse plane, the force field and trapping potential-well can be tailored to trap/manipulate nanoparticles at different off-axis distance at the subwavelength scale. Our work provides new insight into optical tweezers and promises applications in optical nanomanipulation, nanoparticle sorting/separation, particle patterning and micro-fabrication on substrates.

Aptamer-based biotherapeutic conjugate for shear responsive release of Von Willebrand factor A1 domain

Smart polymers that mimic and even surpass the functionality of natural responsive materials have been actively researched. This study explores the design and characterization of a Single-MOlecule-based material REsponsive to Shear (SMORES) for the targeted release of A1, the platelet binding domain of the blood clotting protein von Willebrand factor (VWF). Each SMORES construct employs an aptamer molecule as the flow transducer and a microparticle to sense and amplify the hydrodynamic force. Within the construct, the aptamer, ARC1172, undergoes conformational changes beyond a shear stress threshold, mimicking the shear-responsive behavior of VWF. This conformational alteration modulates the bioavailability of its target, the VWF-A1 domain, ultimately releasing it at elevated shear. Through optical tweezer-based single-molecule force measurement, ARC1172s role as a force transducer was assessed by examining its unfolding under constant pulling force. We also investigated its refolding rate as a function of force under varied relaxation periods. These analyses revealed a narrow range of threshold forces (3-7 pN) governing the transition between folded and unfolded states. We subsequently constructed the SMORES material by conjugating ARC1172 and a microbead, and immobilizing the other end of the aptamer on a substrate. Single-molecule flow experiments on immobilized SMORES constructs revealed a peak A1 domain release within a flow rate range of (40-70 μL min-1). A COMSOL Multiphysics model translated these flow rates to total forces of 3.10 pN-5.63 pN experienced by the aptamers, aligning with single-molecule force microscopy predictions. Evaluation under variable flow conditions showed a peak binding of A1 to the platelet glycoprotein Ib (GPIB) within the same force range, confirming released payload functionality. Building on knowledge of aptamer biomechanics, this study presents a new strategy to create shear-stimulated biomaterials based on single biomolecules.

Isolation and Analysis of Rare Enzymatic Events with Multiplex Flow Magnetic Tweezers

Our understanding of biomolecular dynamics has been revolutionized with the advent of techniques that enable the manipulation of forces and torques at the single-molecule level. However, the characterization of rare intermediates has proven challenging due to limited throughput. In this chapter, we present a method that dramatically enhances the throughput of force spectroscopy measurements with topological control. The method allows for routine imaging of tens of thousands of individual molecules undergoing millions of reaction cycles in parallel. The improvement in throughput enables the discovery of rare enzymatic events. Here, we describe the experimental procedures for the observation and analysis of supercoiling dynamics by DNA gyrase. To efficiently quantify diverse dynamic behaviors and rare events, we introduce a software platform with an incorporated automated feature classification pipeline. This method and accompanying software can be freely adapted for investigations into a wide array of complex, multistep enzymatic pathways where the characterization of rare intermediates has been hindered by limited throughput.

Optical tweezers in biomedical research - progress and techniques

Optical tweezers, which leverage the forces exerted by radiation pressure, have emerged as a pivotal technique for precisely manipulating and analyzing microscopic particles. Since Arthur Ashkin's ground-breaking work in the 1970s and the subsequent development of the single-beam optical trap in 1986, the capabilities of optical tweezers have expanded significantly, enabling the intricate manipulation of biological specimens at the micro- and nanoscale. This review elucidates the foundational principles of optical trapping and their extensive applications in the biomedical sciences. The applications of optical tweezers in biomedicine are vast, ranging from the investigation of cellular mechanical properties, such as cell stretching, membrane elasticity, and stiffness, to single-molecule studies encompassing DNA and protein mechanics, protein-DNA interactions, molecular motor functions, and pathogen-host interactions. Advancement of optical tweezers in this field includes their integration with holography, fluorescence microscopy, microfluidics, and enhancements in force sensitivity and positional accuracy. These tools have profoundly impacted the study of cellular mechanics, drug discovery processes, and disease diagnostics, providing unparalleled insights into the biophysical mechanisms underlying health and pathology.

Temperature-dependent ejection evolution arising from active and passive effects in DNA viruses

Recent experiments have demonstrated that the ejection velocity of different species of DNA viruses is temperature dependent, potentially influencing the cellular infection mechanisms of these viruses. However, due to the challenge in quantifying the multiscale characteristics of DNA virus systems, there is currently a lack of systematic theoretical research on the temperature-dependent evolution of ejection dynamics. This work presents a multiscale model to quantitatively explore the temperature-dependent mechanical properties during the virus ejection process, and unveil the underlying mechanisms. Two different assumptions of DNA structures, featuring two or single domains, are used for the early and later stages of ejection, respectively. Temperature is introduced as an influencing variable into the mesoscopic energy model by considering the temperature dependence of Debye length, DNA persistence length, molecular kinetic energy, and other parameters. The results indicate that temperature variations alter the energy landscape associated with DNA structure, leading to the changes in the energy minimum and corresponding DNA structure remaining in the capsid. These changes affect both the active ejection force and passive friction during the DNA ejection, ultimately leading to a significant increase in ejection velocity at higher temperatures. Furthermore, our model supports the previous hypothesis that temperature-induced changes in the size of viral portal pore could dramatically enhance DNA ejection velocity.

DNA Mechanics: From Single Stranded to Self-Assembled

DNA encodes genetic information and forms various structural conformations with distinct physical, chemical, and biological properties. Over the past 30 years, advancements in force manipulation technology have enabled the precise manipulation of DNA at nanometer and piconewton resolutions. This mini-review discusses these force manipulation techniques for exploring the mechanical properties of DNA at the single-molecule level. We summarize the distinct mechanical features of different DNA forms while considering the impact of the force geometry. We highlight the role of DNA mechanics in origami structures that serve as self-assembled building blocks or mechanically responsive/active nanomachines. Accordingly, we emphasize how DNA mechanics are integral to the functionality of origami structures for achieving mechanical capabilities. Finally, we provide an outlook on the intrinsic mechanical properties of DNA, from single stranded to self-assembled higher-dimensional structures. This understanding is expected to inspire new design strategies in DNA mechanics, paving the way for innovative applications and technologies.

Ten Thousand Recaptures of a Single DNA Molecule in a Nanopore and Variance Reduction of Translocation Characteristics

Nanopores have emerged as highly sensitive biosensors operating at the single-molecule level. However, the majority of nanopore experiments still rely on averaging signals from multiple molecules, introducing systematic errors. To overcome this limitation and obtain accurate information from a single molecule, the molecular ping-pong methodology provides a precise approach involving repeated captures of a single molecule. In this study, we have enhanced the molecular ping-pong technique by incorporating a customized electronic system and control algorithm, resulting in a recapture number exceeding 10,000. During the ping-pong process, we observed a significant reduction in the variance of translocation characteristics, providing fresh insights into single-molecule translocation dynamics. An inhomogeneous translocation velocity of folded DNA has been revealed, illustrating a strong interaction between the molecule and the solid-state nanopore. The results not only promise heightened experimental efficiency with reduced sample volume but also increase the precision in statistical analysis of translocation events, marking a significant stride toward authentic single-molecule nanopore sensing.

Exploring ssDNA translocation through α-hemolysin using coarse-grained steered molecular dynamics

Protein nanopores have proven to be effective for single-molecule studies, particularly for single-stranded DNA (ssDNA) translocation. Previous experiments demonstrated their ability to distinguish differences in purine and pyrimidine bases and in the orientation of the ssDNA molecule inside nanopores. Unfortunately, the microscopic details of ssDNA translocation over experimental time scales, which are not accessible through all-atom molecular dynamics (MD), have yet to be examined. However, coarse-grained (CG) MD simulations enable systems to be simulated over longer characteristic times closer to experiments than all-atom MD. This paper studies ssDNA translocation through α-hemolysin nanopores exploiting steered MD using the MARTINI CG force field. The impacts of the sequence length, orientation inside the nanopore and DNA charges on translocation dynamics as well as the conformational dynamics of ssDNA during the translocation are explored. Our results highlight the efficacy of CG molecular dynamics in capturing the experimental properties of ssDNA translocation, including a wide distribution in translocation times per base. In particular, the phosphate charges of the DNA molecule are crucial in the translocation dynamics and impact the translocation rate. Additionally, the influence of the ssDNA molecule orientation on the translocation rate is explained by the conformational differences of ssDNA inside the nanopore during its translocation. Our study emphasizes the significance of obtaining sufficient statistics via CG MD, which can elucidate the great variety of translocation processes.

Enzyme Engineering by Force: DNA Springs for the Modulation of Biocatalytic Trajectories

The engineering of enzymatic activity generally involves alteration of the protein primary sequences, which introduce structural changes that give rise to functional improvements. Mechanical forces have been used to interrogate protein biophysics, leading to deep mechanistic insights in single-molecule studies. Here, we use simple DNA springs to apply small pulling forces to perturb the active site of a thermostable alcohol dehydrogenase. Methods were developed to enable the study of different spring lengths and spring orientations under bulk catalysis conditions. Tension applied across the active site expanded the binding pocket volume and shifted the preference of the enzyme for longer chain-length substrates, which could be tuned by altering the spring length and the resultant applied force. The substrate specificity changes did not occur when the DNA spring was either severed or rotated by ∼90°. These findings demonstrate an alternative approach in protein engineering, where active site architectures can be dynamically and reversibly remodeled using applied mechanical forces.

Optical trapping and manipulating with a transmissive and polarization-insensitive metalens

Trapping and manipulating micro-objects and achieving high-precision measurements of tiny forces and displacements are of paramount importance in both physical and biological research. While conventional optical tweezers rely on tightly focused beams generated by bulky microscope systems, the emergence of flat lenses, particularly metalenses, has revolutionized miniature optical tweezers applications. In contrast to traditional objectives, the metalenses can be seamlessly integrated into sample chambers, facilitating flat-optics-based light manipulation. In this study, we propose an experimentally realized transmissive and polarization-insensitive water-immersion metalens, constructed using adaptive nano-antennas. This metalens boasts an ultra-high numerical aperture of 1.28 and achieves a remarkable focusing efficiency of approximately 50 % at a wavelength of 532 nm. Employing this metalens, we successfully demonstrate stable optical trapping, achieving lateral trapping stiffness exceeding 500 pN/(μm W). This stiffness magnitude aligns with that of conventional objectives and surpasses the performance of previously reported flat lenses. Furthermore, our bead steering experiment showcases a lateral manipulation range exceeding 2 μm, including a region of around 0.5 μm exhibiting minimal changes in stiffness for smoothly optical manipulation. We believe that this metalens paves the way for flat-optics-based optical tweezers, simplifying and enhancing optical trapping and manipulation processes, attributing ease of use, reliability, high performance, and compatibility with prevalent optical tweezers applications, including single-molecule and single-cell experiments.

Ebola Virus Glycoprotein Strongly Binds to Membranes in the Absence of Receptor Engagement

Ebola virus (EBOV) is an enveloped virus that must fuse with the host cell membrane in order to release its genome and initiate infection. This process requires the action of the EBOV envelope glycoprotein (GP), encoded by the virus, which resides in the viral envelope and consists of a receptor binding subunit, GP1, and a membrane fusion subunit, GP2. Despite extensive research, a mechanistic understanding of the viral fusion process is incomplete. To investigate GP-membrane association, a key step in the fusion process, we used two approaches: high-throughput measurements of single-particle diffusion and single-molecule measurements with optical tweezers. Using these methods, we show that the presence of the endosomal Niemann-Pick C1 (NPC1) receptor is not required for primed GP-membrane binding. In addition, we demonstrate this binding is very strong, likely attributed to the interaction between the GP fusion loop and the membrane's hydrophobic core. Our results also align with previously reported findings, emphasizing the significance of acidic pH in the protein-membrane interaction. Beyond Ebola virus research, our approach provides a powerful toolkit for studying other protein-membrane interactions, opening new avenues for a better understanding of protein-mediated membrane fusion events.

Localized Plasmonic Heating for Single-Molecule DNA Rupture Measurements in Optical Tweezers

To date, studies on the thermodynamic and kinetic processes that underlie biological function and nanomachine actuation in biological- and biology-inspired molecular constructs have primarily focused on photothermal heating of ensemble systems, highlighting the need for probes that are localized within the molecular construct and capable of resolving single-molecule response. Here we present an experimental demonstration of wavelength-selective, localized heating at the single-molecule level using the surface plasmon resonance of a 15 nm gold nanoparticle (AuNP). Our approach is compatible with force-spectroscopy measurements and can be applied to studies of the single-molecule thermodynamic properties of DNA origami nanomachines as well as biomolecular complexes. We further demonstrate wavelength selectivity and establish the temperature dependence of the reaction coordinate for base-pair disruption in the shear-rupture geometry, demonstrating the utility and flexibility of this approach for both fundamental studies of local (nanometer-scale) temperature gradients and rapid and multiplexed nanomachine actuation.

Magnetic tweezers characterization of the entropic elasticity of intrinsically disordered proteins and peptoids

Understanding the conformational behavior of biopolymers is essential to unlocking knowledge of their biophysical mechanisms and functional roles. Single-molecule force spectroscopy can provide a unique perspective on this by exploiting entropic elasticity to uncover key biopolymer structural parameters. A particularly powerful approach involves the use of magnetic tweezers, which can easily generate lower stretching forces (0.1-20 pN). For forces at the low end of this range, the elastic response of biopolymers is sensitive to excluded volume effects, and they can be described by Pincus blob elasticity model that allow robust extraction of the Flory polymer scaling exponent. Here, we detail protocols for the use of magnetic tweezers for force-extension measurements of intrinsically disordered proteins and peptoids. We also discuss procedures for fitting low-force elastic curves to the predictions of polymer physics models to extract key conformational parameters.

Shear-activation of mechanochemical reactions through molecular deformation

Mechanical stress can directly activate chemical reactions by reducing the reaction energy barrier. A possible mechanism of such mechanochemical activation is structural deformation of the reactant species. However, the effect of deformation on the reaction energetics is unclear, especially, for shear stress-driven reactions. Here, we investigated shear stress-driven oligomerization reactions of cyclohexene on silica using a combination of reactive molecular dynamics simulations and ball-on-flat tribometer experiments. Both simulations and experiments captured an exponential increase in reaction yield with shear stress. Elemental analysis of ball-on-flat reaction products revealed the presence of oxygen in the polymers, a trend corroborated by the simulations, highlighting the critical role of surface oxygen atoms in oligomerization reactions. Structural analysis of the reacting molecules in simulations indicated the reactants were deformed just before a reaction occurred. Quantitative evidence of shear-induced deformation was established by comparing bond lengths in cyclohexene molecules in equilibrium and prior to reactions. Nudged elastic band calculations showed that the deformation had a small effect on the transition state energy but notably increased the reactant state energy, ultimately leading to a reduction in the energy barrier. Finally, a quantitative relationship was developed between molecular deformation and energy barrier reduction by mechanical stress.

Molecular Adhesion of a Pilus-Derived Peptide Involved in Pseudomonas aeruginosa Biofilm Formation on Non-Polar ZnO-Surfaces

Bacterial colonization and biofilm formation on abiotic surfaces are initiated by the adhesion of peptides and proteins. Understanding the adhesion of such peptides and proteins at a molecular level thus represents an important step toward controlling and suppressing biofilm formation on technological and medical materials. This study investigates the molecular adhesion of a pilus-derived peptide that facilitates biofilm formation of Pseudomonas aeruginosa, a multidrug-resistant opportunistic pathogen frequently encountered in healthcare settings. Single-molecule force spectroscopy (SMFS) was performed on chemically etched ZnO11 2 ‾ 0 ${\left(11\bar{2}0\right)}$ surfaces to gather insights about peptide adsorption force and its kinetics. Metal-free click chemistry for the fabrication of peptide-terminated SMFS cantilevers was performed on amine-terminated gold cantilevers and verified by X-ray photoelectron spectroscopy (XPS) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Atomic force microscopy (AFM) and XPS analyses reveal stable topographies and surface chemistries of the substrates that are not affected by SMFS. Rupture events described by the worm-like chain model (WLC) up to 600 pN were detected for the non-polar ZnO surfaces. The dissociation barrier energy at zero force ΔG(0), the transition state distance xb and bound-unbound dissociation rate at zero force koff (0) for the single crystalline substrate indicate that coordination and hydrogen bonds dominate the peptide/surface interaction.

Unravelling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers

Genomes carry the genetic blueprint of all living organisms. Their organization requires strong condensation as well as carefully regulated accessibility to specific genes for proper functioning of their hosts. The study of the structure and dynamics of the proteins that organize the genome has benefited tremendously from the development of single-molecule force spectroscopy techniques that allow for real-time, nanometer accuracy measurements of the compaction of DNA and manipulation with pico-Newton scale forces. Magnetic tweezers, in particular, have the unique ability to complement such force spectroscopy with the control over the linking number of the DNA molecule, which plays an important role when DNA-organizing proteins form or release wraps, loops, and bends in DNA. Here, we describe all the necessary steps to prepare DNA substrates for magnetic tweezers experiments, assemble flow cells, tether DNA to a magnetic bead inside a flow cell, and manipulate and record the extension of such DNA tethers. Furthermore, we explain how mechanical parameters of nucleoprotein filaments can be extracted from the data.

Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy

Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.

Electrokinetic Torque Generation by DNA Nanorobotic Arms Studied via Single-Molecule Fluctuation Analysis

DNA nanotechnology has enabled the creation of supramolecular machines, whose shape and function are inspired from traditional mechanical engineering as well as from biological examples. As DNA inherently is a highly charged biopolymer, the external application of electric fields provides a versatile, computer-programmable way to control the movement of DNA-based machines. However, the details of the electrohydrodynamic interactions underlying the electrical manipulation of these machines are complex, as the influence of their intrinsic charge, the surrounding cloud of counterions, and the effect of electrokinetic fluid flow have to be taken into account. In this work, we identify the relevant effects involved in this actuation mechanism by determining the electric response of an established DNA-based nanorobotic arm to varying design and operation parameters. Borrowing an approach from single-molecule biophysics, we determined the electrical torque exerted on the nanorobotic arms by analyzing their thermal fluctuations when oriented in an electric field. We analyze the influence of various experimental and design parameters on the "actuatability" of the nanostructures and optimize the generated torque according to these parameters. Our findings give insight into the physical processes involved in the actuation mechanism and provide general guidelines that aid in designing and efficiently operating electrically driven nanorobotic devices made from DNA.

The Free Energy of Nucleosomal DNA Based on the Landau Model and Topology

The free energy of nucleosomal DNA plays a key role in the formation of nucleosomes in eukaryotes. Some work on the free energy of nucleosomal DNA have been carried out in experiments. However, the relationships between the free energy of nucleosomal DNA and its conformation, especially its topology, remain unclear in theory. By combining the Landau theory, the Hopfion model and experimental data, we find that the free energy of nucleosomal DNA is at the lower level. With the help of the energy minimum principle, we conclude that nucleosomal DNA stays in a stable state. Moreover, we discover that small perturbations on nucleosomal DNA have little effect on its free energy. This implies that nucleosomal DNA has a certain redundancy in order to stay stable. This explains why nucleosomal DNA will not change significantly due to small perturbations.

Mechanics of dynamic and deformable DNA nanostructures

In DNA nanotechnology, DNA molecules are designed, engineered, and assembled into arbitrary-shaped architectures with predesigned functions. Static DNA assemblies often have delicate designs with structural rigidity to overcome thermal fluctuations. Dynamic structures reconfigure in response to external cues, which have been explored to create functional nanodevices for environmental sensing and other applications. However, the precise control of reconfiguration dynamics has been a challenge due partly to flexible single-stranded DNA connections between moving parts. Deformable structures are special dynamic constructs with deformation on double-stranded parts and single-stranded hinges during transformation. These structures often have better control in programmed deformation. However, related deformability and mechanics including transformation mechanisms are not well understood or documented. In this review, we summarize the development of dynamic and deformable DNA nanostructures from a mechanical perspective. We present deformation mechanisms such as single-stranded DNA hinges with lock-and-release pairs, jack edges, helicity modulation, and external loading. Theoretical and computational models are discussed for understanding their associated deformations and mechanics. We elucidate the pros and cons of each model and recommend design processes based on the models. The design guidelines should be useful for those who have limited knowledge in mechanics as well as expert DNA designers.

Inhalation delivery of nucleic acid gene therapies in preclinical drug development

INTRODUCTION

Inhaled gene therapy programs targeting diseases of the lung have seen increasing interest in recent years, though as of yet no product has successfully entered the market. Preclinical research to support such programs is critically important in maximizing the chances of developing successful candidates.

AREAS COVERED

Aspects of inhalation delivery of gene therapies are reviewed, with a focus on preclinical research in animal models. Various barriers to inhalation delivery of gene therapies are discussed, including aerosolization stresses, aerosol behavior in the respiratory tract, and disposition processes post-deposition. Important aspects of animal models are considered, including determinations of biologically relevant determinations of dose and issues related to translatability.

EXPERT OPINION

Development of clinically-efficacious inhaled gene therapies has proven difficult owing to numerous challenges. Fit-for-purpose experimental and analytical methods are necessary for determinations of biologically relevant doses in preclinical animal models. Further developments in disease-specific animal models may aid in improving the translatability of results in future work, and we expect to see accelerated interests in inhalation gene therapies for various diseases. Sponsors, researchers, and regulators are encouraged to engage in early and frequent discussion regarding candidate therapies, and additional dissemination of preclinical methodologies would be of immense value in avoiding common pitfalls.

Horizontal Magnetic Tweezers to Directly Measure the Force-Velocity Relationship for Multiple Kinesin Motors

Transport of intracellular cargo along cytoskeletal filaments is often achieved by the concerted action of multiple motor molecules. While single-molecule studies have provided profound insight into the mechano-chemical principles and force generation of individual motors, studies on multi-motor systems are less advanced. Here, a horizontal magnetic-tweezers setup is applied, capable of producing up to 150 pN of horizontal force onto 2.8 µm superparamagnetic beads, to motor-propelled cytoskeletal filaments. It is found that kinesin-1 driven microtubules decorated with individual beads display frequent transitions in their gliding velocities which we attribute to dynamic changes in the number of engaged motors. Applying defined temporal force-ramps the force-velocity relationship is directly measured for multi-motor transport. It is found that the stall forces of individual motors are approximately additive and collective backward motion of the transport system under super-stall forces is observed. The magnetic-tweezers apparatus is expected to be readily applicable to a wide range of molecular and cellular motility assays.

Type 2B von Willebrand disease mutations differentially perturb autoinhibition of the A1 domain

Type 2B von Willebrand disease (VWD) is an inherited bleeding disorder in which a subset of point mutations in the von Willebrand factor (VWF) A1 domain and recently identified autoinhibitory module (AIM) cause spontaneous binding to glycoprotein Ibα (GPIbα) on the platelet surface. All reported type 2B VWD mutations share this enhanced binding; however, type 2B VWD manifests as variable bleeding complications and platelet levels in patients, depending on the underlying mutation. Understanding how these mutations localizing to a similar region can result in such disparate patient outcomes is essential for detailing our understanding of VWF regulatory and activation mechanisms. In this study, we produced recombinant glycosylated AIM-A1 fragments bearing type 2B VWD mutations and examined how each mutation affects the A1 domain's thermodynamic stability, conformational dynamics, and biomechanical regulation of the AIM. We found that the A1 domain with mutations associated with severe bleeding occupy a higher affinity state correlating with enhanced flexibility in the secondary GPIbα-binding sites. Conversely, mutation P1266L, associated with normal platelet levels, has similar proportions of high-affinity molecules to wild-type (WT) but shares regions of solvent accessibility with both WT and other type 2B VWD mutations. V1316M exhibited exceptional instability and solvent exposure compared with all variants. Lastly, examination of the mechanical stability of each variant revealed variable AIM unfolding. Together, these studies illustrate that the heterogeneity among type 2B VWD mutations is evident in AIM-A1 fragments.

Investigation of Soft Matter Nanomechanics by Atomic Force Microscopy and Optical Tweezers: A Comprehensive Review

Soft matter exhibits a multitude of intrinsic physico-chemical attributes. Their mechanical properties are crucial characteristics to define their performance. In this context, the rigidity of these systems under exerted load forces is covered by the field of biomechanics. Moreover, cellular transduction processes which are involved in health and disease conditions are significantly affected by exogenous biomechanical actions. In this framework, atomic force microscopy (AFM) and optical tweezers (OT) can play an important role to determine the biomechanical parameters of the investigated systems at the single-molecule level. This review aims to fully comprehend the interplay between mechanical forces and soft matter systems. In particular, we outline the capabilities of AFM and OT compared to other classical bulk techniques to determine nanomechanical parameters such as Young's modulus. We also provide some recent examples of nanomechanical measurements performed using AFM and OT in hydrogels, biopolymers and cellular systems, among others. We expect the present manuscript will aid potential readers and stakeholders to fully understand the potential applications of AFM and OT to soft matter systems.

Siloxane Molecules: Nonlinear Elastic Behavior and Fracture Characteristics

Fracture phenomena in soft materials span multiple length and time scales. This poses a major challenge in computational modeling and predictive materials design. To pass quantitatively from molecular to continuum scales, a precise representation of the material response at the molecular level is vital. Here, we derive the nonlinear elastic response and fracture characteristics of individual siloxane molecules using molecular dynamics (MD) studies. For short chains, we find deviations from classical scalings for both the effective stiffness and mean chain rupture times. A simple model of a nonuniform chain of Kuhn segments captures the observed effect and agrees well with MD data. We find that the dominating fracture mechanism depends on the applied force scale in a nonmonotonic fashion. This analysis suggests that common polydimethylsiloxane (PDMS) networks fail at cross-linking points. Our results can be readily lumped into coarse-grained models. Although focusing on PDMS as a model system, our study presents a general procedure to pass beyond the window of accessible rupture times in MD studies employing mean first passage time theory, which can be exploited for arbitrary molecular systems.

A predictive model for the thermomechanical melting transition of double stranded DNA

By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical response of DNA under stretching at variable values of temperature, number of base pairs and intrachains and interchains bonds stiffness. In order to compare elasticity and temperature effects, we first analyze the system in the zero temperature mechanical limit, important to describe several experimental effects including possible hysteresis. We then analyze temperature effects in the framework of equilibrium Statistical Mechanics. In particular, we obtain an analytical expression for the temperature-dependent melting force and unzipping assigned displacement in the thermodynamical limit, also depending on the relative stability of intra vs. inter molecular bonds. Such results coincide with the purely mechanical model in the limit of zero temperature and with the denaturation temperature that we obtain with the classical transfer integral method. Based on our analytical results, we obtain explicitly phase diagrams and cooperativity parameters, where also discreteness effect can be accounted for. The obtained results are successfully applied in reproducing the thermomechanical experimental melting of DNA and the response of DNA hairpins. Due to the generality of the model, exemplified in the proposed analysis of both overstretching and unzipping experiments, we argue that the proposed approach can be extended to other thermomechanically induced molecular melting phenomena. STATEMENT OF SIGNIFICANCE: We obtain a fully analytical description of the complex wiggly energy landscape of two stranded macromolecules under unzipping loading. Based on Equilibrium Statistical Mechanics, we describe the combined thermomechanical effects and the melting transition of double stranded molecules such as nucleic acids. This is proved by quantitatively predicting the experimental behavior of both melting of DNA and DNA hairpins opening. While analytical results have been previously attained under special conditions on the relative stiffness of the covalent vs. non-covalent bonds of the base pairs, our model is completely general in this respect, thus representing a tool in the perspective of the design at the molecular scale. We show that the obtained model can be fully inscribed in the theory of phase transitions giving a new interpretation of the thermomechanical behavior of double stranded molecules.

Engineered Spore-Forming Bacillus as a Microbial Vessel for Long-Term DNA Data Storage

DNA data storage technology may supersede conventional chip or magnetic data storage medium, providing long-term stability, high density, and sustainable storage. Due to its error-correcting capability, DNA data stored in living organisms exhibits high fidelity in information replication. Here we report the development of a Bacillus chassis integrated with an inducible artificially assembled bacterial chromosome to facilitate random data access. We generated three sets of data in the form of DNA sequences using a rudimentary coding system accessible by the regulatory promoter. Sporulated Bacillus harboring the genes were used for long-term storage, where viability assays of spores were subjected to harsh environmental stresses to evaluate the data storage stability. The data accuracy remained above 99% after high temperature and oxidative stress treatment, whereas UV irradiation treatment provided above 96% accuracy. The developed Bacillus chassis and artificial chromosome facilitate the long-term storage of larger datum volume by using other DNA digital encoding and decoding programs.

Mechanical Constraint Effect on DNA Persistence Length

Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning's statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA.

Mechanical deformation behaviors and structural properties of ligated DNA crystals

DNA self-assembly has emerged as a powerful strategy for constructing complex nanostructures. While the mechanics of individual DNA strands have been studied extensively, the deformation behaviors and structural properties of self-assembled architectures are not well understood. This is partly due to the small dimensions and limited experimental methods available. DNA crystals are macroscopic crystalline structures assembled from nanoscale motifs via sticky-end association. The large DNA constructs may thus be an ideal platform to study structural mechanics. Here, we investigate the fundamental mechanical properties and behaviors of ligated DNA crystals made of tensegrity triangular motifs. We perform coarse-grained molecular dynamics simulations and confirm the results with nanoindentation experiments using atomic force microscopy. We observe various deformation modes, including untension, linear elasticity, duplex dissociation, and single-stranded component stretch. We find that the mechanical properties of a DNA architecture are correlated with those of its components. However, the structure shows complex behaviors which may not be predicted by components alone and the architectural design must be considered.

Autoinhibitory module underlies species difference in shear activation of von Willebrand factor

BACKGROUND

Von Willebrand factor (VWF) is a multimeric plasma protein that bridges the gap between vessel injury and platelet capture at high shear rates. Under high shear or tension, VWF can become activated upon the unfolding of its autoinhibitory module (AIM). AIM unfolding exposes the A1 domain, allowing for binding to platelet glycoprotein (GP)Ibα to initiate primary hemostasis. The characteristics of the AIM and its inhibitory properties within mouse VWF are unknown.

OBJECTIVES

To determine and characterize the autoinhibitory properties of mouse VWF.

METHODS

Recombinant mouse VWF A1 fragments containing or lacking the flanking regions around the A1 domain were generated. We tested the ability of these fragments to bind to human or mouse GPIbα and platelets. We compared the unfolding of mouse AIM-A1 to human AIM-A1 by single-molecule force spectroscopy.

RESULTS

Recombinant mouse AIM-A1 binds with higher affinity to GPIbα than its human counterpart. Recombinant mouse proteins lacking part of the AIM show increased binding to GPIbα. Activated A1 fragments lacking the AIM can effectively agglutinate platelets across the species barrier. Using single-molecule force spectroscopy, we determined that the mouse AIM unfolds under forces similar to the human AIM. Additionally, the human AIM paired with mouse A1 largely recapitulates the behavior of human AIM-A1.

CONCLUSIONS

Our results suggest that the regulation of VWF-GPIbα binding has been specifically tuned to work optimally in different rheological architectures. Differences in the AIM sequence may contribute to the difference in VWF shear response between human and mice.

Search and processing of Holliday junctions within long DNA by junction-resolving enzymes

Resolution of Holliday junctions is a critical intermediate step of homologous recombination in which junctions are processed by junction-resolving endonucleases. Although binding and cleavage are well understood, the question remains how the enzymes locate their substrate within long duplex DNA. Here we track fluorescent dimers of endonuclease I on DNA, presenting the complete single-molecule reaction trajectory for a junction-resolving enzyme finding and cleaving a Holliday junction. We show that the enzyme binds remotely to dsDNA and then undergoes 1D diffusion. Upon encountering a four-way junction, a catalytically-impaired mutant remains bound at that point. An active enzyme, however, cleaves the junction after a few seconds. Quantitative analysis provides a comprehensive description of the facilitated diffusion mechanism. We show that the eukaryotic junction-resolving enzyme GEN1 also undergoes facilitated diffusion on dsDNA until it becomes located at a junction, so that the general resolution trajectory is probably applicable to many junction resolving enzymes.

Active and thermal fluctuations in multi-scale polymer structure and dynamics

The presence of athermal noise or biological fluctuations control and maintain crucial life-processes. In this work, we present an exact analytical treatment of the dynamic behavior of a flexible polymer chain that is subjected to both thermal and active forces. Our model for active forces incorporates temporal correlation associated with the characteristic time scale and processivity of enzymatic function (driven by ATP hydrolysis), leading to an active-force time scale that competes with relaxation processes within the polymer chain. We analyze the structure and dynamics of an active-Brownian polymer using our exact results for the dynamic structure factor and the looping time for the chain ends. The spectrum of relaxation times within a polymer chain implies two different behaviors at small and large length scales. Small length-scale relaxation is faster than the active-force time scale, and the dynamic and structural behavior at these scales are oblivious to active forces and, are thus governed by the true thermal temperature. Large length-scale behavior is governed by relaxation times that are much longer than the active-force time scale, resulting in an effective active-Brownian temperature that dramatically alters structural and dynamic behavior. These complex multi-scale effects imply a time-dependent temperature that governs living and non-equilibrium systems, serving as a unifying concept for interpreting and predicting their physical behavior.

Temperature-dependent elastic properties of DNA

Knowledge of the elastic properties, e.g., the persistence length or interphosphate distance, of single-stranded (ss) and double-stranded (ds) DNA under different experimental conditions is critical to characterizing molecular reactions studied with single-molecule techniques. While previous experiments have addressed the dependence of the elastic parameters upon varying ionic strength and contour length, temperature-dependent effects are less studied. Here, we examine the temperature-dependent elasticity of ssDNA and dsDNA in the range 5°C-50°C using a temperature-jump optical trap. We find a temperature softening for dsDNA and a temperature stiffening for ssDNA. Our results highlight the need for a general theory explaining the phenomenology observed.

The primeval optical evolving matter by optical binding inside and outside the photon beam

Optical binding has recently gained considerable attention because it enables the light-induced assembly of many-body systems; however, this phenomenon has only been described between directly irradiated particles. Here, we demonstrate that optical binding can occur outside the focal spot of a single tightly focused laser beam. By trapping at an interface, we assemble up to three gold nanoparticles with a linear arrangement which fully-occupies the laser focus. The trapping laser is efficiently scattered by this linear alignment and interacts with particles outside the focus area, generating several discrete arc-shape potential wells with a half-wavelength periodicity. Those external nanoparticles inside the arcs show a correlated motion not only with the linear aligned particles, but also between themselves even both are not directly illuminated. We propose that the particles are optically bound outside the focal spot by the back-scattered light and multi-channel light scattering, forming a dynamic optical binding network.

Nanoscale packing of DNA tiles into DNA macromolecular lattices

Nanoscale double-crossovers (DX), antiparallel (A), and even half-turns-perimeter (E) DNA tiles (DAE-tiles) with rectangular shapes can be packed into large arrays of micrometer-scale lattices. But the features and mechanical strength of DNA assembly made from differently shaped large-sized DAE DNA tiles and the effects of various geometries on the final DNA assembly are yet to be explored. Herein, we focused on examining DNA lattices synthesized from DX bi-triangular, DNA tiles (T) with concave and convex regions along the perimeter of the tiles. The bi-triangular DNA tiles "T(A) and T(B)" were synthesized by self-assembling the freshly prepared short circular scaffold (S) strands "S(A) and S(B)", each of 106 nucleotides (NT) lengths. The tiles "T(A) and T(B)" were then coupled together to get assembled via sticky ends. It resulted in the polymerization of DNA tiles into large-sized DNA lattices with giant micrometer-scale dimensions to form the "T(A) + T(B)" assembly. These DNA macro-frameworks were visualized "in the air" under atomic force microscopy (AFM) employing tapping mode. We have characterized how curvature in DNA tiles may undergo transitions and transformations to adjust the overall torque, strain, twists, and the topology of the final self-assembly array of DNA tiles. According to our results, our large-span DX tiles assembly "T(A) + T(B)" despite the complicated curvatures and mechanics, was successfully packed into giant DNA lattices of the width of 30-500 nm and lengths of 500 nm to over 10 μm. Conclusively, the micrometer-scale "T(A) + T(B)" framework assembly was rigid, stable, stiff, and exhibited enough tensile strength to form monocrystalline lattices.

Quantum machine learning corrects classical forcefields: Stretching DNA base pairs in explicit solvent

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange-correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software.

Unfolding of crumpled thin sheets

Crumpled thin sheets are complex fractal structures whose physical properties are influenced by a hierarchy of ridges. In this paper, we report experiments that measure the stress-strain relation and show the coexistence of phases in the stretching of crumpled surfaces. The pull stress showed a change from a linear Hookean regime to a sublinear scaling with an exponent of 0.65±0.03, which is identified with the Hurst exponent of the crumpled sheets. The stress fluctuations are studied. The statistical distribution of force peaks is analyzed. It is shown that the unpacking of crumpled sheets is guided by a hierarchical order of ridges.

Optimal control with a strong harmonic trap

Quadratic trapping potentials are widely used to experimentally probe biopolymers and molecular machines and drive transitions in steered molecular-dynamics simulations. Approximating energy landscapes as locally quadratic, we design multidimensional trapping protocols that minimize dissipation. The designed protocols are easily solvable and applicable to a wide range of systems. The approximation does not rely on either fast or slow limits and is valid for any duration provided the trapping potential is sufficiently strong. We demonstrate the utility of the designed protocols with a simple model of a periodically driven rotary motor. Our results elucidate principles of effective single-molecule manipulation and efficient nonequilibrium free-energy estimation.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Stretching of Long Double-Stranded DNA and RNA Described by the Same Approach

We propose an approach to help interpret polymer force-extension curves that exhibit plateau regimes. When coupled to a bead-spring dynamic model, the approach accurately reproduces a variety of experimental force-extension curves of long double-stranded DNA and RNA, including torsionally constrained and unconstrained DNA and negatively supercoiled DNA. A key feature of the model is a specific nonconvex energy function of the spring. We provide an algorithm to obtain the five required parameters of the model from experimental force-extension curves. The applicability of the approach to the force-extension curves of double-stranded (ds) DNA of variable GC content as well as to a DNA/RNA hybrid structure is explored and confirmed. We use the approach to explain counterintuitive sequence-dependent trends and make predictions. In the plateau region of the force-extension curves, our molecular dynamics simulations show that the polymer separates into a mix of weakly and strongly stretched states without forming macroscopically distinct phases. The distribution of these states is predicted to depend on the sequence.

Modeling multiple duplex DNA attachments in a force-extension experiment

Optical tweezers-based DNA stretching often relies on tethering a single end-activated DNA molecule between optically manipulated end-binding beads. Measurement success can depend on DNA concentration. At lower DNA concentrations tethering is less common, and many trials may be required to observe a single-molecule stretch. At higher DNA concentrations tethering is more common; however, the resulting force-extensions observed are more complex and may vary from measurement to measurement. Typically these more complex results are attributed to the formation of multiple tethers between the beads; however, to date there does not appear to have been a critical examination of this hypothesis or the potential usefulness of such data. Here we examine stretches at a higher DNA concentration and use analysis and simulation to show how the more complex force-extensions observed can be understood in terms of multiple DNA attachments.

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.

Kinetics of DNA looping by Anabaena sensory rhodopsin transducer (ASRT) by using DNA cyclization assay

DNA cyclization assay together with single-molecule FRET was employed to monitor protein-mediated bending of a short dsDNA (~ 100 bp). This method provides a simple and easy way to monitor the structural change of DNA in real-time without necessitating prior knowledge of the molecular structures for the optimal dye-labeling. This assay was applied to study how Anabaena sensory rhodopsin transducer (ASRT) facilitates loop formation of DNA as a possible mechanism for gene regulation. The ASRT-induced DNA looping was maximized at 50 mM of Na⁺, while Mg²⁺ also played an essential role in the loop formation.

Modulating the chemo-mechanical response of structured DNA assemblies through binding molecules

Recent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.

Virus self-assembly proceeds through contact-rich energy minima

Self-assembly of supramolecular complexes such as viral capsids occurs prominently in nature. Nonetheless, the mechanisms underlying these processes remain poorly understood. Here, we uncover the assembly pathway of hepatitis B virus (HBV), applying fluorescence optical tweezers and high-speed atomic force microscopy. This allows tracking the assembly process in real time with single-molecule resolution. Our results identify a specific, contact-rich pentameric arrangement of HBV capsid proteins as a key on-path assembly intermediate and reveal the energy balance of the self-assembly process. Real-time nucleic acid packaging experiments show that a free energy change of ~1.4 k_BT per condensed nucleotide is used to drive protein oligomerization. The finding that HBV assembly occurs via contact-rich energy minima has implications for our understanding of the assembly of HBV and other viruses and also for the development of new antiviral strategies and the rational design of self-assembling nanomaterials.

DNA origami nano-mechanics

Invention of DNA origami has transformed the fabrication and application of biological nanomaterials. In this review, we discuss DNA origami nanoassemblies according to their four fundamental mechanical properties in response to external forces: elasticity, pliability, plasticity and stability. While elasticity and pliability refer to reversible changes in structures and associated properties, plasticity shows irreversible variation in topologies. The irreversible property is also inherent in the disintegration of DNA nanoassemblies, which is manifested by its mechanical stability. Disparate DNA origami devices in the past decade have exploited the mechanical regimes of pliability, elasticity, and plasticity, among which plasticity has shown its dominating potential in biomechanical and physiochemical applications. On the other hand, the mechanical stability of the DNA origami has been used to understand the mechanics of the assembly and disassembly of DNA nano-devices. At the end of this review, we discuss the challenges and future development of DNA origami nanoassemblies, again, from these fundamental mechanical perspectives.

A nanoscale DNA force spectrometer capable of applying tension and compression on biomolecules

Single molecule force spectroscopy is a powerful approach to probe the structure, conformational changes, and kinetic properties of biological and synthetic macromolecules. However, common approaches to apply forces to biomolecules require expensive and cumbersome equipment and relatively large probes such as beads or cantilevers, which limits their use for many environments and makes integrating with other methods challenging. Furthermore, existing methods have key limitations such as an inability to apply compressive forces on single molecules. We report a nanoscale DNA force spectrometer (nDFS), which is based on a DNA origami hinge with tunable mechanical and dynamic properties. The angular free energy landscape of the nDFS can be engineered across a wide range through substitution of less than 5% of the strand components. We further incorporate a removable strut that enables reversible toggling of the nDFS between open and closed states to allow for actuated application of tensile and compressive forces. We demonstrate the ability to apply compressive forces by inducing a large bend in a 249bp DNA molecule, and tensile forces by inducing DNA unwrapping of a nucleosome sample. These results establish a versatile tool for force spectroscopy and robust methods for designing nanoscale mechanical devices with tunable force application.