Concentrated DNA Rheology and Microrheology

From Bioreactor to Bulk Rheology: Achieving Scalable Production of Highly Concentrated Circular DNA

DNA serves as a model system in polymer physics due to its ability to be obtained as a uniform polymer with controllable topology and nonequilibrium behavior. Currently, a major obstacle in the widespread adoption of DNA is obtaining it on a scale and cost basis that accommodates bulk rheology and high-throughput screening. To address this, recent advancements in bioreactor-based plasmid DNA production is coupled with anion exchange chromatography producing a unified approach to generating gram-scale quantities of monodisperse DNA. With this method, 1.1 grams of DNA is obtained per batch to generate solutions with concentrations up to 116 mg mL-1. This solution of uniform supercoiled and relaxed circular plasmid DNA, is roughly 69 times greater than the overlap concentration. The utility of this method is demonstrated by performing bulk rheology measurements at sample volumes up to 1 mL on DNA of different lengths, topologies, and concentrations. The measured elastic moduli are orders of magnitude larger than those previously reported for DNA and allowed for the construction of a time-concentration superposition curve that spans 12 decades of frequency. Ultimately, these results can provide important insights into the dynamics of ring polymers and the nature of highly condensed DNA dynamics.

Passive and Active Microrheology for Biomedical Systems

Microrheology encompasses a range of methods to measure the mechanical properties of soft materials. By characterizing the motion of embedded microscopic particles, microrheology extends the probing length scale and frequency range of conventional bulk rheology. Microrheology can be characterized into either passive or active methods based on the driving force exerted on probe particles. Tracer particles are driven by thermal energy in passive methods, applying minimal deformation to the assessed medium. In active techniques, particles are manipulated by an external force, most commonly produced through optical and magnetic fields. Small-scale rheology holds significant advantages over conventional bulk rheology, such as eliminating the need for large sample sizes, the ability to probe fragile materials non-destructively, and a wider probing frequency range. More importantly, some microrheological techniques can obtain spatiotemporal information of local microenvironments and accurately describe the heterogeneity of structurally complex fluids. Recently, there has been significant growth in using these minimally invasive techniques to investigate a wide range of biomedical systems both in vitro and in vivo. Here, we review the latest applications and advancements of microrheology in mammalian cells, tissues, and biofluids and discuss the current challenges and potential future advances on the horizon.

Diffusing wave microrheology of highly scattering concentrated monodisperse emulsions

Motivated by improvements in diffusing wave spectroscopy (DWS) for nonergodic, highly optically scattering soft matter and by cursory treatment of collective scattering effects in prior DWS microrheology experiments, we investigate the low-frequency plateau elastic shear moduli [Formula: see text] of concentrated, monodisperse, disordered oil-in-water emulsions as droplets jam. In such experiments, the droplets play dual roles both as optical probes and as the jammed objects that impart shear elasticity. Here, we demonstrate that collective scattering significantly affects DWS mean-square displacements (MSDs) in dense colloidal emulsions. By measuring and analyzing the scattering mean free path as a function of droplet volume fraction φ, we obtain a φ-dependent average structure factor. We use this to correct DWS MSDs by up to a factor of 4 and then calculate [Formula: see text] predicted by the generalized Stokes-Einstein relation. We show that DWS-microrheological [Formula: see text] agrees well with mechanically measured [Formula: see text] over about three orders of magnitude when droplets are jammed but only weakly deformed. Moreover, both of these measurements are consistent with predictions of an entropic-electrostatic-interfacial (EEI) model, based on quasi-equilibrium free-energy minimization of disordered, screened-charge-stabilized, deformable droplets, which accurately describes prior mechanical measurements of [Formula: see text] made on similar disordered monodisperse emulsions over a wide range of droplet radii and φ. This very good quantitative agreement between DWS microrheology, mechanical rheometry, and the EEI model provides a comprehensive and self-consistent view of weakly jammed emulsions. Extensions of this approach may improve DWS microrheology on other systems of dense, jammed colloids that are highly scattering.

Decorrelation correction for nanoparticle tracking analysis of dilute polydisperse suspensions in bulk flow

Nanoparticle tracking analysis, a multiprobe single particle tracking technique, is a widely used method to quickly determine the concentration and size distribution of colloidal particle suspensions. Many popular tools remove non-Brownian components of particle motion by subtracting the ensemble-average displacement at each time step, which is termed dedrifting. Though critical for accurate size measurements, dedrifting is shown here to introduce significant biasing error and can fundamentally limit the dynamic range of particle size that can be measured for dilute heterogeneous suspensions such as biological extracellular vesicles. We report a more accurate estimate of particle mean-square displacement, which we call decorrelation analysis, that accounts for correlations between individual and ensemble particle motion, which are spuriously introduced by dedrifting. Particle tracking simulation and experimental results show that this approach more accurately determines particle diameters for low-concentration polydisperse suspensions when compared with standard dedrifting techniques.

Local collective motion analysis for multi-probe dynamic imaging and microrheology

Dynamical artifacts, such as mechanical drift, advection, and hydrodynamic flow, can adversely affect multi-probe dynamic imaging and passive particle-tracking microrheology experiments. Alternatively, active driving by molecular motors can cause interesting non-Brownian motion of probes in local regions. Existing drift-correction techniques, which require large ensembles of probes or fast temporal sampling, are inadequate for handling complex spatio-temporal drifts and non-Brownian motion of localized domains containing relatively few probes. Here, we report an analytical method based on local collective motion (LCM) analysis of as few as two probes for detecting the presence of non-Brownian motion and for accurately eliminating it to reveal the underlying Brownian motion. By calculating an ensemble-average, time-dependent, LCM mean square displacement (MSD) of two or more localized probes and comparing this MSD to constituent single-probe MSDs, we can identify temporal regimes during which either thermal or athermal motion dominates. Single-probe motion, when referenced relative to the moving frame attached to the multi-probe LCM trajectory, provides a true Brownian MSD after scaling by an appropriate correction factor that depends on the number of probes used in LCM analysis. We show that LCM analysis can be used to correct many different dynamical artifacts, including spatially varying drifts, gradient flows, cell motion, time-dependent drift, and temporally varying oscillatory advection, thereby offering a significant improvement over existing approaches.

Parallel temperature-dependent microrheological measurements in a microfluidic chip

Microfluidic stickers are used as a sample environment to measure the microrheology of monoclonal antibody (mAb) protein solutions. A Peltier-based microscope stage is implemented and validated, and is capable of controlling the sample temperature over the range 0.9-40 °C. The design accounts for heat transfer to and from the objective, controls the sample environment humidity to mitigate condensation, and provides adequate damping to reduce vibration from the cooling system. A concentrated sucrose solution is used as a standard sample to provide an in situ temperature measurement by the Stokes-Einstein-Sutherland relation. By combining microfluidic stickers and microrheology, 72 temperature-concentration viscosity measurements of mAb solutions can be made in 1 day, a significant increase in throughput over conventional rheometry.

On the correction of errors in some multiple particle tracking experiments

A common source of error in particle tracking experiments is identified, and a theoretical model for the magnitude of the error is offered. In many cases, the error is small, but in systems where only a few particles are being tracked, the measured mean squared displacement can be up to 50% smaller than the actual value. The theoretical model predictions are confirmed using numerical simulations and experimental observations of polystyrene microspheres in water.

Control of the flow properties of DNA by topoisomerase II and its targeting inhibitor

The flow properties of DNA are important for understanding cell division and, indirectly, cancer therapy. DNA topology controlling enzymes such as topoisomerase II are thought to play an essential role. We report experiments showing how double-strand passage facilitated by topoisomerase II controls DNA rheology. For this purpose, we have measured the elastic storage and viscous loss moduli of a model system comprising bacteriophage λ-DNA and human topoisomerase IIα using video tracking of the Brownian motion of colloidal probe particles. We found that the rheology is critically dependent on the formation of temporal entanglements among the DNA molecules with a relaxation time of ∼1 s. We observed that topoisomerase II effectively removes these entanglements and transforms the solution from an elastic physical gel to a viscous fluid depending on the consumption of ATP. A second aspect of this study is the effect of the generic topoisomerase II inhibitor adenylyl-imidodiphosphate (AMP-PNP). In mixtures of AMP-PNP and ATP, the double-strand passage reaction gets blocked and progressively fewer entanglements are relaxed. A total replacement of ATP by AMP-PNP results in a temporal increase in elasticity at higher frequencies, but no transition to an elastic gel with fixed cross-links.

The mechanics of F-actin microenvironments depend on the chemistry of probing surfaces

To understand the microscopic mechanical properties of actin networks, we monitor the motion of embedded particles with controlled surface properties. The highly resolved Brownian motions of these particles reveal the viscoelastic character of the microenvironments around them. In both non-cross-linked and highly cross-linked actin networks, particles that bind F-actin report viscoelastic moduli comparable to those determined by macroscopic rheology experiments. By contrast, particles modified to prevent actin binding have weak microenvironments that are surprisingly insensitive to the introduction of filament cross-links. Even when adjacent in the same cross-linked gel, actin-binding and nonbinding particles report viscoelastic moduli that differ by two orders of magnitude at low frequencies (0.5-1.5 rad/s) but converge at high frequencies (> 10(4) rad/s). For all particle chemistries, electron and light microscopies show no F-actin recruitment or depletion, so F-actin microheterogeneities cannot explain the deep penetration (approximately 100 nm) of nonbinding particles. Instead, we hypothesize that a local depletion of cross-linking around nonbinding particles explains the phenomena. With implications for organelle mobility in cells, our results show that actin binding is required for microenvironments to reflect macroscopic properties, and conversely, releasing actin enhances particle mobility beyond the effects of mere biochemical untethering.

Mechanics of living cells measured by laser tracking microrheology

To establish laser-tracking microrheology (LTM) as a new technique for quantifying cytoskeletal mechanics, we measure viscoelastic moduli with wide bandwidth (5 decades) within living cells. With the first subcellular measurements of viscoelastic phase angles, LTM provides estimates of solid versus liquid behavior at different frequencies. In LTM, the viscoelastic shear moduli are inferred from the Brownian motion of particles embedded in the cytoskeletal network. Custom laser optoelectronics provide sub-nanometer and near-microsecond resolution of particle trajectories. The kidney epithelial cell line, COS7, has numerous spherical lipid-storage granules that are ideal probes for noninvasive LTM. Although most granules are percolating through perinuclear spaces, a subset of perinuclear granules is embedded in dense viscoelastic cytoplasm. Over all time scales embedded particles exhibit subdiffusive behavior and are not merely tethered by molecular motors. At low frequencies, lamellar regions (820 +/- 520 dyne/cm(2)) are more rigid than viscoelastic perinuclear regions (330 +/- 250 dyne/cm(2), p < 0.0001), but spectra converge at high frequencies. Although the actin-disrupting agent, latrunculin A, softens and liquefies lamellae, physiological levels of F-actin, alone (11 +/- 1.2 dyne/cm(2)) are approximately 70-fold softer than lamellae. Therefore, F-actin is necessary for lamellae mechanics, but not sufficient. Furthermore, in time-lapse of apparently quiescent cells, individual lamellar granules can show approximately 4-fold changes in moduli that last >10 s. Over a broad range of frequencies (0.1-30, 000 rad/s), LTM provides a unique ability to noninvasively quantify dynamic, local changes in cell viscoelasticity.

Diffusing wave spectroscopy microrheology of actin filament networks

Filamentous actin (F-actin), one of the constituents of the cytoskeleton, is believed to be the most important participant in the motion and mechanical integrity of eukaryotic cells. Traditionally, the viscoelastic moduli of F-actin networks have been measured by imposing a small mechanical strain and quantifying the resulting stress. The magnitude of the viscoelastic moduli, their concentration dependence and strain dependence, as well as the viscoelastic nature (solid-like or liquid-like) of networks of uncross-linked F-actin, have been the subjects of debate. Although this paper helps to resolve the debate and establishes the extent of the linear regime of F-actin networks' rheology, we report novel measurements of the high-frequency behavior of networks of F-actin, using a noninvasive light-scattering based technique, diffusing wave spectroscopy (DWS). Because no external strain is applied, our optical assay generates measurements of the mechanical properties of F-actin networks that avoid many ambiguities inherent in mechanical measurements. We observe that the elastic modulus has a small magnitude, no strain dependence, and a weak concentration dependence. Therefore, F-actin alone is not sufficient to generate the elastic modulus necessary to sustain the structural rigidity of most cells or support new cellular protrusions. Unlike previous studies, our measurements show that the mechanical properties of F-actin are highly dependent on the frequency content of the deformation. We show that the loss modulus unexpectedly dominates the elastic modulus at high frequencies, which are key for fast transitions. Finally, the measured mean square displacement of the optical probes, which is also generated by DWS measurements, offers new insight into the local bending fluctuations of the individual actin filaments and shows how they generate enhanced dissipation at short time scales.