Double-Stranded DNA Diffusion in Slitlike Nanochannels

Directly Characterizing the Capture Radius of Tethered Double-Stranded DNA by Single-Molecule Nanopipette Manipulation

The tethered molecule exhibits characteristics of both free and fixed states, with the electrodynamics involved in its diffusion, electrophoresis, and stretching processes still not fully understood. We developed a Single-Molecule Manipulation, Identification, and Length Examination (SMILE) system by integrating piezoelectric devices with nanopipettes. This system enabled successful capture and stretching of tethered double-stranded DNA within the nanopore. Our research unveiled distinct capture (rcapture) and stretch radii (rstretch) surrounding the DNA's anchor point. Notably, consistent ratios of capture radius for DNA of varying lengths (2k, 4k, and 6k base pairs) were observed across different capturing voltages, approximately 1:1.4:1.83, showing a resemblance to their gyration radius ratios. However, the ratios of stretch radius are consistent to their contour length (L0), with the stretching ratio (rstretch/L0) increasing from 70 to 90% as the voltage rose from 100 to 1000 mV. Additionally, through numerical simulations, we identified the origin of capture and stretch radii, determined by the entropic elasticity-induced capture barrier and the electric field-dominant escape barrier. This research introduces an innovative methodology and outlines research perspectives for a comprehensive exploration of the conformational, electrical, and diffusion characteristics of tethered molecules.

Crowding and confinement act in concert to slow DNA diffusion within cell-sized droplets

Dynamics of biological macromolecules, such as DNA, in crowded and confined environments are critical to understanding cellular processes such as transcription, infection, and replication. However, the combined effects of cellular confinement and crowding on macromolecular dynamics remain poorly understood. Here, we use differential dynamic microscopy to investigate the diffusion of large DNA molecules confined in cell-sized droplets and crowded by dextran polymers. We show that confined and crowded DNA molecules exhibit universal anomalous subdiffusion with scaling that is insensitive to the degree of confinement and crowding. However, effective DNA diffusion coefficients Deff decrease up to 2 orders of magnitude as droplet size decreases—an effect that is enhanced by increased crowding. We mathematically model the coupling of crowding and confinement by combining polymer scaling theories with confinement-induced depletion effects. The generality and tunability of our system and models render them applicable to elucidating wide-ranging crowded and confined systems.

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DNA diffusion measured in cell-sized droplets with differential dynamic microscopy

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Combination of crowding and confinement leads to subdiffusion and slowing

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Diffusion coefficients of DNA decrease strongly with decreasing droplet size

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Polymer scaling theories and depletion effects predict observed dynamics

Diffusive dynamics of charged nanoparticles in convex lens-induced confinement

Transport through heterogeneous confined geometries is encountered in many processes and applications such as filtration, drug delivery, and enhanced oil recovery. We have used differential dynamic microscopy (DDM) and particle tracking to investigate dynamics of 36 nm negatively-charged polystyrene particles in convex lens-induced confinement (CLiC). The confinement gap height was controlled from 0.085 μm to 3.6 mm by sandwiching the aqueous particle solution between a glass coverslip and a convex lens using a homemade sample holder. With an inverted fluorescence microscope, sequences of micrographs were taken at various radial positions and gap heights for five particle concentrations (i.e. φ = 0.5 × 10^-5, 1 × 10^-5, 5 × 10^-5, 10 × 10^-5, 50 × 10^-5) and ionic strengths ranging from 10^-3 to 150 mM. The resulting image structure functions were fitted with a simple exponential model to extract the ensemble-averaged diffusive dynamics. It was found that particle diffusion was more hindered as a function of increased confinement. In addition, the ensemble-averaged diffusion coefficient was found to depend on the bulk concentration, and the concentration dependence increased as a function of confinement. Increasing particle and salt concentration led to confinement-dependent adsorption onto the geometry surface. Overall, we show that CLiC devices are simple and effective and can be used to study dynamics in continuous confinement from sub 100 nm to 100's of μm. These findings could lead to better understanding of separations and interactions in confining devices.

Diffusion of Short Semiflexible DNA Polymer Chains in Strong and Moderate Confinement

In many technological applications, DNA is confined within nanoenvironments that are smaller than the size of the unconfined polymer in solution. However, the dependence of the diffusion coefficient on molecular weight and characteristic confinement dimension remains poorly understood in this regime. Here, convex lens-induced confinement (CLiC) was leveraged to examine how the diffusion of short DNA fragments varied as a function of slit height by using single-molecule fluorescence tracking microscopy. The diffusion coefficient followed approximate power law behavior versus confinement height, with exponents of 0.27 ± 0.01, 0.32 ± 0.02, and 0.42 ± 0.06 for 692, 1343, and 2686 base pair chains, respectively. The weak dependence on slit height suggests that shorter semiflexible chains may adopt increasingly rodlike conformations and therefore experience weaker excluded-volume interactions as the confinement dimension is reduced. The diffusion coefficient versus molecular weight also exhibited apparent power law behavior, with exponents that varied slightly (from -0.89 to -0.85) with slit height, consistent with hydrodynamic interactions intermediate between Rouse and Zimm model predictions.

Translocation of DNA through Ultrathin Nanoslits

2D nanoslit devices, where two crystals with atomically flat surfaces are separated by only a few nanometers, have attracted considerable attention because their tunable control over the confinement allows for the discovery of unusual transport behavior of gas, water, and ions. Here, the passage of double-stranded DNA molecules is studied through nanoslits fabricated from exfoliated 2D materials, such as graphene or hexagonal boron nitride, and the DNA polymer behavior is examined in this tight confinement. Two types of events are observed in the ionic current: long current blockades that signal DNA translocation and short spikes where DNA enters the slits but withdraws. DNA translocation events exhibit three distinct phases in their current-blockade traces-loading, translation, and exit. Coarse-grained molecular dynamics simulation allows the different polymer configurations of these phases to be identified. DNA molecules, including folds and knots in their polymer structure, are observed to slide through the slits with near-uniform velocity without noticeable frictional interactions of DNA with the confining graphene surfaces. It is anticipated that this new class of 2D-nanoslit devices will provide unique ways to study polymer physics and enable lab-on-a-chip biotechnology.

Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity

Here we present a pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution. Using a principle familiar from classic devices based on soft-lithography, the system uses pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit. We use this system to quantify the interactions of multiple confined DNA chains, a key problem in polymer physics with important implications for nanofluidic device performance and DNA partitioning/organization in bacteria and the eukaryotes. In particular, we focus on the problem of two-chain confinement, using differential staining of the chains to independently assess the chain conformation, determine the degree of partitioning/mixing in the cavities and assess coupled diffusion of the chain center-of-mass positions. We find that confinement of more than one chain in the cavity can have a drastic impact on the polymer dynamics and conformation.

Relaxation of surface-tethered polymers under moderate confinement

We study the relaxation of surface-tethered polymers in microchannels under moderate confinement (i.e. h ∼ Rg, where h is the channel height and Rg is the radius of gyration of the polymer) by experiments with fluorescence-marked DNA molecules and coupled lattice-Boltzmann/molecular dynamics simulations. The determined scaling exponent suggests that the relaxation is dominated by Zimm-dynamics with significant intra-chain hydrodynamic interactions. The relaxation of the DNA molecules is slower in shallower channels, indicating a pronounced effect of confinement on the longest relaxation time. An experimental correlation is obtained for the longest relaxation time as a function of the molecular contour length and the channel height. Good agreement between the experimental and the simulation results is found.

Knots modify the coil-stretch transition in linear DNA polymers

We perform single-molecule DNA experiments to investigate the relaxation dynamics of knotted polymers and examine the steady-state behavior of knotted polymers in elongational fields. The occurrence of a knot reduces the relaxation time of a molecule and leads to a shift in the molecule's coil-stretch transition to larger strain rates. We measure chain extension and extension fluctuations as a function of strain rate for unknotted and knotted molecules. The curves for knotted molecules can be collapsed onto the unknotted curves by defining an effective Weissenberg number based on the measured knotted relaxation time in the low extension regime, or a relaxation time based on Rouse/Zimm scaling theories in the high extension regime. Because a knot reduces a molecule's relaxation time, we observe that knot untying near the coil-stretch transition can result in dramatic changes in the molecule's conformation. For example, a knotted molecule at a given strain rate can experience a stretch-coil transition, followed by a coil-stretch transition, after the knot partially or fully unties.

Evaluation of Blob Theory for the Diffusion of DNA in Nanochannels

We have measured the diffusivity of λ-DNA molecules in approximately square nanochannels with effective sizes ranging from 117 nm to 260 nm at moderate ionic strength. The experimental results do not agree with the non-draining scaling predicted by blob theory. Rather, the data are consistent with the predictions of previous simulations of the Kirkwood diffusivity of a discrete wormlike chain model, without the need for any fitting parameters.

Wall depletion length of a channel-confined polymer

Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well-defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths.

Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers

We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of "giant acceleration of diffusion." The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.

Polymer globule with fractal properties caused by intramolecular nanostructuring and spatial constrains

By means of computer simulation, we studied macromolecules composed of N dumbbell amphiphilic monomer units with attractive pendant groups. In poor solvents, these macromolecules form spherical globules that are dense in the case of short chains (the gyration radius RG∼N(1/3)), or hollow inside and obey the RG∼N(1/2) law when the macromolecules are sufficiently long. Due to the specific intramolecular nanostructuring, the vesicle-like globules of long amphiphilic macromolecules posses some properties of fractal globules, by which they (i) could demonstrate the same scaling statistics for the entire macromolecule and for short subchains with m monomer units and (ii) possess a specific territorial structure. Within a narrow slit, the globule loses its inner cavity, takes a disk-like shape and scales as N(1/2) for much shorter macromolecules. However, the field of end-to-end distance r(m) ∼m(1/2) dependence for subchains becomes visibly smaller. The results obtained were compared with the homopolymer case.

The polymer physics of single DNA confined in nanochannels

In recent years, applications and experimental studies of DNA in nanochannels have stimulated the investigation of the polymer physics of DNA in confinement. Recent advances in the physics of confined polymers, using DNA as a model polymer, have moved beyond the classic Odijk theory for the strong confinement, and the classic blob theory for the weak confinement. In this review, we present the current understanding of the behaviors of confined polymers while briefly reviewing classic theories. Three aspects of confined DNA are presented: static, dynamic, and topological properties. The relevant simulation methods are also summarized. In addition, comparisons of confined DNA with DNA under tension and DNA in semidilute solution are made to emphasize universal behaviors. Finally, an outlook of the possible future research for confined DNA is given.

Slowing DNA Translocation in a Nanofluidic Field-Effect Transistor

Here, we present an experimental demonstration of slowing DNA translocation across a nanochannel by modulating the channel surface charge through an externally applied gate bias. The experiments were performed on a nanofluidic field-effect transistor, which is a monolithic integrated platform featuring a 50 nm-diameter in-plane alumina nanocapillary whose entire length is surrounded by a gate electrode. The field-effect transistor behavior was validated on the gating of ionic conductance and protein transport. The gating of DNA translocation was subsequently studied by measuring discrete current dips associated with single λ-DNA translocation events under a source-to-drain bias of 1 V. The translocation speeds under various gate bias conditions were extracted by fitting event histograms of the measured translocation time to the first passage time distributions obtained from a simple 1D biased diffusion model. A positive gate bias was observed to slow the translocation of single λ-DNA chains markedly; the translocation speed was reduced by an order of magnitude from 18.4 mm/s obtained under a floating gate down to 1.33 mm/s under a positive gate bias of 9 V. Therefore, a dynamic and flexible regulation of the DNA translocation speed, which is vital for single-molecule sequencing, can be achieved on this device by simply tuning the gate bias. The device is realized in a conventional semiconductor microfabrication process without the requirement of advanced lithography, and can be potentially further developed into a compact electronic single-molecule sequencer.

Recent advancements in ion concentration polarization

Advancements in ion concentration polarization made over the past three years are highlighted.

Coil-globule transition of a single semiflexible chain in slitlike confinement

Single polymer chains undergo a phase transition from coiled conformations to globular conformations as the effective attraction between monomers becomes strong enough. In this work, we investigated the coil-globule transition of a semiflexible chain confined between two parallel plates, i.e. a slit, using the lattice model and Pruned-enriched Rosenbluth method (PERM) algorithm. We find that as the slit height decreases, the critical attraction for the coil-globule transition changes non-monotonically due to the competition of the confinement free energies of the coiled and globular states. In wide (narrow) slits, the coiled state experiences more (less) confinement free energy, and hence the transition becomes easier (more difficult). In addition, we find that the transition becomes less sharp with the decreasing slit height. Here, the sharpness refers to the sensitivity of thermodynamic quantities when varying the attraction around the critical value. The relevant experiments can be performed for DNA condensation in microfluidic devices.

Coarse-grained model of conformation-dependent electrophoretic mobility and its influence on DNA dynamics

The electrophoretic mobility of molecules such as λ-DNA depends on the conformation of the molecule. It has been shown that electrohydrodynamic interactions between parts of the molecule lead to a mobility that depends on conformation and can explain some experimental observations. We have developed a new coarse-grained model that incorporates these changes of mobility into a bead-spring chain model. Brownian dynamics simulations have been performed using this model. The model reproduces the cross-stream migration that occurs in capillary electrophoresis when pressure-driven flow is applied parallel or antiparallel to the electric field. The model also reproduces the change of mobility when the molecule is stretched significantly in an extensional field. We find that the conformation-dependent mobility can lead to a new type of unraveling of the molecule in strong fields. This occurs when different parts of the molecule have different mobilities and the electric field is large.

Rigorous study of molecular dynamics of a single dsDNA confined in a nanochannel: Introduction of a critical mobility behaviour

The essential and effective characteristics of a double-stranded DNA (dsDNA) confined in a nanochannel is revisited by employing the rigorous full numerical approach of Molecular Dynamics (MD). The deformation of dsDNA and wall-biomolecule interaction which is critical in highly confined regime has been precisely imposed in numerical simulations. The numerical approach has been justified against available theoretical outcomes. A new and general expression for DNA electrophoretic mobility versus DNA length is extracted from numerical simulation which is out of reach of experimental methods due to practical shortcomings. The newly derived expression suggests an essential correction in the previously proposed expression for the critical case of small DNA molecules and reveals an astonishingly unbeknown trend of small DNA's mobility. Sub-molecular phenomenon of dsDNA melting under the condition of large external force is also studied. Assuming strong electric field exertion, the MD approach aptly demonstrates the elaborate melting phenomenon for dsDNA in sub-molecular scale.

Kirkwood diffusivity of long semiflexible chains in nanochannel confinement

We compute the axial diffusivity of asymptotically long semiflexible polymers confined in square channels. Our calculations employ the Kirkwood approximation of the mobility tensor by combining computational fluid dynamics (CFD) calculations of the hydrodynamic tensor in channel confinement with pruned-enriched Rosenbluth method (PERM) simulations of a discrete wormlike chain model. Three key results emerge from our study. First, for the classic de Gennes regime, we confirm that Brochard and de Gennes' blob theory correctly predicts the scaling of the axial diffusivity, contrary to the conclusions of previous analyses. Second, for the extended de Gennes regime, we show that a modified blob theory, which has been used to incorporate the effect of local stiffness on DNA diffusion in nanoslits, explains the deviation from the prediction of classic blob theory for diffusion in nanochannels. Third, we provide a calculation similar to the modified blob theory to explain the relative insensitivity of the diffusivity to channel size for channels between the extended de Gennes regime and the Odijk regime, which is the most relevant regime for experiments and technological applications of DNA confinement in nanochannels. Our results are not only relevant to the dynamics of confined semiflexible polymers such as DNA, but also reveal interesting analogies between confinement in channels and slits.

Stretching self-entangled DNA molecules in elongational fields

We present experiments of self-entangled DNA molecules stretching under a planar elongational field, and their stretching dynamics are compared to identical molecules without entanglements. Self-entangled molecules stretch in a stage-wise fashion, persisting in an "arrested" state for decades of strain prior to rapidly stretching, slowing down the stretching dynamics by an order of magnitude compared to unentangled molecules. Self-entangled molecules are shown to proceed through a transient state where one or two ends of the molecule are protruding from an entangled, knotted core. This phenomenon sharply contrasts with the wide array of transient configurations shown here and by others for stretching polymers without entanglements. The rate at which self-entangled molecules stretch through this transient state is demonstrably slower than unentangled molecules, providing the first direct experimental evidence of a topological friction. These experimental observations are shown to be qualitatively and semi-quantitatively reproduced by a dumbbell model with two fitting parameters, the values of which are reasonable in light of previous experiments of knotted DNA.

Electrophoretic Mobility of Polyelectrolytes within a Confining Well

We present a numerical study of polyelectrolytes electrophoresing in free solution while squeezed by an axisymmetric confinement force transverse to their net displacement. Hybrid multiparticle collision dynamics and molecular dynamics simulations with mean-field finite Debye layers show that even though the polyelectrolyte chains remain "free-draining" their electrophoretic mobility increases with confinement in nanoconfining potential wells. The primary mechanism leading to the increase in mobility above the free-solution value, despite long-range hydrodynamic screening by counterion layers, is the orientation of polymer segments within Debye layers. The observed length dependence of the electrophoretic mobility arises due to secondary effects of counterion condensation related to confinement compactification.

Critical effect of pore characteristics on capillary infiltration in mesoporous films

Capillary phenomena governing the mass-transport (capillary filling, condensation/evaporation) has been experimentally investigated in around 20 different silica thin films exhibiting various porosities with pores dimension ranging from 2 to 200 nm. Films have been prepared by sol-gel chemistry combined with soft-templating approaches and controlled dip coating process. Environmental ellipsometric porosimetry combined with electronic microscopy were used to assess the porosity characteristics. Investigation of lateral capillary filling was performed by following the natural infiltration of water and ionic liquids at the edge of a sessile drop in open air or underneath a PDMS cover. The Washburn model was applied to the displacement of the liquid front within the films to deduce the kinetic constants. The role of the different capillary phenomena were discussed with respect to the porosity characteristics (porosity vol%, pore dimensions and constrictions). We show that correlation between capillary filling rate and pore dimensions is not straightforward. Generally, with a minimum of constrictions, faster filling is observed for larger pores. In the case of mesopores (<50 nm in diameter), the presence of bottle necks considerably slows down the infiltration rate. At such a small dimension, evaporation/capillary condensation dynamics, taking place at the meniscus inside the porosity, has to be considered to explain the transport mode. This fundamental study is of interest for applications involving liquids at the interface of mesoporous networks such as nanofluidics, purification, separation, water harvesting or heat transfer.

DNA motion induced by electrokinetic flow near an Au coated nanopore surface as voltage controlled gate

We used fluorescence microscopy to investigate the diffusion and drift motion of λ DNA molecules on an Au-coated membrane surface near nanopores, prior to their translocation through solid-state nanopores. With the capability of controlling electric potential at the Au surface as a gate voltage, Vgate, the motions of DNA molecules, which are presumably generated by electrokinetic flow, vary dramatically near the nanopores in our observations. We carefully investigate these DNA motions with different values of Vgate in order to alter the densities and polarities of the counterions, which are expected to change the flow speed or direction, respectively. Depending on Vgate, our observations have revealed the critical distance from a nanopore for DNA molecules to be attracted or repelled-DNA's anisotropic and unsteady drifting motions and accumulations of DNA molecules near the nanopore entrance. Further finite element method (FEM) numerical simulations indicate that the electrokinetic flow could qualitatively explain these unusual DNA motions near metal-collated gated nanopores. Finally, we demonstrate the possibility of controlling the speed and direction of DNA motion near or through a nanopore, as in the case of recapturing a single DNA molecule multiple times with alternating current voltages on the Vgate.

Flexible and in situ fabrication of nanochannels with high aspect ratios and nanopillar arrays in fused silica substrates utilizing focused ion beam

We present a general methodology for the fabrication of fused silica nanochannels with high aspect ratios and nanopillar arrays using FIB milling.

Creating sub-50 nm nanofluidic junctions in a PDMS microchip via self-assembly process of colloidal silica beads for electrokinetic concentration of biomolecules

In this work we describe a novel and simple self-assembly process of colloidal silica beads to create a nanofluidic junction between two microchannels. The nanoporous membrane was used to induce ion concentration polarization inside the microchannel and this electrokinetic preconcentration system allowed rapid concentration of DNA samples by ~1700 times and of protein samples by ~100 times within 5 minutes.

Hydrodynamics of DNA confined in nanoslits and nanochannels

Modeling the dynamics of a confined, semi exible polymer is a challenging problem, owing to the complicated interplay between the configurations of the chain, which are strongly affected by the length scale for the confinement relative to the persistence length of the chain, and the polymer-wall hydrodynamic interactions. At the same time, understanding these dynamics are crucial to the advancement of emerging genomic technologies that use confinement to stretch out DNA and "read" a genomic signature. In this mini-review, we begin by considering what is known experimentally and theoretically about the friction of a wormlike chain such as DNA confined in a slit or a channel. We then discuss how to estimate the friction coefficient of such a chain, either with dynamic simulations or via Monte Carlo sampling and the Kirk-wood pre-averaging approximation. We then review our recent work on computing the diffusivity of DNA in nanoslits and nanochannels, and conclude with some promising avenues for future work and caveats about our approach.

DNA translocation through short nanofluidic channels under asymmetric pulsed electric field

Investigation of single molecule DNA dynamics in confined environments has led to important applications in DNA analysis, separation, and sequencing. Here, we studied the electrophoretic transport of DNA molecules through nanochannels shorter than the DNA contour length and calculated the associated translocation time curves. We found that the longer T4 DNA molecules required a longer time to traverse a fixed length nanochannel than shorter λ DNA molecules and that the translocation time decreased with increasing electric field which agreed with theoretical predictions. We applied this knowledge to design an asymmetric electric pulse and demonstrate the different responses of λ and T4 DNA to the pulses. We used Brownian dynamics simulations to corroborate our experimental results on DNA translocation behaviour. This work contributes to the fundamental understanding of polymer transport through nanochannels and may help in designing better separation techniques in the future.

Simulations of DNA stretching by flow field in microchannels with complex geometry

Recently, we have reported the experimental results of DNA stretching by flow field in three microchannels (C. H. Lee and C. C. Hsieh, Biomicrofluidics 7(1), 014109 (2013)) designed specifically for the purpose of preconditioning DNA conformation for easier stretching. The experimental results do not only demonstrate the superiority of the new devices but also provides detailed observation of DNA behavior in complex flow field that was not available before. In this study, we use Brownian dynamics-finite element method (BD-FEM) to simulate DNA behavior in these microchannels, and compare the results against the experiments. Although the hydrodynamic interaction (HI) between DNA segments and between DNA and the device boundaries was not included in the simulations, the simulation results are in fairly good agreement with the experimental data from either the aspect of the single molecule behavior or from the aspect of ensemble averaged properties. The discrepancy between the simulation and the experimental results can be explained by the neglect of HI effect in the simulations. Considering the huge savings on the computational cost from neglecting HI, we conclude that BD-FEM can be used as an efficient and economic designing tool for developing new microfluidic device for DNA manipulation.

Precision platform for convex lens-induced confinement microscopy

We present the conception, fabrication, and demonstration of a versatile, computer-controlled microscopy device which transforms a standard inverted fluorescence microscope into a precision single-molecule imaging station. The device uses the principle of convex lens-induced confinement [S. R. Leslie, A. P. Fields, and A. E. Cohen, Anal. Chem. 82, 6224 (2010)], which employs a tunable imaging chamber to enhance background rejection and extend diffusion-limited observation periods. Using nanopositioning stages, this device achieves repeatable and dynamic control over the geometry of the sample chamber on scales as small as the size of individual molecules, enabling regulation of their configurations and dynamics. Using microfluidics, this device enables serial insertion as well as sample recovery, facilitating temporally controlled, high-throughput measurements of multiple reagents. We report on the simulation and experimental characterization of this tunable chamber geometry, and its influence upon the diffusion and conformations of DNA molecules over extended observation periods. This new microscopy platform has the potential to capture, probe, and influence the configurations of single molecules, with dramatically improved imaging conditions in comparison to existing technologies. These capabilities are of immediate interest to a wide range of research and industry sectors in biotechnology, biophysics, materials, and chemistry.

The diffusion and relaxation of Gaussian chains in narrow rectangular slits

The confinement of a polymer to volumes whose characteristic linear dimensions are comparable to or smaller than its bulk radius of gyration R(G,bulk) can produce significant changes in its static and dynamic properties, with important implications for the understanding of single-molecule processes in biology and chemistry. In this paper, we present calculations of the effects of a narrow rectangular slit of thickness d on the scaling behavior of the diffusivity D and relaxation time τr of a Gaussian chain of polymerization index N and persistence length l0. The calculations are based on the Rouse-Zimm model of chain dynamics, with the pre-averaged hydrodynamic interaction being obtained from the solutions to Stokes equations for an incompressible fluid in a parallel plate geometry in the limit of small d. They go beyond de Gennes' purely phenomenological analysis of the problem based on blobs, which has so far been the only analytical route to the determination of chain scaling behavior for this particular geometry. The present model predicts that D ∼ dN(-1)ln (N∕d(2)) and τr ∼ N(2)d(-1)[ln (N∕d(2))](-1) in the regime of moderate confinement, where l0 ≪ d < R(G,bulk). The corresponding results for the blob model have exactly the same power law behavior, but contain no logarithmic corrections; the difference suggests that segments within a blob may actually be partially draining and not non-draining as generally assumed.

Revisiting blob theory for DNA diffusivity in slitlike confinement

Blob theory has been widely applied to describe polymer conformations and dynamics in nanoconfinement. In slit confinement, blob theory predicts a scaling exponent of 2/3 for polymer diffusivity as a function of slit height, yet a large body of experimental studies using DNA produce a scaling exponent significantly less than 2/3. In this work, we develop a theory that predicts that this discrepancy occurs because the segment correlation function for a semiflexible chain such as DNA does not follow the Flory exponent for length scales smaller than the persistence length. We show that these short length scale effects contribute significantly to the scaling for the DNA diffusivity, but do not appreciably affect the scalings for static properties. Our theory is fully supported by Monte Carlo simulations, quantitative agreement with DNA experiments, and the results reconcile this outstanding problem for confined polymers.