Entropic unfolding of DNA molecules in nanofluidic channels

Fluorescence Microscopy of Nanochannel-Confined DNA

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level, and the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments, and analyze the data.

Sculpturing wafer-scale nanofluidic devices for DNA single molecule analysis

We present micro- and nanofluidic devices with 3D structures and nanochannels with multiple depths for the analysis of single molecules of DNA. Interfacing the nanochannels with graded and 3D inlets allows the improvement of the flow and controls not only the translocation speed of the DNA but also its conformation inside the nanochannels. The complex, multilevel, multiscale fluidic circuits are patterned in a simple, two-minute imprinting step. The stamp, the key of the technology, is directly milled by focused ion beam, which allows patterning nanochannels with different cross sections and depths, together with 3D transient inlets, all at once. Having such a variety of structures integrated in the same sample allows studying, optimizing and directly comparing their effect on the DNA flow. Here, DNA translocation is studied in long (160 µm) and short (5-40 µm) nanochannels. We study the homogeneity of the stretched molecules in long, meander nanochannels made with this technology. In addition, we analyze the effect of the different types of inlet structures interfacing short nanochannels. We observe pre-stretching and an optimal flow, and no hairpin formation, when the inlets have gradually decreasing widths and depths. In contrast, when the nanochannels are faced with an abrupt transition, we observe clogging and hairpin formation. In addition, 3D inlets strongly decrease the DNA molecules' speed before they enter the nanochannels, and help capturing more DNA molecules. The robustness and versatility of this technology and DNA testing results evidence the potential of imprinted devices in biomedical applications as low cost, disposable lab-on-a-chip devices.

Stochastic unfolding of nanoconfined DNA: Experiments, model and Bayesian analysis

Nanochannels provide a means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. Here we introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients are the entropic unfolding force and the friction coefficient for the unfolding process, and we describe the associated dynamics by a non-linear Langevin equation. By analyzing experimental data where DNA molecules are photo-cut and unfolded inside a nanochannel, our model allows us to extract values for the unfolding force as well as the friction coefficient for the first time. In order to extract numerical values for these physical quantities, we employ a recently introduced Bayesian inference framework. We find that the determined unfolding force is in agreement with estimates from a simple Flory-type argument. The estimated friction coefficient is in agreement with theoretical estimates for motion of a cylinder in a channel. We further validate the estimated friction constant by extracting this parameter from DNA's center-of-mass motion before and after unfolding, yielding decent agreement. We provide publically available software for performing the required image and Bayesian analysis.

Nanoplumbing with 2D Metamaterials

Complex manipulations of DNA in a nanofluidic device require channels with branches and junctions. However, the dynamic response of DNA in such nanofluidic networks is relatively unexplored. Here, the transport of DNA in a 2D metamaterial made by arrays of nanochannel junctions is investigated. The mechanism of transport is explained as Brownian motion through an energy landscape formed by the combination of the confinement free energy of DNA and the effective potential of hydrodynamic flow, which both can be tuned independently within the device. For the quantitative understanding of DNA transport, a dynamic mean-field model of DNA at a nanochannel junction is proposed. It is shown that the dynamics of DNA in a nanofluidic device with branched channels and junctions is well described by the model.

Distribution of label spacings for genome mapping in nanochannels

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.

A nanofluidic knot factory based on compression of single DNA in nanochannels

Knots form when polymers self-entangle, a process enhanced by compaction with important implications in biological and artificial systems involving chain confinement. In particular, new experimental tools are needed to assess the impact of multiple variables influencing knotting probability. Here, we introduce a nanofluidic knot factory for efficient knot formation and detection. Knots are produced during hydrodynamic compression of single DNA molecules against barriers in a nanochannel; subsequent extension of the chain enables direct assessment of the number of independently evolving knots. Knotting probability increases with chain compression as well as with waiting time in the compressed state. Using a free energy derived from scaling arguments, we develop a knot-formation model that can quantify the effect of interactions and the breakdown of Poisson statistics at high compression. Our model suggests that highly compressed knotted states are stabilized by a decreased free energy as knotted contour contributes a lower self-exclusion derived free energy.

Hairpins in the conformations of a confined polymer

If a semiflexible polymer confined to a narrow channel bends around by 180°, the polymer is said to exhibit a hairpin. The equilibrium extension statistics of the confined polymer are well understood when hairpins are vanishingly rare or when they are plentiful. Here, we analyze the extension statistics in the intermediate situation via experiments with DNA coated by the protein RecA, which enhances the stiffness of the DNA molecule by approximately one order of magnitude. We find that the extension distribution is highly non-Gaussian, in good agreement with Monte-Carlo simulations of confined discrete wormlike chains. We develop a simple model that qualitatively explains the form of the extension distribution. The model shows that the tail of the distribution at short extensions is determined by conformations with one hairpin.

Odijk excluded volume interactions during the unfolding of DNA confined in a nanochannel

We report experimental data on the unfolding of human and E. coli genomic DNA molecules shortly after injection into a 45 nm nanochannel. The unfolding dynamics are deterministic, consistent with previous experiments and modeling in larger channels, and do not depend on the biological origin of the DNA. The measured entropic unfolding force per friction per unit contour length agrees with that predicted by combining the Odijk excluded volume with numerical calculations of the Kirkwood diffusivity of confined DNA. The time scale emerging from our analysis has implications for genome mapping in nanochannels, especially as the technology moves towards longer DNA, by setting a lower bound for the delay time before making a measurement.

Fluorescence Microscopy of Nanochannel-Confined DNA

Stretching of DNA in nanoscale confinement allows for several important studies. The genetic contents of the DNA can be visualized on the single DNA molecule level and both the polymer physics of confined DNA and also DNA/protein and other DNA/DNA-binding molecule interactions can be explored. This chapter describes the basic steps to fabricate the nanostructures, perform the experiments and analyze the data.

Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family

Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.

Thermoplastic nanofluidic devices for biomedical applications

Microfluidics is now moving into a developmental stage where basic discoveries are being transitioned into the commercial sector so that these discoveries can affect, for example, healthcare. Thus, high production rate microfabrication technologies, such as thermal embossing and/or injection molding, are being used to produce low-cost consumables appropriate for commercial applications. Based on recent reports, it is clear that nanofluidics offers some attractive process capabilities that may provide unique venues for biomolecular analyses that cannot be realized at the microscale. Thus, it would be attractive to consider early in the developmental cycle of nanofluidics production pipelines that can generate devices possessing sub-150 nm dimensions in a high production mode and at low-cost to accommodate the commercialization of this exciting technology. Recently, functional sub-150 nm thermoplastic nanofluidic devices have been reported that can provide high process yield rates, which can enable commercial translation of nanofluidics. This review presents an overview of recent advancements in the fabrication, assembly, surface modification and the characterization of thermoplastic nanofluidic devices. Also, several examples in which nanoscale phenomena have been exploited for the analysis of biomolecules are highlighted. Lastly, some general conclusions and future outlooks are presented.

Exploring DNA–protein interactions on the single DNA molecule level using nanofluidic tools

This review highlights the use of nanofluidic channels for studying DNA–protein interactions on the single DNA molecule level.

Flow of DNA in micro/nanofluidics: From fundamentals to applications

Thanks to direct observation and manipulation of DNA in micro/nanofluidic devices, we are now able to elucidate the relationship between the polymer microstructure and its rheological properties, as well as to design new single-molecule platforms for biophysics and biomedicine. This allows exploration of many new mechanisms and phenomena, which were previously unachievable with conventional methods such as bulk rheometry tests. For instance, the field of polymer rheology is at a turning point to relate the complex molecular conformations to the nonlinear viscoelasticity of polymeric fluids (such as coil-stretch transition, shear thinning, and stress overshoot in startup shear). In addition, nanofluidic devices provided a starting point for manipulating single DNA molecules by applying basic principles of polymer physics, which is highly relevant to numerous processes in biosciences. In this article, we review recent progress regarding the flow and deformation of DNA in micro/nanofluidic systems from both fundamental and application perspectives. We particularly focus on advances in the understanding of polymer rheology and identify the emerging research trends and challenges, especially with respect to future applications of nanofluidics in the biomedical field.

A simple approach for an optically transparent nanochannel device prototype

Compared with microfluidic devices, the fabrication of structure-controllable and designable nanochannel devices has been considered to have high costs and complex procedures, which require expensive equipment and high-quality raw materials. Exploring fast, simple and inexpensive approaches in nanochannel fabrication will be greatly helpful to speed up laboratory studies of nanofluidics. Here we developed a simple and inexpensive approach to fabricate a nanochannel device with a glass/epoxy resin/glass structure. The grooves were engraved using a UV laser on an aluminum sacrificial layer on the substrate glass, and epoxy resin was coated on the substrate and stuffed fully into the grooves. Another glass plate with holes for fluidic inlets and outlets was bonded on the top of the resin layer. The nanochannels were formed by etching thin sacrificial layers electrochemically. Meanwhile, the microstructures of the fluidic outlets and inlets could be fabricated simultaneously to the nanochannel formation. The total processing time for the simple nanochannel device took less than 10 hours. Optically transparent nanochannels with a depth of up to 20 nm were achieved. Nanofluidic behaviors in the nanochannels were observed under both optical and fluorescence microscopes.

A novel 2D silicon nano-mold fabrication technique for linear nanochannels over a 4 inch diameter substrate

A novel low-cost 2D silicon nano-mold fabrication technique was developed based on Cu inclined-deposition and Ar⁺ (argon ion) etching. With this technique, sub-100 nm 2D (two dimensional) nano-channels can be etched economically over the whole area of a 4 inch n-type <100> silicon wafer. The fabricating process consists of only 4 steps, UV (Ultraviolet) lithography, inclined Cu deposition, Ar⁺ sputter etching, and photoresist & Cu removing. During this nano-mold fabrication process, we investigated the influence of the deposition angle on the width of the nano-channels and the effect of Ar⁺ etching time on their depth. Post-etching measurements showed the accuracy of the nanochannels over the whole area: the variation in width is 10%, in depth it is 11%. However, post-etching measurements also showed the accuracy of the nanochannels between chips: the variation in width is 2%, in depth it is 5%. With this newly developed technology, low-cost and large scale 2D nano-molds can be fabricated, which allows commercial manufacturing of nano-components over large areas.

Knotting dynamics of DNA chains of different length confined in nanochannels

Langevin dynamics simulations are used to characterize the typical mechanisms governing the spontaneous tying, untying and the dynamical evolution of knots in coarse-grained models of DNA chains confined in nanochannels. In particular we focus on how these mechanisms depend on the chain contour length, Lc, at a fixed channel width D = 56 nm corresponding to the onset of the Odijk scaling regime where chain backfoldings and hence knots are disfavoured but not suppressed altogether. We find that the lifetime of knots grows significantly with Lc, while that of unknots varies to a lesser extent. The underlying kinetic mechanisms are clarified by analysing the evolution of the knot position along the chain. At the considered confinement, in fact, knots are typically tied by local backfoldings of the chain termini where they are eventually untied after a stochastic motion along the chain. Consequently, the lifetime of unknots is mostly controlled by backfoldings events at the chain ends, which is largely independent of Lc. The lifetime of knots, instead, increases significantly with Lc because knots can, on average, travel farther along the chain before being untied. The observed interplay of knots and unknots lifetimes underpins the growth of the equilibrium knotting probability of longer and longer chains at fixed channel confinement.

DNA Brushing Shoulders: Targeted Looping and Scanning of Large DNA Strands

We present a nanofluidic device for targeted manipulations in the quarternary structure of single DNA molecules. We demonstrate the folding and unfolding of hairpin-shaped regions, similar to chromatin loops. These loops are stable for minutes at nanochannel junctions. We demonstrate continuous scanning of two DNA segments that occupy a common nanovolume. We present a model governing the stability of loop folds and discuss how the system achieves specific DNA configurations without operator intervention.

Topological events in single molecules of E. coli DNA confined in nanochannels

We present experimental data concerning potential topological events such as folds, internal backfolds, and/or knots within long molecules of double-stranded DNA when they are stretched by confinement in a nanochannel. Genomic DNA from E. coli was labeled near the 'GCTCTTC' sequence with a fluorescently labeled dUTP analog and stained with the DNA intercalator YOYO. Individual long molecules of DNA were then linearized and imaged using methods based on the NanoChannel Array technology (Irys® System) available from BioNano Genomics. Data were collected on 189 153 molecules of length greater than 50 kilobases. A custom code was developed to search for abnormal intensity spikes in the YOYO backbone profile along the length of individual molecules. By correlating the YOYO intensity spikes with the aligned barcode pattern to the reference, we were able to correlate the bright intensity regions of YOYO with abnormal stretching in the molecule, which suggests these events were either a knot or a region of internal backfolding within the DNA. We interpret the results of our experiments involving molecules exceeding 50 kilobases in the context of existing simulation data for relatively short DNA, typically several kilobases. The frequency of these events is lower than the predictions from simulations, while the size of the events is larger than simulation predictions and often exceeds the molecular weight of the simulated molecules. We also identified DNA molecules that exhibit large, single folds as they enter the nanochannels. Overall, topological events occur at a low frequency (∼7% of all molecules) and pose an easily surmountable obstacle for the practice of genome mapping in nanochannels.

Polymers under confinement: single polymers, how they interact, and as model chromosomes

How confinement or a physical constraint modifies polymer chains is not only a classical problem in polymer physics but also relevant in a variety of contexts such as single-molecule manipulations, nanofabrication in narrow pores, and modelling of chromosome organization. Here, we review recent progress in our understanding of polymers in a confined (and crowded) space. To this end, we highlight converging views of these systems from computational, experimental, and theoretical approaches, and then clarify what remains to be clarified. In particular, we focus on exploring how cylindrical confinement reshapes individual chains and induces segregation forces between them - by pointing to the relationships between intra-chain organization and chain segregation. In the presence of crowders, chain molecules can be entropically phase-separated into a condensed state. We include a kernel of discussions on the nature of chain compaction by crowders, especially in a confined space. Finally, we discuss the relevance of confined polymers for the nucleoid, an intracellular space in which the bacterial chromosome is tightly packed, in part by cytoplasmic crowders.

Hydrodynamics of diamond-shaped gradient nanopillar arrays for effective DNA translocation into nanochannels

Effective DNA translocation into nanochannels is critical for advancing genome mapping and future single-molecule DNA sequencing technologies. We present the design and hydrodynamic study of a diamond-shaped gradient pillar array connected to nanochannels for enhancing the success of DNA translocation events. Single-molecule fluorescence imaging is utilized to interrogate the hydrodynamic interactions of the DNA with this unique structure, evaluate key DNA translocation parameters, including speed, extension, and translocation time, and provide a detailed mapping of the translocation events in nanopillar arrays coupled with 10 and 50 μm long channels. Our analysis reveals the important roles of diamond-shaped nanopillars in guiding DNA into as small as 30 nm channels with minimized clogging, stretching DNA to nearly 100% of their dyed contour length, inducing location-specific straddling of DNA at nanopillar interfaces, and modulating DNA speeds by pillar geometries. Importantly, all critical features down to 30 nm wide nanochannels are defined using standard photolithography and fabrication processes, a feat aligned with the requirement of high-volume, low-cost production.

Surface charge, electroosmotic flow and DNA extension in chemically modified thermoplastic nanoslits and nanochannels

Thermoplastics have become attractive alternatives to glass/quartz for microfluidics, but the realization of thermoplastic nanofluidic devices has been slow in spite of the rather simple fabrication techniques that can be used to produce these devices. This slow transition has in part been attributed to insufficient understanding of surface charge effects on the transport properties of single molecules through thermoplastic nanochannels. We report the surface modification of thermoplastic nanochannels and an assessment of the associated surface charge density, zeta potential and electroosmotic flow (EOF). Mixed-scale fluidic networks were fabricated in poly(methylmethacrylate), PMMA. Oxygen plasma was used to generate surface-confined carboxylic acids with devices assembled using low temperature fusion bonding. Amination of the carboxylated surfaces using ethylenediamine (EDA) was accomplished via EDC coupling. XPS and ATR-FTIR revealed the presence of carboxyl and amine groups on the appropriately prepared surfaces. A modified conductance equation for nanochannels was developed to determine their surface conductance and was found to be in good agreement with our experimental results. The measured surface charge density and zeta potential of these devices were lower than glass nanofluidic devices and dependent on the surface modification adopted, as well as the size of the channel. This property, coupled to an apparent increase in fluid viscosity due to nanoconfinement, contributed to the suppression of the EOF in PMMA nanofluidic devices by an order of magnitude compared to the micro-scale devices. Carboxylated PMMA nanochannels were efficient for the transport and elongation of λ-DNA while these same DNA molecules were unable to translocate through aminated nanochannels.

A novel hybrid patterning technique for micro and nanochannel fabrication by integrating hot embossing and inverse UV photolithography

Nanofluidic devices with micro and nanostructures are becoming increasingly important for biological and chemical applications. However, the majority of the present fabrication methods suffer from a low pattern transfer quality during the simultaneous embossing of the microscale and nanoscale patterns into a thermoplastic polymer due to insufficient polymer flow. In this work, a novel hybrid patterning technique, integrating hot embossing and inverse ultraviolet (UV) photolithography, is developed to fabricate micro and nanochannels with a high replication precision of the SU-8 layer. The influence of embossing temperature and time on the replication precision was investigated. The effect of UV lithography parameters on the micro and nanochannel pattern was analyzed. To improve the SU-8 bonding strength, the influence of the O2 plasma treatment parameters on the water contact angles of the exposed and unexposed SU-8 layer were studied. A complete SU-8 nanofluidic chip with 130 nm wide and 150 nm deep nanochannels was successfully fabricated with a replication precision of 99.5%. Compared with most of the current processing methods, this fabrication technique has great potential due to its low cost and high pattern transfer quality of the SU-8 micro and nanochannels.

Probing transient protein-mediated DNA linkages using nanoconfinement

We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNApolymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches.

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.

Modeling the relaxation time of DNA confined in a nanochannel

Using a mapping between a Rouse dumbbell model and fine-grained Monte Carlo simulations, we have computed the relaxation time of λ-DNA in a high ionic strength buffer confined in a nanochannel. The relaxation time thus obtained agrees quantitatively with experimental data [Reisner et al., Phys. Rev. Lett. 94, 196101 (2005)] using only a single O(1) fitting parameter to account for the uncertainty in model parameters. In addition to validating our mapping, this agreement supports our previous estimates of the friction coefficient of DNA confined in a nanochannel [Tree et al., Phys. Rev. Lett. 108, 228105 (2012)], which have been difficult to validate due to the lack of direct experimental data. Furthermore, the model calculation shows that as the channel size passes below approximately 100 nm (or roughly the Kuhn length of DNA) there is a dramatic drop in the relaxation time. Inasmuch as the chain friction rises with decreasing channel size, the reduction in the relaxation time can be solely attributed to the sharp decline in the fluctuations of the chain extension. Practically, the low variance in the observed DNA extension in such small channels has important implications for genome mapping.

Field-flow fractionation and hydrodynamic chromatography on a microfluidic chip

We present gravitational field-flow fractionation and hydrodynamic chromatography of colloids eluting through 18 μm microchannels. Using video microscopy and mesoscopic simulations, we investigate the average retention ratio of colloids with both a large specific weight and neutral buoyancy. We consider the entire range of colloid sizes, including particles that barely fit in the microchannel and nanoscopic particles. Ideal theory predicts four operational modes, from hydrodynamic chromatography to Faxén-mode field-flow fractionation. We experimentally demonstrate, for the first time, the existence of the Faxén-mode field-flow fractionation and the transition from hydrodynamic chromatography to normal-mode field-flow fractionation. Furthermore, video microscopy and simulations show that the retention ratios are largely reduced above the steric-inversion point, causing the variation of the retention ratio in the steric- and Faxén-mode regimes to be suppressed due to increased drag. We demonstrate that theory can accurately predict retention ratios if hydrodynamic interactions with the microchannel walls (wall drag) are added to the ideal theory. Rather than limiting the applicability, these effects allow the microfluidic channel size to be tuned to ensure high selectivity. Our findings indicate that particle velocimetry methods must account for the wall-induced lag when determining flow rates in highly confining systems.

Review article: Fabrication of nanofluidic devices

Thanks to its unique features at the nanoscale, nanofluidics, the study and application of fluid flow in nanochannels/nanopores with at least one characteristic size smaller than 100 nm, has enabled the occurrence of many interesting transport phenomena and has shown great potential in both bio- and energy-related fields. The unprecedented growth of this research field is apparently attributed to the rapid development of micro/nanofabrication techniques. In this review, we summarize recent activities and achievements of nanofabrication for nanofluidic devices, especially those reported in the past four years. Three major nanofabrication strategies, including nanolithography, microelectromechanical system based techniques, and methods using various nanomaterials, are introduced with specific fabrication approaches. Other unconventional fabrication attempts which utilize special polymer properties, various microfabrication failure mechanisms, and macro/microscale machining techniques are also presented. Based on these fabrication techniques, an inclusive guideline for materials and processes selection in the preparation of nanofluidic devices is provided. Finally, technical challenges along with possible opportunities in the present nanofabrication for nanofluidic study are discussed.

Electrokinetically-driven transport of DNA through focused ion beam milled nanofluidic channels

The electrophoretically driven transport of double-stranded λ-phage DNA through focused ion beam (FIB) milled nanochannels is described. Nanochannels were fabricated having critical dimensions (width and depth) corresponding to 0.5×, 1×, and 2× the DNA persistence length, or 25 nm, 50 nm, and 100 nm, respectively. The threshold field strength required to drive transport, the threading mobility, and the transport mobility were measured as a function of nanochannel size. As the nanochannel dimensions decreased, the entropic barrier to translocation increased and transport became more constrained. Equilibrium models of confinement provide a framework in which to understand the observed trends, although the dynamic nature of the experiments resulted in significant deviations from theory. It was also demonstrated that the use of dynamic wall coatings for the purpose of electroosmotic flow suppression can have a significant impact on transport dynamics that may obfuscate entropic contributions. The nonintermittent DNA transport through the FIB milled nanochannels demonstrates that they are well suited for use in nanofluidic devices. We expect that an understanding of the dynamic transport properties reported here will facilitate the incorporation of FIB-milled nanochannels in devices for single molecule and ensemble analyses.

Chain conformation of ring polymers under a cylindrical nanochannel confinement

We investigate the chain conformation of ring polymers confined to a cylindrical nanochannel using both theoretical analysis and three-dimensional Langevin dynamics simulations. We predict that the longitudinal size of a ring polymer scales with the chain length and the diameter of the channel in the same manner as that for linear chains based on scaling analysis and Flory-type theory. Moreover, Flory-type theory also gives the ratio of the longitudinal sizes for a ring polymer and a linear chain with identical chain length. These theoretical predictions are confirmed by numerical simulations. Finally, our simulation results show that this ratio first decreases and then saturates with increasing the chain stiffness, which explains the discrepancy in experiments. Our results have biological significance.

Nanofluidic devices towards single DNA molecule sequence mapping

Nanofluidics enables the imaging of stretched single molecules with potential applications for single molecule sequence mapping. Lab-on-a-chip devices for single cell trapping and lyzing, genomic DNA extraction from single cells, and optical mapping of genomic length DNA has been demonstrated separately. Yet the pursuit for applying DNA optical mapping to solve real genomics challenges is still to come. We review lab-on-a-chip devices from literature that could be part of a complete system for the sequence mapping of single DNA molecules.

DNA molecules descending a nanofluidic staircase by entropophoresis

A complex entropy gradient for confined DNA molecules was engineered for the first time. Following the second law of thermodynamics, this enabled the directed self-transport and self-concentration of DNA molecules. This new nanofluidic method is termed entropophoresis. As implemented in experiments, long DNA molecules were dyed with cyanine dimers, dispersed in a high ionic strength buffer, and confined by a nanofluidic channel with a depth profile approximated by a staircase function. The staircase step depths spanned the transition from strong to moderate confinement. The diffusion of DNA molecules across slitlike steps was ratcheted by entropic forces applied at step edges, so that DNA molecules descended and collected at the bottom of the staircase, as observed by fluorescence microscopy. Different DNA morphologies, lengths, and stoichiometric base pair to dye molecule ratios were tested and determined to influence the rate of transport by entropophoresis. A model of ratcheted diffusion was used to interpret a shifting balance of forces applied to linear DNA molecules of standard length in a complex free energy landscape. Related metrics for the overall and optimum performance of entropophoresis were developed. The device and method reported here transcend current limitations in nanofluidics and present new possibilities in polymer physics, biophysics, separation science, and lab-on-a-chip technology.