Electrophoretic manipulation of single DNA molecules in nanofabricated capillaries

Unmasking the Resolution-Throughput Tradespace of Focused-Ion-Beam Machining

Focused-ion-beam machining is a powerful process to fabricate complex nanostructures, often through a sacrificial mask that enables milling beyond the resolution limit of the ion beam. However, current understanding of this super-resolution effect is empirical in the spatial domain and nonexistent in the temporal domain. This article reports the primary study of this fundamental tradespace of resolution and throughput. Chromia functions well as a masking material due to its smooth, uniform, and amorphous structure. An efficient method of in-line metrology enables characterization of ion-beam focus by scanning electron microscopy. Fabrication and characterization of complex test structures through chromia and into silica probe the response of the bilayer to a focused beam of gallium cations, demonstrating super-resolution factors of up to 6 ± 2 and improvements to volume throughput of at least factors of 42 ± 2, with uncertainties denoting 95% coverage intervals. Tractable theory models the essential aspects of the super-resolution effect for various nanostructures. Application of the new tradespace increases the volume throughput of machining Fresnel lenses by a factor of 75, enabling the introduction of projection standards for optical microscopy. These results enable paradigm shifts of sacrificial masking from empirical to engineering design and from prototyping to manufacturing.

Nonlinear electrophoretic velocity of DNA in slitlike confinement

We have applied zero-time-averaged alternating electric fields to DNA molecules in a cross-shaped nanofluidic slit. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device, we derive an estimate for the second-order electrophoretic mobility, μ_{2}. We observe that focusing is absent at a dipole rotation frequency >20 Hz, which suggests that μ_{2} depends on the frequency of the alternating fields. The observation of a nonzero μ_{2} raises the possibility of frequency-dependent electrophoretic DNA separation by length achievable in the absence of a sieving matrix.

Label-Free Identification of Single Mononucleotides by Nanoscale Electrophoresis

Nanoscale electrophoresis allows for unique separations of single molecules, such as DNA/RNA nucleobases, and thus has the potential to be used as single molecular sensors for exonuclease sequencing. For this to be envisioned, label-free detection of the nucleotides to determine their electrophoretic mobility (i.e., time-of-flight, TOF) for highly accurate identification must be realized. Here, for the first time a novel nanosensor is shown that allows discriminating four 2-deoxyribonucleoside 5'-monophosphates, dNMPs, molecules in a label-free manner by nanoscale electrophoresis. This is made possible by positioning two sub-10 nm in-plane pores at both ends of a nanochannel column used for nanoscale electrophoresis and measuring the longitudinal transient current during translocation of the molecules. The dual nanopore TOF sensor with 0.5, 1, and 5 µm long nanochannel column lengths discriminates different dNMPs with a mean accuracy of 55, 66, and 94%, respectively. This nanosensor format can broadly be applicable to label-free detection and discrimination of other single molecules, vesicles, and particles by changing the dimensions of the nanochannel column and in-plane nanopores and integrating different pre- and postprocessing units to the nanosensor. This is simple to accomplish because the nanosensor is contained within a fluidic network made in plastic via replication.

Characterisation of optically driven microstructures for manipulating single DNA molecules under a fluorescence microscope

Optical tweezers are powerful tools for manipulating single DNA molecules using fluorescence microscopy, particularly in nanotechnology-based DNA analysis. We previously proposed a manipulation technique using microstructures driven by optical tweezers that allows the handling of single giant DNA molecules of millimetre length that cannot be manipulated by conventional techniques. To further develop this technique, the authors characterised the microstructures quantitatively from the view point of fabrication and efficiency of DNA manipulation under a fluorescence microscope. The success rate and precision of the fabrications were evaluated. The results indicate that the microstructures are obtained in an aqueous solution with a precision ∼50 nm at concentrations in the order of 10(6) particles/ml. The visibility of these microstructures under a fluorescence microscope was also characterised, along with the elucidation of the fabrication parameters needed to fine tune visibility. Manipulating yeast chromosomal DNA molecules with the microstructures illustrated the relationship between the efficiency of manipulation and the geometrical shape of the microstructure. This report provides the guidelines for designing microstructures used in single DNA molecule analysis based on on-site DNA manipulation, and is expected to broaden the applications of this technique in the future.

Optimized holographic femtosecond laser patterning method towards rapid integration of high-quality functional devices in microchannels

Rapid integration of high-quality functional devices in microchannels is in highly demand for miniature lab-on-a-chip applications. This paper demonstrates the embellishment of existing microfluidic devices with integrated micropatterns via femtosecond laser MRAF-based holographic patterning (MHP) microfabrication, which proves two-photon polymerization (TPP) based on spatial light modulator (SLM) to be a rapid and powerful technology for chip functionalization. Optimized mixed region amplitude freedom (MRAF) algorithm has been used to generate high-quality shaped focus field. Base on the optimized parameters, a single-exposure approach is developed to fabricate 200 × 200 μm microstructure arrays in less than 240 ms. Moreover, microtraps, QR code and letters are integrated into a microdevice by the advanced method for particles capture and device identification. These results indicate that such a holographic laser embellishment of microfluidic devices is simple, flexible and easy to access, which has great potential in lab-on-a-chip applications of biological culture, chemical analyses and optofluidic devices.

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.

Electrophoretic Separation of Single Particles Using Nanoscale Thermoplastic Columns

Phenomena associated with microscale electrophoresis separations cannot, in many cases, be applied to the nanoscale. Thus, understanding the electrophoretic characteristics associated with the nanoscale will help formulate relevant strategies that can optimize the performance of separations carried out on columns with at least one dimension below 150 nm. Electric double layer (EDL) overlap, diffusion, and adsorption/desorption properties and/or dielectrophoretic effects giving rise to stick/slip motion are some of the processes that can play a role in determining the efficiency of nanoscale electrophoretic separations. We investigated the performance characteristics of electrophoretic separations carried out in nanoslits fabricated in poly(methyl methacrylate), PMMA, devices. Silver nanoparticles (AgNPs) were used as the model system with tracking of their transport via dark field microscopy and localized surface plasmon resonance. AgNPs capped with citrate groups and the negatively charged PMMA walls (induced by O2 plasma modification of the nanoslit walls) enabled separations that were not apparent when these particles were electrophoresed in microscale columns. The separation of AgNPs based on their size without the need for buffer additives using PMMA nanoslit devices is demonstrated herein. Operational parameters such as the electric field strength, nanoslit dimensions, and buffer composition were evaluated as to their effects on the electrophoretic performance, both in terms of efficiency (plate numbers) and resolution. Electrophoretic separations performed at high electric field strengths (>200 V/cm) resulted in higher plate numbers compared to lower fields due to the absence of stick/slip motion at the higher electric field strengths. Indeed, 60 nm AgNPs could be separated from 100 nm particles in free solution using nanoscale electrophoresis with 100 μm long columns.

Conductivity-based detection techniques in nanofluidic devices

This review covers conductivity detection in fabricated nanochannels and nanopores. Improvements in nanoscale sensing are a direct result of advances in fabrication techniques, which produce devices with channels and pores with reproducible dimensions and in a variety of materials. Analytes of interest are detected by measuring changes in conductance as the analyte accumulates in the channel or passes transiently through the pore. These detection methods take advantage of phenomena enhanced at the nanoscale, such as ion current rectification, surface conductance, and dimensions comparable to the analytes of interest. The end result is the development of sensing technologies for a broad range of analytes, e.g., ions, small molecules, proteins, nucleic acids, and particles.

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.

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.

Single-particle electrophoresis in nanochannels

Electrophoretic mobilities and particle sizes of individual Hepatitis B Virus (HBV) capsids were measured in nanofluidic channels with two nanopores in series. The channels and pores had three-dimensional topography and were milled directly in glass substrates with a focused ion beam instrument assisted by an electron flood gun. The nanochannel between the two pores was 300 nm wide, 100 nm deep, and 2.5 μm long, and the nanopores at each end had dimensions 45 nm wide, 45 nm deep, and 400 nm long. With resistive-pulse sensing, the nanopores fully resolved pulse amplitude distributions of T = 3 HBV capsids (32 nm outer diameter) and T = 4 HBV capsids (35 nm outer diameter) and had sufficient peak capacity to discriminate intermediate species from the T = 3 and T = 4 capsid distributions in an assembly reaction. Because the T = 3 and T = 4 capsids have a wiffle-ball geometry with a hollow core, the observed change in current due to the capsid transiting the nanopore is proportional to the volume of electrolyte displaced by the volume of capsid protein, not the volume of the entire capsid. Both the signal-to-noise ratio of the pulse amplitude and resolution between the T = 3 and T = 4 distributions of the pulse amplitudes increase as the electric field strength is increased. At low field strengths, transport of the larger T = 4 capsid through the nanopores is hindered relative to the smaller T = 3 capsid due to interaction with the pores, but at sufficiently high field strengths, the T = 3 and T = 4 capsids had the same electrophoretic mobilities (7.4 × 10(-5) cm(2) V(-1) s(-1)) in the nanopores and in the nanochannel with the larger cross-sectional area.

Electrokinetics and Rare-Cell Detection

Lab-on-a-chip devices perform functions which are not feasible or difficult to achieve with macroscale devices. Importantly, isolating and enriching rare cells is key in health and environmental applications, such as detecting circulating tumor cells from body fluid biopsies, or pathogens from water. Within a microdevice, the dominant mechanical force on a suspended particle is the drag force as it flows through the fluid. Electrokinetic forces such as dielectrophoresis - the motion of a particle due to its polarization in the presence of a non-uniform electric field - may also be applied to manipulate particles. For instance, separation of particles can be achieved using a combination of drag and dielectrophoretic forces to precisely manipulate a particle. Understanding the interaction of electrokinetic forces, particles, and fluid flow is critical for engineering novel microsystems used for cell sorting. Determining this interaction is even more complicated when dealing with bioparticles, especially cells, due to their intrinsic complex biological properties which influence their electrical and mechanical behaviors. In order to design novel and more practical microdevices for medical, biological, and chemical applications, it is essential to have a comprehensive understanding of the mechanics of particle-fluid interaction and the dynamics of particle movement. This chapter will describe the role of electrokinetic techniques in rare cell detection and the behavior of electrokinetic microsystems.

Design of a microchannel-nanochannel-microchannel array based nanoelectroporation system for precise gene transfection

A micro/nano-fabrication process of a nanochannel electroporation (NEP) array and its application for precise delivery of plasmid for non-viral gene transfection is described. A dip-combing device is optimized to produce DNA nanowires across a microridge array patterned on the polydimethylsiloxane (PDMS) surface with a yield up to 95%. Molecular imprinting based on a low viscosity resin, 1,4-butanediol diacrylate (1,4-BDDA), adopted to convert the microridge-nanowire-microridge array into a microchannel-nanochannel-microchannel (MNM) array. Secondary machining by femtosecond laser ablation is applied to shorten one side of microchannels from 3000 to 50 μm to facilitate cell loading and unloading. The biochip is then sealed in a packaging case with reservoirs and microfluidic channels to enable cell and plasmid loading, and to protect the biochip from leakage and contamination. The package case can be opened for cell unloading after NEP to allow for the follow-up cell culture and analysis. These NEP cases can be placed in a spinning disc and up to ten discs can be piled together for spinning. The resulting centrifugal force can simultaneously manipulate hundreds or thousands of cells into microchannels of NEP arrays within 3 minutes. To demonstrate its application, a 13 kbp OSKM plasmid of induced pluripotent stem cell (iPSC) is injected into mouse embryonic fibroblasts cells (MEFCs). Fluorescence detection of transfected cells within the NEP biochips shows that the delivered dosage is high and much more uniform compared with similar gene transfection carried out by the conventional bulk electroporation (BEP) method.

A nanochannel based on-line universal logic ion sensing platform

In this work, a novel ion sensing platform was constructed in a microfluidic chip based on a very easy nano-fabrication technique, with which the nanoscale channel generated along the junction of the PDMS and metal strip could serve as a salt bridge for electrochemical measurements. More importantly, we have proposed a flexible and universal ion sensing strategy based on Boolean logic, which can rapidly report the concentration of analyte by the approach method. Firstly, the performance of the nanochannel based salt bridge was characterized, and the results showed that the nanoscale salt bridge behaved comparably to the traditional ones. To illustrate the promising applications of this wonderful design, an IrOx electrode was employed to construct the on-line pH sensing device as an example, and a wide linearity range (pH 2-12) was obtained with a really high sensitivity of 74.15 mV per pH unit. Owing to the use of the logic sensing strategy, we achieved rapid identification of the sample pH on-line, and demonstrated the broad potential of our system in designing sensing devices with extremely high integration, automation and throughput.

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.

A device for performing lateral conductance measurements on individual double-stranded DNA molecules

A nanofluidic device is described that is capable of electrically monitoring the driven translocation of DNA molecules through a nanochannel. This is achieved by intersecting a long transport channel with a shorter orthogonal nanochannel. The ionic conductance of this transverse nanochannel is monitored while DNA is electrokinetically driven through the transport channel. When DNA passes the intersection, the transverse conductance is altered, resulting in a transient current response. In 1 M KCl solutions, this was found to be a current enhancement of 5-25%, relative to the baseline transverse ionic current. Two different device geometries were investigated. In one device, the DNA was detected after it was fully inserted into and translocating through the transport nanochannel. In the other device, the DNA was detected while it was in the process of entering the nanochannel. It was found that these two conditions are characterized by different transport dynamics. Simultaneous optical and electrical monitoring of DNA translocation confirmed that the transient events originated from DNA transport through the nanochannel intersection.

High throughput fabrication of disposable nanofluidic lab-on-chip devices for single molecule studies

An easy method is introduced allowing fast polydimethylsiloxane (PDMS) replication of nanofluidic lab-on-chip devices using accurately fabricated molds featuring cross-sections down to 60 nm. A high quality master is obtained through proton beam writing and UV lithography. This master can be used more than 200 times to replicate nanofluidic devices capable of handling single DNA molecules. This method allows to fabricate nanofluidic devices through simple PDMS casting. The extensions of YOYO-1 stained bacteriophage T4 and λ-DNA inside these nanochannels have been investigated using fluorescence microscopy and follow the scaling prediction of a large, locally coiled polymer chain confined in nanochannels.

Electric-field-controlled flow in nanoscale-thin wetting films

A novel nanofluidic system based on electroosmotic flow in nanoscale-thin aqueous wetting films is reported. The water films formed spontaneously on mica substrates in a saturation humidity environment. The film thickness was determined to be a few tens of nanometers by optical interference and fluorescence intensity measurements and was consistent with a theoretical evaluation of the thickness of a film based on the competing forces of electrostatic repulsion and capillary pressure. Lateral flow was induced by applying a dc electric field tangential to the film and characterized by tracking the position of a fluorescent probe. The mobilities of the thin fluid layer and the flow marker were lower than the predictions of the electrokinetic theory, which may be a result of adsorption of the fluorescent molecules to the mica. Confinement of the film to two-dimensional "channels" was achieved by microcontact printing of patterned hydrophobic monolayers onto the substrate. This system has the advantage of simple and inexpensive fabrication in comparison to nanofluidic devices made by traditional lithography techniques.

Parallel sub-micrometre channels with different dimensions for laser scattering detection

A novel and simple approach for the realization of polymer sub-micrometre channels is introduced by exploiting replica molding of Pt wires deposited by focused ion beam. We fabricate arrays of parallel channels with typical dimensions down to 600 nm and with variable height. We characterize the pressure-driven transport of polymer colloids through the channels in terms of the translocation frequency, amplitude and duration by implementing a laser scattering detection technique. We propose a prototype application of the presented platform such as the in situ sizing and sensing of populations of particles with different dimensions down to 50 nm.

Optical biosensors to analyze novel biomarkers in oncology

Many cancer types are characterized by poor survival and unpredictable therapy response. Easy-to-perform molecular analyses may help patient stratification and treatment tailoring. Several integrated devices have been proposed to overcome current analysis equipment limitations. They offer improved sensitivity and easy availability of parallel detection. Particularly, unlabelled optical biosensors combine the manifold advantages of integrated sensors (e.g. easy handling, portability and low-volume requirement) with detection of target molecules in their original form. Here, we review integrated optical biosensor current features, and discuss their possible application to the detection of protein variants from body fluids, with particular regard to histone modifications. Indeed, histone post-translational modifications are a set of epigenetic markers frequently deregulated in cancer. Available technology does not allow a comprehensive analysis of all histone modifications in a single patient. Thus, label-free optical biosensors may pave the way to the discovery and detection of a novel class of biomarkers in oncology.

Atomic layer deposition on phase-shift lithography generated photoresist patterns for 1D nanochannel fabrication

A versatile, low-cost, and flexible approach is presented for the fabrication of millimeter-long, sub-100 nm wide 1D nanochannels with tunable wall properties (wall thickness and material) over wafer-scale areas on glass, alumina, and silicon surfaces. This approach includes three fabrication steps. First, sub-100 nm photoresist line patterns were generated by near-field contact phase-shift lithography (NFC-PSL) using an inexpensive homemade borosilicate mask (NFC-PSM). Second, various metal oxides were directly coated on the resist patterns with low-temperature atomic layer deposition (ALD). Finally, the remaining photoresist was removed via an acetone dip, and then planar nanochannel arrays were formed on the substrate. In contrast to all the previous fabrication routes, the sub-100 nm photoresist line patterns produced by NFC-PSL are directly employed as a sacrificial layer for the creation of nanochannels. Because both the NFC-PSL and the ALD deposition are highly reproducible processes, the strategy proposed here can be regarded as a general route for nanochannel fabrication in a simplified and reliable manner. In addition, the fabricated nanochannels were used as templates to synthesize various organic and inorganic 1D nanostructures on the substrate surface.

Integrated extended-nano chemical systems on a chip

In a past decade, new research fields utilizing microfluidics have been formed. General micro-integration methods were proposed, and the supporting fundamental technologies were widely developed. These methodologies made various applications in analytical and chemical synthesis fields, and their superior performances such as rapid, simple, and high efficient processing have been proved. Recently, the space is further downscaling to the 10(1)-10(2) nm scale (extended-nano space). The extended-nano space is located between conventional nanotechnology (10(0)-10(1) nm) and microtechnology (>1 mum), and the research tools are not well established. In addition, the extended-nano space is a transient space from single molecules to bulk condensed phase, and fluidics and chemistry are unknown. For these purposes, basic methodologies were developed, and new specific phenomena in fluidics and chemistry were found. These new phenomena were applied to unique chemical operations such as concentration and ion selection. The new research fields are now being created which are quite different with those in microspace. In this tutorial review, we focus on the basic researches in extended-nano space and survey the fundamental technologies for extended-nano space and reported specific liquid properties. Then, several unique chemical operations utilizing the properties are introduced. Finally, we show the future perspectives by showing the problems to be solved and illustrating the applications in development and in near future.

High aspect ratio taper-free microchannel fabrication using femtosecond Bessel beams

We present a systematic study of femtosecond laser microchannel machining in glass using nondiffracting Bessel beams. In particular, our results identify a source and focusing parameter working window where high aspect ratio taper-free microchannels can be reproducibly produced without sample translation. With appropriate source parameters, we machine channels of 2 microm diameter and with aspect ratios up to 40. We propose the filamentation stability of the Bessel beam propagation as the critical factor underlying the controlled and reproducible results that have been obtained.

Electrophoretic separation of DNA in gels and nanostructures

The development of nanostructure devices has opened the door to new DNA separation techniques and fundamental investigations. With advanced nanotechnologies, artificial gels (e.g. nanopillar arrays, nanofilters) can be manufactured with controlled and ordered geometries. This contrast with gels, where the pores are disordered and the range of available pore sizes is limited by the level of cross-linking and the mechanical properties of the gel. In this review, we recall the theories developed for free-solution and gel electrophoresis (extended Ogston model, biased reptation and entropic trapping) and from this perspective, suggestions for future concepts for fast DNA separation using nanostructures will be given.

Manipulation of single DNA molecules by using optically projected images

A new platform is presented that is capable of manipulating a single DNA molecule based on optically-induced dielectrophoretic forces. The ends of a single DNA molecule are bound with a micro-bead, which is then manipulated by interactions with optical images projected from a commercially available projector. Thus a single DNA molecule is indirectly manipulated by a projected animation pre-programmed using simple computer software. Real-time observation of the manipulation process is made possible by using a fluorescent dye and an oxygen scavenging buffer. Two types of DNA manipulation modes, specifically DNA elongation and rotation, are successfully demonstrated and are characterized. The maximum stretching force can be as high as 61.3 pN for a 10.1 microm bead. Experimental data show that the force-extension curve measured using this platform fits reasonably with the worm-like chain model. The developed platform can be a promising and flexible tool for further applications requiring single molecule manipulation.

Field-dependent DNA mobility in 20 nm high nanoslits

The transport behavior of lambda-DNA (48 kbp) in fused silica nanoslits is investigated upon application of electrical fields of different strengths. The slit dimensions are 20 nm in height, 3 microm in width, and 500 microm in length. With fields of 30 kV/m or below, the molecules move fluently through the slits, while at higher electrical fields, the DNA molecules move intermittently, resulting in a strongly reduced mobility. We propose that the behavior can be explained by mechanical and/or field-induced dielectrophoretic DNA trapping due to the surface roughness in the nanoslits. The observation of preferential pathways and trapping sites of the lambda-DNA molecules through the nanoslits supports this hypothesis and indicates that the classical viscous friction models to explain the DNA movement in nanoslits needs to be modified to include these effects. Preliminary experiments with the smaller XbaI-digested litmus-DNA (2.8 kbp) show that the behavior is size-dependent, suggesting that the high field electrophoresis in nanoslits can be used for DNA separation.

DNA linearization through confinement in nanofluidic channels

Stretching DNA has emerged as a vital process for studying the physical and biological properties of these molecules. Over the past decade, there has been increasing research interest in utilizing nanoscale fluidic channels to confine and stretch single DNA molecules. Nanofabricated systems for linearizing DNA have revealed new and important insights into the conformation changes of DNA molecules. They also have emerged as innovative techniques for efficiently separating DNA molecules based on size and for physically mapping genetic information along the genome. This review describes physical theories of DNA linearization, current DNA stretching techniques based on nanofabricated channels, and breakthroughs resulting from the use of nanofluidic channels for DNA linearization.

Nanochannels in SU-8 with floor and ceiling metal electrodes and integrated microchannels

Sacrificially etched 2-D nanofluidic channels and nanospaces with integrated floor and ceiling electrodes and arbitrary channel geometries have been demonstrated with channel heights from 20 nm to 400 nm, widths from 800 nm to 40 microm, and lengths up to 3 mm, using SU-8 as the channel structural material.

An integrated system for enzymatic cleavage and electrostretching of freely-suspended single DNA molecules

A novel polyacrylamide gel-based femtolitre microchamber system for performing single-molecule restriction enzyme assay on freely-suspended DNA molecules and subsequent DNA electrostretching by applying an alternating electric field has been developed. We attempted the integration by firstly initiating restriction enzyme reaction on a fluorescent-stained lambdaDNA molecule, encapsulated in a microchamber, using magnesium as an external trigger. Upon complete digestion, the cleaved DNA fragments were electrostretched to analyze the DNA lengths optically. The critical parameters for electrostretching of encapsulated DNA were investigated and optimum stretching was achieved by using 1.5 kHz pulses with electric field strength in the order of 10(3) V cm(-1) in 7% linear polyacrylamide (LPA) solution. LPA was adopted to minimize the adverse effects of ionic thermal agitation on molecular dielectrophoretic elongation in the microchamber. In our experiments, as the fragments were not immobilized throughout the entire protocol, it was found from repeated tests that digestion always occurred, producing the expected number of cleaved fragments. This versatile microchamber approach realized direct observation of these biological reactions on real-time basis at a single-molecule level. Furthermore, with the employment of porous polyacrylamide gel, the effective manipulation of DNA assays and the ability to combine conventionally independent bioanalytical processes have been demonstrated.

A simple polysilsesquioxane sealing of nanofluidic channels below 10 nm at room temperature

We present a simple sealing method to fabricate nanofluidic channels, where plasma treated polysilsesquioxane (PSQ) thin film on a rigid support is used to bond to a hydrophilic glass surface permanently at room temperature. This method shows precise dimension control below 10 nm with easy experimental setup. Using this method, one dimensional confined shallow nanochannels with a depth as small as 8 nm and an aspect ratio of <4 x 10(-5), two dimensional confined nanochannel arrays, and integrated nano/microchannel devices with a micro-to-nano interface have been demonstrated. Smooth transfer of DNA fragments from microchannel to nanochannel through the interface area was observed.

Single DNA Molecule Isolation and Trapping in a Microfluidic Device

This paper presents a systematic method to isolate and trap long single DNA segments between integrated electrodes in a microfluidic environment. Double stranded lambda-DNA molecules are introduced in a microchip and are isolated by electrophoretic force through microfluidic channels. Downstream, each individual molecule is extended and oriented by ac dielectrophoresis (900 kHz, 1 MV m(-1)) and anchored between aluminium electrodes. With a proper design, a long DNA segment (up to 10 microm) can be instantly captured in stretched conformation, opening way for further assays.

Poly(dimethylsiloxane)-based protein preconcentration using a nanogap generated by junction gap breakdown

Simple and efficient sample concentration tools are the key to the application of proteomics in a biological system. In this paper, we developed a method to realize a nanofluidic preconcentrator on a poly(dimethylsiloxane) (PDMS)-based microfluidic channel. The originality of our preconcentration device is the simple nanogap formation using the junction gap breakdown phenomenon between two PDMS microchannels, without using any photolithography and etching techniques. From the dc current measurement, we confirm that the nanogap formed between two microchannel junctions with approximately 80 nm depth. Using this device, we achieve the concentration volume of beta-phycoerythrin protein as high as 70 pL, which is 120-fold larger than that from our previous reports, with a concentration factor as high as 10(4) within 1 h. Also we show the availability of protein preconcentration under several different buffers (phosphate, acetate) at several different pH values (pH 5 to pH 9).

Tuneable elastomeric nanochannels for nanofluidic manipulation

Fluidic transport through nanochannels offers new opportunities to probe fundamental nanoscale transport phenomena and to develop tools for manipulating DNA, proteins, small molecules and nanoparticles. The small size of nanofabricated devices and the accompanying increase in the effect of surface forces, however, pose challenges in designing and fabricating flexible nanofluidic systems that can dynamically adjust their transport characteristics according to the handling needs of various molecules and nanoparticles. Here, we describe the use of nanoscale fracturing of oxidized poly(dimethylsiloxane) to conveniently fabricate nanofluidic systems with arrays of nanochannels that can actively manipulate nanofluidic transport through dynamic modulation of the channel cross-section. We present the design parameters for engineering material properties and channel geometry to achieve reversible nanochannel deformation using remarkably small forces. We demonstrate the versatility of the elastomeric nanochannels through tuneable sieving and trapping of nanoparticles, dynamic manipulation of the conformation of single DNA molecules and in situ photofabrication of movable polymeric nanostructures.

Nanofluidic structures for single biomolecule fluorescent detection

Fluid-filled nanofabricated cavities can be used to increase the spatial resolution of single molecule confocal microscopy based techniques by creating smaller and more uniformly illuminated probe volumes. Such structures may also be used to temporarily stretch single macromolecules, permitting the resolution of molecular details that would otherwise be beyond the capabilities of a diffraction limited system.

Conformational analysis of single DNA molecules undergoing entropically induced motion in nanochannels

We have used the interface between a nanochannel and a microchannel as a tool for applying controlled forces on a DNA molecule. A molecule, with a radius of gyration larger than the nanochannel width, that straddles such an interface is subject to an essentially constant entropic force, which can be balanced against other forces such as the electrophoretic force from an applied electric field. By controlling the applied field we can position the molecule as desired and observe the conformation of the molecule as it stretches, relaxes, and recoils from the nanochannel. We quantify and present models for the molecular motion in response to the entropic, electrophoretic, and frictional forces acting on it. By determining the magnitude of the drag coefficients for DNA molecules in the nanostructure, we are able to estimate the confinement-induced recoil force. Finally, we demonstrate that we can use a controlled applied field and the entropic interfacial forces to unfold molecules, which can then be manipulated and positioned in their simple extended morphology.

Future lab-on-a-chip technologies for interrogating individual molecules

Advances in technology have allowed chemical sampling with high spatial resolution and the manipulation and measurement of individual molecules. Adaptation of these approaches to lab-on-a-chip formats is providing a new class of research tools for the investigation of biochemistry and life processes.

Fabrication and validation of a multi-channel type microfluidic chip for electrokinetic streaming potential devices

To elaborate on the applicability of the electrokinetic micro power generation, we designed and fabricated the silicon-glass as well as the PDMS-glass microfluidic chips with the unique features of a multi-channel. Besides miniaturizing the device, the key advantage of our microfluidic chip utilization lies in the reduction in water flow rate. Both a distributor and a collector taking the tapered duct geometry are positioned aiming the uniform distribution of water flow into all individual channels of the chip, in which several hundreds of single microchannels are assembled in parallel. A proper methodology is developed accompanying the deep reactive ion etching as well as the anodic bonding, and optimum process conditions necessary for hard and soft micromachining are presented. It has been shown experimentally and theoretically that the silicon-based microchannel leads to increasing streaming potential and higher external current compared to those of the PDMS-based one. A proper comparison between experimental results and theoretical computations allows justification of the validity of our novel devices. It is useful to recognize that a material inducing a higher magnitude of zeta potential has an advantage for obtaining higher power density under the same external resistance.