Electromigration of Single Molecules of DNA in a Crystalline Array of 300-nm Silica Colloids

Submicron Nonporous Silica Particles for Enhanced Separation Performance in pCEC

Applications of submicron-scale particles are of rising interest in separation science due to their favorable surface-to-volume ratio and their fabrication of highly ordered structures. The uniformly dense packing beds in columns assembled from nanoparticles combined with an electroosmotic flow-driven system has great potential in a highly efficient separation system. Here, we packed capillary columns using a gravity method with synthesized nanoscale C18-SiO₂ particles having diameters of 300-900 nm. The separation of small molecules and proteins was evaluated in the packed columns on a pressurized capillary electrochromatography platform. The run-to-run reproducibility regarding retention time and peak area for the PAHs using a column packed with 300 nm C18-SiO₂ particles were less than 1.61% and 3.17%, respectively. Our study exhibited a systematic separation analysis of small molecules and proteins based on the columns packed with submicron particles combined with the pressurized capillary electrochromatography (pCEC) platform. This study may provide a promising analytical approach with extraordinary column efficiency, resolution, and speed for the separation of complex samples.

Emergent slow dynamics of collapsed polymers flowing through porous media

Using hydrodynamic simulations, we study the single polymers flowing through model porous media (close-packed colloidal crystal). In good solvent or high flow rates, the polymer transport is similar to gel electrophoresis, with size-dependent sieving for L_{c}/L≲1 and size-independent biased reptation for L_{c}/L≳1 (L_{c} is the polymer contour length and L is the diameter of colloids forming the porous media). Importantly, in bad solvent and low flow rates, the polymers show an extra window of size-dependent velocity for 1≲L_{c}/L≲2, where the polymer transport is controlled by a globule-stretch transition at pore throats, and the transport velocity is much slower than reptation.

Entropic trap purification of long DNA

Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.

Nanofluidic crystals: nanofluidics in a close-packed nanoparticle array

With various promising applications demonstrated, nanofluidics has been of broad research interest in the past decade. As nanofluidics matures from a proof of concept towards practical applications, it faces two major barriers: expensive nanofabrication and ultra-low throughput. To date, the only material that enables nanofabrication-free, high-throughput, yet precisely controllable nanofluidic systems is the close-packed nanoparticle array, i.e. nanofluidic crystals. Recently, significant progress in nanofluidics has been made using nanofluidic crystals, including high-current ionic diodes, high-power energy harvesters, efficient biomolecular separation, and facile biosensors. Nanofluidic crystals are seen as a key to applying nanofluidic concepts to real-world applications. In this review, we introduce the key concepts and models in nanofluidic crystals, summarize the fabrication methods, and discuss the various applications of nanofluidic crystals in depth, highlighting their advantages in terms of simple fabrication, low cost, flexibility, and high throughput. Finally, we provide our perspectives on the future of nanofluidic crystals and their potential impacts.

Deceleration of single-stranded DNA passing through a nanopore using a nanometre-sized bead structure

DNA sequencing with a solid-state nanopore requires a reduction of the translocation speeds of single-stranded DNA (ssDNA) over 10 μs/base. In this study, we report that a nanometre-sized bead structure constructed around a nanopore can reduce the moving speed of ssDNA to 270 μs/base by adjusting the diameter of the bead and its surface chemical group. This decelerating effect originates from the strong interaction between ssDNA and the chemical group on the surface of the bead. This nanostructure was simply prepared by dip coating in which a substrate with a nanopore was immersed in a silica bead solution and then dried in an oven. As compared with conventional approaches, our novel method is less laborious, simpler to perform and more effective in reducing ssDNA translocation speed.

Mechanism of DNA trapping in nanoporous structures during asymmetric pulsed-field electrophoresis

We investigate the trapping mechanism of individual DNA molecules in ordered nanoporous structures generated by crystalline particle arrays. Two requisites for trapping are revealed by the dynamics of single trapped DNA, fully-stretched U/J shapes and hernia formation. The experimental results show there is a stronger possibility for hernias to lead the reorientation upon switching directions of the voltage at high field strengths, where trapping occurs. Fully stretched DNA has longer unhooking times than expected by a classic rope-on-pulley model. We propose a dielectrophoretic (DEP) force reduces the mobility of segments at the apex of the U or J, where field gradients are highest, based on simulations and observations of the trapping force dependence on field strength. A modified model for unhooking time is obtained after the DEP force is introduced. The new model explains the unhooking time data by predicting an infinite trapping time when the ratio of arm length differences (of the U or J) to molecule length Δx/L < β, where β is a DEP parameter that is found to strongly increase with electric field. The DNA polarizability calculated with the DEP model and experimental value of β is of the same magnitude of reported value. The results indicate the tension at the apex of U/J shape DNA is the primary reason for DNA trapping during pulsed field separation, instead of hernias.

Surface-modified silica colloidal crystals: nanoporous films and membranes with controlled ionic and molecular transport

Nanoporous membranes are important for the study of the transport of small molecules and macromolecules through confined spaces and in applications ranging from separation of biomacromolecules and pharmaceuticals to sensing and controlled release of drugs. For many of these applications, chemists need to gate the ionic and molecular flux through the nanopores, which in turn depends on the ability to control the nanopore geometry and surface chemistry. Most commonly used nanoporous membrane materials are based on polymers. However, the nanostructure of polymeric membranes is not well-defined, and their surface is hard to modify. Inorganic nanoporous materials are attractive alternatives for polymers in the preparation of nanoporous membranes. In this Account, we describe the preparation and surface modification of inorganic nanoporous films and membranes self-assembled from silica colloidal spheres. These spheres form colloidal crystals with close-packed face centered cubic lattices upon vertical deposition from colloidal solutions. Silica colloidal crystals contain ordered arrays of interconnected three dimensional voids, which function as nanopores. We can prepare silica colloidal crystals as supported thin films on various flat solid surfaces or obtain free-standing silica colloidal membranes by sintering the colloidal crystals above 1000 °C. Unmodified silica colloidal membranes are capable of size-selective separation of macromolecules, and we can surface-modify them in a well-defined and controlled manner with small molecules and polymers. For the surface modification with small molecules, we use silanol chemistry. We grow polymer brushes with narrow molecular weight distribution and controlled length on the colloidal nanopore surface using atom transfer radical polymerization or ring-opening polymerization. We can control the flux in the resulting surface-modified nanoporous films and membranes by pH and ionic strength, temperature, light, and small molecule binding. When we modify the surface of the colloidal nanopores with ionizable moieties, they can generate an electric field inside the nanopores, which repels ions of the same charge and attracts ions of the opposite charge. This allows us to electrostatically gate the ionic flux through colloidal nanopores, controlled by pH and ionic strength of the solution when surface amines or sulfonic acids are present or by irradiation with light in the case of surface spiropyran moieties. When we modify the surface of the colloidal nanopores with chiral moieties capable of stereoselective binding of enantiomers, we generate colloidal films with chiral permselectivity. By filling the colloidal nanopores with polymer brushes attached to the pore surface, we can control the ionic flux through the corresponding films and membranes electrostatically using reversibly ionizable polymer brushes. By filling the colloidal nanopores with polymer brushes whose conformation reversibly changes in response to pH, ionic strength, temperature, or small molecule binding, we can control the molecular flux sterically. There are various potential applications for surface-modified silica colloidal films and membranes. Due to their ordered nanoporous structure and mechanical durability, they are beneficial in nanofluidics, nanofiltration, separations, and fuel cells and as catalyst supports. Reversible gating of flux by external stimuli may be useful in drug release, in size-, charge-, and structure-selective separations, and in microfluidic and sensing devices.

Nonmonotonous variation of DNA angular separation during asymmetric pulsed field electrophoresis

Asymmetric pulsed field electrophoresis within crystalline arrays is used to generate angular separation of DNA molecules. Four regimes of the frequency response are observed, a low frequency rise in angular separation, a plateau, a subsequent decline, and a second plateau at higher frequencies. It is shown that the frequency response for different sized DNA is governed by the relation between pulse time and the reorientation time of DNA molecules. The decline in angular separation at higher frequencies has not previously been analyzed. Real-time videos of single DNA molecules migrating under high frequency-pulsed electric field show the molecules no longer follow the head to tail switching, ratchet mechanism seen at lower frequencies. Once the pulse period is shorter than the reorientation time, the migration mechanism changes significantly. The molecule reptates along the average direction of the two electric fields, which reduces the angular separation. A freely jointed chain model of DNA is developed where the porous structure is represented with a hexagonal array of obstacles. The model qualitatively predicts the variation of DNA angular separation with respect to frequency.

A systematic evaluation of the role of crystalline order in nanoporous materials on DNA separation

The role of order within a porous separation matrix on the separation efficiency of DNA was studied systematically. DNA separation was based on a ratchet mechanism. Monodisperse colloidal suspensions of nanoparticles were used to fabricate highly ordered separation media with a hexagonal close-packed structure. Doping with a second particle size yielded structures with different degrees of disorder, depending upon the volume fraction of each particle size. Radial distribution functions and orientational order parameters were calculated from electron micrographs to characterize the scale of disorder. The peak separation distance, band broadening, and separation resolution of DNA molecules was quantified for each structure. DNA separation parameters using pulsed fields and the ratchet effect showed a strong dependence on order within the porous nanoparticle array. Ordered structures gave large separation distances, smaller band broadening and better resolution than highly disordered, nearly random, porous structures. The effect dominated these three parameters when compared to the effect of pore size. However, the effect of order on separation performance was not monotonic. A small, but statistically significant improvement was seen in structures with short range order compared to those with long range order.

Ion transport in sulfonated nanoporous colloidal films

The surface of self-assembled nanoporous silica colloidal crystalline films comprised of 184-nm-diameter silica spheres has been sulfonated using 1,3-propanesultone. The transport of ions through the sulfonated films has been studied using cyclic voltammetry in water as a function of ion charge, pH, and solution ionic strength. We found that the flux of anions through the sulfonated colloidal films is reduced, while the flux of cations is increased, compared to the unmodified colloidal films. This behavior is pH-dependent and is due to electrostatic repulsion/attraction that can be modulated by changing the ionic strength of the contacting solution.

Fundamentals of protein separations: 50 years of nanotechnology, and growing

The separation of proteins in biology samples has long been recognized as an important and daunting endeavor that continues to have enormous impact on human health. Today's technology for protein separations has its origins in the early nanotechnology of the 1950s and 1960s, and the methods include immunoassays and other affinity extractions, electrophoresis, and chromatography. What is different today is the need to resolve and identify many low-abundance proteins within complex biological matrices. Multidimensional separations are the rule, high speed is needed, and the separations must be able to work with mass spectrometry for protein identification. Hybrid approaches that combine disparate separation tools (including recognition, electrophoresis, and chromatography) take advantage of the fact that no single class of separation can resolve the proteins in a biological matrix. Protein separations represent a developing area technologically, and understanding the principles of protein separations from a molecular and nanoscale viewpoint will enable today's researchers to invent tomorrow's technology.

Monolithic integration of well-ordered nanoporous structures in the microfluidic channels for bioseparation

Gel electrophoresis and capillary gel electrophoresis are widely used for the separation of biomolecules. With increasing demand in the miniaturized devices such as lab-on-a-chip, it is necessary to integrate such a separation component into a chip format. Here, we describe a simple approach to fabricate robust three-dimensional periodic porous nanostructures inside the microchannels for the separation of DNA molecules. In our approach, the colloidal crystals were first grown inside the microchannel using evaporation assisted self-assembly process. Then the void spaces among the colloidal crystals were filled with epoxy-based negative tone photoresist (SU-8). UV radiation was used to cure the photoresist at the desired area inside the microchannel. After subsequent development and nanoparticle removal, the well-ordered nanoporous structures inside the microchannel were obtained. Our results indicated that it was possible to construct periodic porous nanostructures inside the microchannels with cavity size around 300 nm and interconnecting pores around 30 nm. The mobility of large DNA molecules with different sizes was measured as a function of the applied electric field in the nanoporous materials. It was also demonstrated that 1 kilo-base pair (kbp) DNA ladders could be separated in such an integrated system within 10 min under moderate electric field.

Confinement effects on electromigration of long DNA molecules in an ordered cavity array

Confinement effects on the electromigration of long dsDNA molecules in an array of well-ordered, molecular sized cavities interconnected by nanopores are described. The array was prepared by replicating the structure of a colloidal crystal of microspheres in a polymer matrix. Both conformation and mobility studies show that the electrophoretic behavior of large DNA molecules is distinct from that in gels and other microfabricated sieves, showing a peak in mobility versus electric field, and an inversion in the separation order with field strength. A simple model was proposed to interpret this unexpected observation qualitatively. We conclude that the molecular behavior of DNA can be modified by the combination of entropic effect and electric trapping as a consequence of both unique geometry and conductivity of this cavity array material. This approach provides insights for design and optimization of on-chip molecular sieving structures for rapid separation of long DNA molecules. It may lead to a promising material for manipulation and size fractionation of other biological macromolecules.

pH- and ionic strength-controlled cation permselectivity in amine-modified nanoporous opal films

The influence of pH and ionic strength on permselective transport in nanoporous opal films prepared from 440 nm silica spheres was investigated by cyclic voltammetry in aqueous and acetonitrile solutions. Three-layer opal films were deposited from a 1.5 wt % colloidal solution of silica spheres onto 25-microm-diameter Pt microdisk electrodes shrouded in glass. The films were chemically modified by immersing them in a dry acetonitrile solution of 3-aminopropyl triethoxysilane. When the surface amino groups of the modified opal films are protonated and there is little or no supporting electrolyte present in solution, the flux of cationic redox species through the opal membrane is blocked because of electrostatic repulsion. The permselectivity is pH-dependent and can be modulated by adjusting the Debye screening length within the nanopores of the opal by changing the ionic strength of the contacting solution.