Electrodeless Dielectrophoresis of Single- and Double-stranded DNA

Biophysical Journal. Oct, 2002  |  Pubmed ID: 12324434

Dielectrophoretic trapping of molecules is typically carried out using metal electrodes to provide high field gradients. In this paper we demonstrate dielectrophoretic trapping using insulating constrictions at far lower frequencies than are feasible with metallic trapping structures because of water electrolysis. We demonstrate that electrodeless dielectrophoresis (EDEP) can be used for concentration and patterning of both single-strand and double-strand DNA. A possible mechanism for DNA polarization in ionic solution is discussed based on the frequency, viscosity, and field dependence of the observed trapping force.

Single-molecule Measurement of Protein Folding Kinetics

Science (New York, N.Y.). Aug, 2003  |  Pubmed ID: 12947198

In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of Förster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.

Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding

Analytical Chemistry. Dec, 2004  |  Pubmed ID: 15595857

We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.

Layer-by-Layer Electrostatic Self-assembly of Polyelectrolyte Nanoshells on Individual Carbon Nanotube Templates

Langmuir : the ACS Journal of Surfaces and Colloids. Feb, 2004  |  Pubmed ID: 15803732

Carbon nanotubes have been featured prominently in the nanotechnology research for some time, yet robust strategies for noncovalent chemical modification of the nanotube surface are still missing. Such strategies are essential for the creation of functional device architectures. Here, we present a new general procedure for carbon nanotube modification based on polyelectrolyte layer-by-layer assembly. We have built multilayer structures around individual carbon nanotube bridges by first modifying the nanotube surface with a pyrene derivative followed by layer-by-layer deposition of polyelectrolyte macroions on the nanotube. Transmission electron microscopy and scanning confocal fluorescence microscopy images confirm the formation of nanometer-thick amorphous polymer nanoshells around the nanotubes. These multilayer polyelectrolyte shells on individual carbon nanotubes introduce nearly unlimited opportunities for the incorporation of various functionalities into nanotube devices, which, in turn, opens up the possibility of building more complex multicomponent structures.

Functional One-dimensional Lipid Bilayers on Carbon Nanotube Templates

Journal of the American Chemical Society. May, 2005  |  Pubmed ID: 15898805

Use of biological machines and environments in novel bioinorganic nanostructures is critical for development of new types of biosensors, bio-NEMS devices, and functional materials. Lipid bilayers that mimic a cell membrane have already played an important role in such applications. We present supported lipid bilayers that spontaneously assemble in a continuous nanoshell around a template of a carbon nanotube wrapped with hydrophilic polymer cushion layers. We demonstrate that such 1-D lipid membranes are fluid and can heal defects, even over repeated damage-recovery cycles. A simple diffusion model can describe mobility of lipid molecules in these 1-D nanoshells. These structures could lead to the development of new classes of biosensors and bioelectronic devices.

Fast Mass Transport Through Sub-2-nanometer Carbon Nanotubes

Science (New York, N.Y.). May, 2006  |  Pubmed ID: 16709781

We report gas and water flow measurements through microfabricated membranes in which aligned carbon nanotubes with diameters of less than 2 nanometers serve as pores. The measured gas flow exceeds predictions of the Knudsen diffusion model by more than an order of magnitude. The measured water flow exceeds values calculated from continuum hydrodynamics models by more than three orders of magnitude and is comparable to flow rates extrapolated from molecular dynamics simulations. The gas and water permeabilities of these nanotube-based membranes are several orders of magnitude higher than those of commercial polycarbonate membranes, despite having pore sizes an order of magnitude smaller. These membranes enable fundamental studies of mass transport in confined environments, as well as more energy-efficient nanoscale filtration.

Bio-assay Based on Single Molecule Fluorescence Detection in Microfluidic Channels

Analytical and Bioanalytical Chemistry. Aug, 2006  |  Pubmed ID: 16802123

A rapid bioassay is described based on the detection of colocalized fluorescent DNA probes bound to DNA targets in a pressure-driven solution flowing through a planar microfluidic channel. By employing total internal reflection excitation of the fluorescent probes and illumination of almost the entire flow channel, single fluorescent molecules can be efficiently detected leading to the rapid analysis of nearly the entire solution flowed through the device. Cross-correlation between images obtained from two spectrally distinct probes is used to determine the target concentration and efficiently reduces the number of false positives. The rapid analysis of DNA targets in the low pM range in less than a minute is demonstrated.

Optimization of a Microfluidic Mixer for Studying Protein Folding Kinetics

Analytical Chemistry. Jul, 2006  |  Pubmed ID: 16808436

We have applied an optimization method in conjunction with numerical simulations to minimize the mixing time of a microfluidic mixer developed for protein folding studies. The optimization method uses a semideterministic algorithm to find the global minimum of the mixing time by varying the mixer geometry and flow conditions. We describe the minimization problem and constraints and give a brief overview of the optimization algorithm. We present results of the optimization, including the optimized geometry and parameter sensitivities, and we demonstrate the improvement in mixing performance with experiments using microfabricated mixers. The dye-quenching experiments of the original and optimized mixer designs show respective mixing times of 7 and 4 mus, a 40% reduction. The new design also provides more uniform mixing across streamlines that enter the mixer. The optimized mixer is the fastest reported continuous flow mixer for protein folding.

Ultrafast Gas Chromatography on Single-wall Carbon Nanotube Stationary Phases in Microfabricated Channels

Analytical Chemistry. Aug, 2006  |  Pubmed ID: 16906706

The key to rapid temperature programmed separations with gas chromatography are a fast, low-volume injection and a short microbore separation column with fast resistive heating. One of the major problems with the reduction of column dimensions for micro gas chromatography is the availability of a stationary phase that provides good separation performance. In this report, we present the first integration of single-wall carbon nanotubes (SWNTs) as a stationary phase into 100 mum x 100 mum square and 50-cm-long microfabricated channels. The small size of this column with integrated resistive heater and the robustness of the SWNT phase allow for fast temperature programming of up to 60 degrees C/s. A combination of the fast temperature programming and the narrow peak width of small-volume injections that can be obtained from a high-speed, dual-valve injection system allows for rapid separations of gas mixtures. We demonstrate highly reproducible separations of four-compound test mixtures on these columns in less than 1 s using fast temperature programming.

Controlled Electrostatic Gating of Carbon Nanotube FET Devices

Nano Letters. Sep, 2006  |  Pubmed ID: 16968029

Carbon nanotube transistors are a promising platform for the next generation of nonoptical biosensors. However, the exact nature of the biomolecule interactions with nanotubes in these devices remains unknown, creating one of the major obstacles to their practical use. We assembled alternating layers of oppositely charged polyelectrolytes on the carbon nanotube transistors to mimic gating of these devices by charged molecules. The devices showed reproducible oscillations of the transistor threshold voltage depending on the polarity of the outer polymer layer in the multilayer film. This behavior shows excellent agreement with the predictions of a simple electrostatic model. Finally, we demonstrate that complex interactions of adsorbed species with the device substrate and the surrounding electrolyte can produce significant and sometimes unexpected effects on the device characteristics.

Mapping Protein Collapse with Single-molecule Fluorescence and Kinetic Synchrotron Radiation Circular Dichroism Spectroscopy

Proceedings of the National Academy of Sciences of the United States of America. Jan, 2007  |  Pubmed ID: 17185422

We have used the combination of single-molecule Förster resonance energy transfer and kinetic synchrotron radiation circular dichroism experiments to probe the conformational ensemble of the collapsed unfolded state of the small cold shock protein CspTm under near-native conditions. This regime is physiologically most relevant but difficult to access experimentally, because the equilibrium signal in ensemble experiments is dominated by folded molecules. Here, we avoid this problem in two ways. One is the use of single-molecule Förster resonance energy transfer, which allows the separation of folded and unfolded subpopulations at equilibrium and provides information on long-range intramolecular distance distributions. From experiments with donor and acceptor chromophores placed at different positions within the chain, we find that the distance distributions in unfolded CspTm agree surprisingly well with a Gaussian chain not only at high concentrations of denaturant, where the polypeptide chain is expanded, but also at low denaturant concentrations, where the chain is collapsed. The second, complementary approach is synchrotron radiation circular dichroism spectroscopy of collapsed unfolded molecules transiently populated with a microfluidic device that enables rapid mixing. The results indicate a beta-structure content of the collapsed unfolded state of approximately 20% compared with the folded protein. This suggests that collapse can induce secondary structure in an unfolded state without interfering with long-range distance distributions characteristic of a random coil, which were previously found only for highly expanded unfolded proteins.

Protein Hydrophobic Collapse and Early Folding Steps Observed in a Microfluidic Mixer

Biophysical Journal. Jul, 2007  |  Pubmed ID: 17416618

We demonstrate that the sub-millisecond protein folding process referred to as "collapse" actually consists of at least two separate processes. We observe the UV fluorescence spectrum from naturally occurring tryptophans in three well-studied proteins, cytochrome c, apomyoglobin, and lysozyme, as a function of time in a microfluidic mixer with a dead time of approximately 20 mus. Single value decomposition of the time-dependent spectra reveal two separate processes: 1), a spectral shift which occurs within the mixing time; and 2), a fluorescence decay occurring between approximately 100 and 300 micros. We attribute the first process to hydrophobic collapse and the second process to the formation of the first native tertiary contacts.

Improvements in Mixing Time and Mixing Uniformity in Devices Designed for Studies of Protein Folding Kinetics

Analytical Chemistry. Aug, 2007  |  Pubmed ID: 17583912

Using a microfluidic laminar flow mixer designed for studies of protein folding kinetics, we demonstrate a mixing time of 1 +/- 1 micros with sample consumption on the order of femtomoles. We recognize two limitations of previously proposed designs: (1) size and shape of the mixing region, which limits mixing uniformity and (2) the formation of Dean vortices at high flow rates, which limits the mixing time. We address these limitations by using a narrow shape-optimized nozzle and by reducing the bend of the side channel streamlines. The final design, which combines both of these features, achieves the best performance. We quantified the mixing performance of the different designs by numerical simulation of coupled Navier-Stokes and convection-diffusion equations and experiments using fluorescence resonance energy-transfer (FRET)-labeled DNA.

Ion Exclusion by Sub-2-nm Carbon Nanotube Pores

Proceedings of the National Academy of Sciences of the United States of America. Nov, 2008  |  Pubmed ID: 18539773

Biological pores regulate the cellular traffic of a large variety of solutes, often with high selectivity and fast flow rates. These pores share several common structural features: the inner surface of the pore is frequently lined with hydrophobic residues, and the selectivity filter regions often contain charged functional groups. Hydrophobic, narrow-diameter carbon nanotubes can provide a simplified model of membrane channels by reproducing these critical features in a simpler and more robust platform. Previous studies demonstrated that carbon nanotube pores can support a water flux comparable to natural aquaporin channels. Here, we investigate ion transport through these pores using a sub-2-nm, aligned carbon nanotube membrane nanofluidic platform. To mimic the charged groups at the selectivity region, we introduce negatively charged groups at the opening of the carbon nanotubes by plasma treatment. Pressure-driven filtration experiments, coupled with capillary electrophoresis analysis of the permeate and feed, are used to quantify ion exclusion in these membranes as a function of solution ionic strength, pH, and ion valence. We show that carbon nanotube membranes exhibit significant ion exclusion that can be as high as 98% under certain conditions. Our results strongly support a Donnan-type rejection mechanism, dominated by electrostatic interactions between fixed membrane charges and mobile ions, whereas steric and hydrodynamic effects appear to be less important.

Microfluidic Mixers for the Investigation of Rapid Protein Folding Kinetics Using Synchrotron Radiation Circular Dichroism Spectroscopy

Analytical Chemistry. Dec, 2008  |  Pubmed ID: 19072266

We have developed a microfluidic mixer optimized for rapid measurements of protein folding kinetics using synchrotron radiation circular dichroism (SRCD) spectroscopy. The combination of fabrication in fused silica and synchrotron radiation allows measurements at wavelengths below 220 nm, the typical limit of commercial instrumentation. At these wavelengths, the discrimination between the different types of protein secondary structure increases sharply. The device was optimized for rapid mixing at moderate sample consumption by employing a serpentine channel design, resulting in a dead time of less than 200 micros. Here, we discuss the design and fabrication of the mixer and quantify the mixing efficiency using wide-field and confocal epi-fluorescence microscopy. We demonstrate the performance of the device in SRCD measurements of the folding kinetics of cytochrome c, a small, fast-folding protein. Our results show that the combination of SRCD with microfluidic mixing opens new possibilities for investigating rapid conformational changes in biological macromolecules that have previously been inaccessible.

Biofunctional Subwavelength Optical Waveguides for Biodetection

ACS Nano. Feb, 2008  |  Pubmed ID: 19206625

We report a versatile biofunctional subwavelength photonic device platform for real-time detection of biological molecules. Our devices contain lipid bilayer membranes fused onto metal oxide nanowire waveguides stretched across polymeric flow channels. The lipid bilayers incorporating target receptors are submersed in the propagating evanescent field of the optical cavity. We show that the lipid bilayers in our devices are continuous, have very high mobile fraction, and are resistant to fouling. We also demonstrate that our platform allows rapid membrane exchange. Finally, we use this device to detect the hybridization of specific DNA target sequences in solution to complementary probe DNA strands anchored to the lipid bilayer. This evanescent wave sensing architecture holds great potential for portable, all-optical detection systems.

Ruggedness in the Folding Landscape of Protein L

HFSP Journal. Dec, 2008  |  Pubmed ID: 19436489

By exploring the folding pathways of the B1 domain of protein L with a series of equilibrium and rapid kinetic experiments, we have found its unfolded state to be more complex than suggested by two-state folding models. Using an ultrarapid mixer to initiate protein folding within approximately 2-4 microseconds, we observe folding kinetics by intrinsic tryptophan fluorescence and fluorescence resonance energy transfer. We detect at least two processes faster than 100 mus that would be hidden within the burst phase of a stopped-flow instrument measuring tryptophan fluorescence. Previously reported measurements of slow intramolecular diffusion are commensurate with the slower of the two observed fast phases. These results suggest that a multidimensional energy landscape is necessary to describe the folding of protein L, and that the dynamics of the unfolded state is dominated by multiple small energy barriers.

Separation Materials: Proteins Make for Finer Filters

Nature Nanotechnology. Jun, 2009  |  Pubmed ID: 19498391

Direct Observation of Downhill Folding of Lambda-repressor in a Microfluidic Mixer

Biophysical Journal. Sep, 2009  |  Pubmed ID: 19751683

The protein lambda(6-85) has been implicated in barrierless folding by observations of kinetic relaxation after nanosecond T-jump. In this work we observed folding of this protein after dilution of a high denaturant in an ultrarapid microfluidic mixer at temperatures far below the thermal midpoint. The observations of total intensity and spectral shift of tryptophan fluorescence yielded distinctly different kinetics and activation energies. These results may be explained as diffusion on a low-barrier, one-dimensional, free-energy surface, with different probes having different sensitivities along the reaction coordinate. Additionally, we observed an extremely fast phase within the mixing time that was not observed by T-jump, suggesting that the ensemble of unfolded states populated at high denaturant is distinct from those accessible at high temperature.

High-speed, Temperature Programmable Gas Chromatography Utilizing a Microfabricated Chip with an Improved Carbon Nanotube Stationary Phase

Talanta. Feb, 2009  |  Pubmed ID: 19084659

A new growth recipe for producing carbon nanotubes (CNTs) combined with a new bonding technique was implemented in a microfabricated gas chromatography (micro-GC) chip. Specifically, the micro-GC chip contained a 30-cm (length) microfabricated channel with a 50 microm x 50 microm square cross-section. A CNT stationary phase "mat" was grown on the bottom of the separation channel prior to the chip bonding. Injections onto the micro-GC chip were made using a previously reported high-speed diaphragm valve technique. A FID was used for detection with a high-speed electrometer board. All together, the result was a highly efficiency, temperature programmable (via low thermal mass, rapid on-chip resistive heating) micro-GC chip. In general, the newly designed micro-GC chip can be operated at significantly lower temperature and pressure than our previously reported micro-GC chip, while producing excellent chemical separations. Scanning electron microscopy (SEM) images show a relatively thin and uniform mat of nanotubes with a thickness of approximately 800 nm inside the channel. The stationary phase was further characterized using Raman spectroscopy. The uniformity of the stationary phase resulted in better separation efficiency and peak symmetry (as compared to our previous report) in the separation of a mixture of five n-alkanes (n-hexane, n-octane, n-nonane, n-decane and n-undecane). The on-chip resistive heater employing a temperature programming rate of 26 degrees C/s produced a peak capacity of eight within a 1.5-s time window.

Mechanism and Kinetics of Growth Termination in Controlled Chemical Vapor Deposition Growth of Multiwall Carbon Nanotube Arrays

Nano Letters. Feb, 2009  |  Pubmed ID: 19146455

We have investigated growth kinetics of multiwall carbon nanotube (MWCNT) arrays produced by catalytic thermal decomposition of ethylene gas in hydrogen, water, and argon mixture. The MWCNT growth rate exhibits a nonmonotonic dependence on total pressure and reaches a maximum at approximately 750 Torr of total pressure. Water concentrations in excess of 3000 ppm lead to the decrease in the observed growth rate. Optimal pressure and water concentration combination results in a reliable growth of well-aligned MWCNT arrays at a maximum growth rate of approximately 30 microm/min. These MWCNT arrays can reach heights of up to 1 mm with typical standard deviations for the array height of less than 8% over a large number of process runs spread over the time of 8 months. Nanotube growth rate in this optimal growth region remains essentially constant until growth reaches an abrupt and irreversible termination. We present a quantitative model that shows how accumulation of the amorphous carbon patches at the catalyst particle surface and the carbon diffusion to the growing nanotube perimeter causes this abrupt growth cessation. The influence of the partial pressures of ethylene and hydrogen on the ethylene decomposition driving force explains the nonlinear behavior of the growth rate as a function of total process pressure.

Extremely Slow Intramolecular Diffusion in Unfolded Protein L

Proceedings of the National Academy of Sciences of the United States of America. Aug, 2010  |  Pubmed ID: 20643973

A crucial parameter in many theories of protein folding is the rate of diffusion over the energy landscape. Using a microfluidic mixer we have observed the rate of intramolecular diffusion within the unfolded B1 domain of protein L before it folds. The diffusion-limited rate of intramolecular contact is about 20 times slower than the rate in 6 M GdnHCl, and because in these conditions the protein is also more compact, the intramolecular diffusion coefficient decreases 100-500 times. The dramatic slowdown in diffusion occurs within the 250 micros mixing time of the mixer, and there appears to be no further evolution of this rate before reaching the transition state of folding. We show that observed folding rates are well predicted by a Kramers model with a denaturant-dependent diffusion coefficient and speculate that this diffusion coefficient is a significant contribution to the observed rate of folding.

PH-tunable Ion Selectivity in Carbon Nanotube Pores

Langmuir : the ACS Journal of Surfaces and Colloids. Sep, 2010  |  Pubmed ID: 20715879

The selectivity of ion transport in nanochannels is of primary importance for a number of physical, chemical, and biological processes ranging from fluid separation to ion-channel-regulated cellular processes. Fundamental understanding of these phenomena requires model nanochannels with well-defined and controllable structural properties. Carbon nanotubes provide an ideal choice for nanofluidic studies because of their simple chemistry and structure, the atomic scale smoothness and chemical inertness of the graphitic walls, and the tunability of their diameter and length. Here, we investigate the selectivity of single and, for the first time, binary salt mixtures transport through narrow carbon nanotubes that act as the only pores in a silicon nitride membrane. We demonstrate that negatively charged carboxylic groups are responsible for the ion rejection performance of carbon nanotube pores and that ion permeation of small salts can be tuned by varying solution pH. Investigation of the effect of solution composition and ion valences for binary electrolytes with common cation in a pressure-driven flow reveals that the addition of slower diffusing multivalent anions to a solution of faster diffusing monovalent anions favors permeation of the monovalent anion. Larger fractions and valences of the added multivalent anions lower the rejection of the monovalent anion. In some cases, we observe negative rejection at low monovalent ion content.

Evidence of Multiple Folding Pathways for the Villin Headpiece Subdomain

The Journal of Physical Chemistry. B. Nov, 2011  |  Pubmed ID: 21923150

The defining property of two-state models of protein folding is that the measured relaxation rates are independent of the starting conditions and only depend on the final conditions. In this work we compare the kinetics of the very fast folding villin subdomain measured after a large change in denaturant concentration using an ultrarapid microfluidic mixer with the kinetics measured after a small temperature change in a laser T-jump experiment and find a significant difference in the observed folding kinetics. The final conditions of temperature and denaturant concentration and the use of tryptophan fluorescence as a probe are the same in both experiments, while the initial conditions are very different. The slower mixing kinetics show no evidence of the faster phase in T-jump experiments, which would support models of on- or off-pathway intermediates. Rather we interpret the combined mixer and T-jump experiments as evidence of an ensemble of unfolded states, some of which are traps. The ensemble after dilution from high denaturant is more expanded than the ensemble after an increase in temperature and, on average, takes longer to reach the native state.