Liquid core waveguide for full imaging of electrophoretic separations

We employed a liquid core waveguide to image both DNA electrophoresis separations and isoelectric focusing of proteins. The utility of the system is demonstrated for DNA fragment sizing and protein separations. The system utilizes the liquid-core waveguide as an efficient window for both the excitation of separated samples and the collection of light through total internal reflectance, with an ability to detect target molecules in the zeptomolar range. Scanning the excitation laser along the length of the electrophoresis capillary excites individually separated analyte bands, while the fluorescence is collected end-on by an optical fiber coupled to a photomultiplier, thus, creating an image of the separation along the length of the capillary.     

Feasibility of a DNA-Based Combinatorial Array Recognition Surface (CARS) in a Polyacrylamide Gel Matrix

We report initial attempts at developing a self-assembled combinatorial DNA biosensor array which may be capable of binding and identifying virtually any soluble analyte that binds the array by pattern recognition, in effect making it a universal biosensor surface. Data are presented for differential binding patterns of various analytes to 1-D arrays of combinatorial deoxyribonucleic acid (DNA) concatamer libraries which are spatially separated according to size and charge by electrophoresis in polyacrylamide gels. These DNA concatamer libraries are essentially composed of single-stranded (ss) random DNA 60 mers, which form a ldquosmearrdquo pattern in gels following electrophoresis. When used to bind and detect various analytes or mixtures of analytes in the gel, we refer to the DNA smear as a ldquocombinatorial array recognition surfacerdquo (CARS). Differences in intrinsic fluorescence scanning patterns of CARS gel strips were compared before and after addition of various analytes to the arrays to detect binding patterns. Scans revealed a high level of reproducibility for individual CARS arrays in a given gel with or without bound analytes. Scan patterns between different CARS gel strips were initially less reproducible, but purification of the DNA library using spin columns prior to electrophoresis improved gel-to-gel reproducibility.     

Automated sampling and imaging of analytes separated on thin-layer chromatography plates using desorption electrospray ionization mass spectrometry

Modest modifications to the atmospheric sampling capillary of a commercial electrospray mass spectrometer and upgrades to an in-house-developed surface positioning control software package (HandsFree TLC/MS) were used to enable the automated sampling and imaging of analytes on and within large area surface substrates using desorption electrospray ionization mass spectrometry. Sampling and imaging of rhodamine dyes separated on TLC plates were used to illustrate some of the practical applications of this system. Examples are shown for user-defined spot sampling from separated bands on a TLC plate (one or multiple spots), scanning of a complete development lane (one or multiple lanes), or imaging of analyte bands in a development lane (i.e., multiple lane scans with close spacing). The post data acquisition processing and data display aspects of the software system are also discussed.     

Fractionation of SWNT/nucleic acid complexes by agarose gel electrophoresis

We show that aqueous dispersions of single-walled carbon nanotubes (SWNTs), prepared with the aid of nucleic acids (NAs) such as RNA or DNA, can be separated into fractions using agarose gel electrophoresis. In a DC electric field, SWNT/NA complexes migrate in the gel in the direction of positive potential to form well-defined bands. Raman spectroscopy as a function of band position shows that nanotubes having different spectroscopic properties possess different electrophoretic mobilities. The migration patterns for SWNT/RNA and SWNT/DNA complexes differ. Parallel elution of the SWNT/NA complexes from the gel during electrophoresis and subsequent characterization by AFM reveals differences in nanotube diameter, length and curvature. The results suggest that fractionation of nanotubes can be achieved by this procedure. We discuss factors affecting the mobility of the nanotube complexes and propose analytical applications of this technique.     

On-line hyphenation of capillary isoelectric focusing and capillary gel electrophoresis by a dialysis interface

An on-line two-dimensional (2D) capillary electrophoresis (CE) system consisting of capillary isoelectric focusing (CIEF) and capillary gel electrophoresis (CGE) was introduced. To validate this 2D system, a dialysis interface was developed by mounting a hollow fiber on a methacrylate resin plate to hyphenate the two CE modes. The two dimensions of capillary shared a cathode fixated into a reservoir in the methacrylate plate; thus, with three electrodes and only one high-voltage source, a 2D CE framework was successfully established. A practical 2D CIEF-CGE experiment was carried out to deal with a target protein, hemoglobin (Hb). After the Hb variants with different isoelectric points (pIs) were focused in various bands in the first-dimension capillary, they were chemically mobilized one after another and fed to the second-dimension capillary for further separation in polyacrylamide gel. During this procedure, a single CIEF band was separated into several peaks due to different molecular weights. The resulting electrophoregram is quite different from that of either CIEF or CGE; therefore, more information about the studied Hb sample can be obtained.     

Separation of tissue proteins of human lung carcinomas by partial-filling capillary electrophoresis

Tissue proteins from human squamous cell lung carcinomas (SQCLC) and small cell lung carcinomas (SCLC) were separated in 0.01% hydroxypylmethyl cellulose (HPMC) linear polymer sieving solutions in the inlet portion of the capillary and next to the outlet of the capillary, followed by capillary zone electrophoresis (CZE) in 40 mM phosphate buffer, pH 2.5. A proper HPMC concentration could cause a molecular sieving effect through the formation of an entangled polymer network. The migration time of the analyte in this matrix depended on the size and electrophoretic mobility of the analyte, the mesh size, and the electric field strength. In the CZE separation, the electroosmotic flow and the charge-to-size ratio of the analyte were important parameters. HPMC concentration and zone length were examined to optimize the separation. Applying this partial-filling technique to the separation of water-soluble proteins from human lung tissues, we found a greatly improved resolution and increased peak intensity. The capillary electrophoresis patterns of normal, SQCLC, and SCLC were obtained and compared for their molecular classifications.     

Capillary affinity gel electrophoresis for combined size- and sequence-dependent separation of oligonucleotides

An interesting new approach to capillary affinity gel electrophoresis (CAGE) has been developed for the selective capture and separation of homopolymer and heteropolymer oligonucleotides. The combination of selectivity of bioaffinity recognition and high-resolution power of capillary gel electrophoresis allows the on-line sequence- and size-specific separation of oligonucleotides. Both rigid gel formulations and viscous replaceable polymer solutions having user-defined, single-stranded oligonucleotides covalently attached as recognition sequences are used. Contrary to most known affinity systems in capillary electrophoresis, which operate in a continuous mode, binding and release are accomplished in two steps, effectively separating the affinity from the separation step. At low temperature, oligonucleotides with complementary sequences in the analyte solution will bind to the immobilized recognition sequence while unrelated oligonucleotides will continue to migrate. This step is a preseparation, removing all nonspecific solutes from the sample. The release of the bound solutes is achieved at elevated temperature, allowing a probe of cross-reactivity for a given biorecognition element. Applications for high-resolution separations of short oligonucleotides and their mismatches are shown, and the potential for on-line preconcentration and separation of dilute analyte solutions, thus effectively enhancing the sensitivity, is demonstrated.     

Integration of isoelectric focusing with parallel sodium dodecyl sulfate gel electrophoresis for multidimensional protein separations in a plastic microfluidic [correction of microfludic] network

An integrated protein concentration/separation system, combining non-native isoelectric focusing (IEF) with sodium dodecyl sulfate (SDS) gel electrophoresis on a polymer microfluidic chip, is reported. The system provides significant analyte concentration and extremely high resolving power for separated protein mixtures. The ability to introduce and isolate multiple separation media in a plastic microfluidic network is one of two key requirements for achieving multidimensional protein separations. The second requirement lies in the quantitative transfer of focused proteins from the first to second separation dimensions without significant loss in the resolution acquired from the first dimension. Rather than sequentially sampling protein analytes eluted from IEF, focused proteins are electrokinetically transferred into an array of orthogonal microchannels and further resolved by SDS gel electrophoresis in a parallel and high-throughput format. Resolved protein analytes are monitored using noncovalent, environment-sensitive, fluorescent probes such as Sypro Red. In comparison with covalently labeling proteins, the use of Sypro staining during electrophoretic separations not only presents a generic detection approach for the analysis of complex protein mixtures such as cell lysates but also avoids additional introduction of protein microheterogeneity as the result of labeling reaction. A comprehensive 2-D protein separation is completed in less than 10 min with an overall peak capacity of approximately 1700 using a chip with planar dimensions of as small as 2 cm x 3 cm. Significant enhancement in the peak capacity can be realized by simply raising the density of microchannels in the array, thereby increasing the number of IEF fractions further analyzed in the size-based separation dimension.     

Comprehensive interpretation of gel electrophoresis data

From temperature analysis of polyacrylamide gel electrophoresis data for rigid-rod DNA analytes, it is proposed that an entropic force term is responsible for the discrepancy between Ogston-Morris-Rodbard-Chrambach model predictions and experimental results. This entropic force originates from reduction of the orientational freedom of anisotropic analytes in small pores of polyacrylamide gels. Time-dependent fluorescence anisotropy decay measurements confirm that, even in the absence of an external field, orientation of anisotropic analytes is restricted in polyacrylamide gels. A new comprehensive model is proposed that takes this effect into consideration. Predictions based on this model are found to compare favorably with experimental data for linear and three-arm asymmetrically branched rigid-rod DNA analytes covering a broad range of molecular aspect ratios and sizes. A new length scale is also proposed for describing the effect of analyte topology on electrophoretic mobility. This length scale reduces to the analyte radius of gyration in the limiting cases of spherically symmetric and linear rigid-rod species. Based on these results, a general approach is proposed for interpreting gel electrophoresis data of charged analytes possessing simple and complex topologies.     

Interactive control of pulsed field gel electrophoresis via real time monitoring.

The migration of DNA fragment bands through a slab gel can be monitored by UV absorption at 254 nm and imaged by a charge-coupled device (CCD) camera. Background correction and immediate viewing of band positions to interactively change the field program in pulsed-field gel electrophoresis is possible throughout the run via this detection scheme. The use of absorption removes the need for staining or radioisotope labelling, thereby simplifying sample preparation and reducing hazardous waste generation. This leaves the DNA in its native state and further analysis can be performed without destaining. The optimization of buffer concentration, electric field strength, temperature, agarose concentration, as well as pulse duration can considerably reduce total run time. For example, DNA from 2 to 850 kb can be separated in 3 h on a 7-cm gel with interactive control of the pulse time, which is 10 times faster than using a constant field program.     

High-throughput DNA droplet assays using picoliter reactor volumes

The online characterization and detection of individual droplets at high speeds, low analyte concentrations, and perfect detection efficiencies is a significant challenge underpinning the application of microfluidic droplet reactors to high-throughput chemistry and biology. Herein, we describe the integration of confocal fluorescence spectroscopy as a high-efficiency detection method for droplet-based microfluidics. Issues such as surface contamination, rapid mixing, and rapid detection, as well as low detections limits have been addressed with the approach described when compared to conventional laminar flow-based fluidics. Using such a system, droplet size, droplet shape, droplet formation frequencies, and droplet compositions can be measured accurately and precisely at kilohertz frequencies. Taking advantage of this approach, we demonstrate a high-throughput biological assay based on fluorescence resonance energy transfer (FRET). By attaching a FRET donor (Alexa Fluor 488) to streptavidin and labeling a FRET acceptor (Alexa Fluor 647) on one DNA strand and biotin on the complementary strand, donor and acceptor molecules are brought in proximity due to streptavidin-biotin binding, resulting in FRET. Fluorescence bursts of the donor and acceptor from each droplet can be monitored simultaneously using separate avalanche photodiode detectors operating in single photon counting mode. Binding assays were investigated and compared between fixed streptavidin and DNA concentrations. Binding curves fit perfectly to Hill-Waud models, and the binding ratio between streptavidin and biotin was evaluated and found to be in agreement with the biotin binding sites on streptavidin. FRET efficiency for this FRET pair was also investigated from the binding results. Efficiency results show that this detection system can precisely measure FRET even at low FRET efficiencies.     

Gateable nanofluidic interconnects for multilayered microfluidic separation systems

The extension of microfluidic devices to include three-dimensional fluidic networks allows complex fluidic and chemical manipulations but requires innovative methods to interface fluidic layers. Externally controllable interconnects, employing nuclear track-etched polycarbonate membranes containing nanometer-diameter capillaries, are described that produce hybrid three-dimensional fluidic architectures. Controllable nanofluidic transfer is achieved by controlling applied bias, polarity, and density of the immobile nanopore surface charge and the impedance of the nanocapillary array relative to the microfluidic channels. Analyte transport between vertically separated microchannels has three stable transfer levels, corresponding to zero, reverse, and forward bias. The transfer can even depend on the properties of the analyte being transferred such as the molecular size, illustrating the flexible character of the analyte transfer. In a specific analysis implementation, nanochannel array gating is applied to capillary electrophoresis separations, allowing selected separated components to be isolated for further manipulation, thereby opening the way for preparative separations at attomole analyte mass levels.     

Effect of affinity for droplet surfaces on the fraction of analyte molecules charged during electrospray droplet fission

The effect of uneven fissioning of mass and charge from electrospray droplets on the amount of analyte charged during the electrospray process was explored. A surface selectivity factor (S) was developed to describe the affinity of an analyte for the droplet surface, and both theoretical and experimental response curves were compared for analytes with various S values. The theoretical response curves were generated by calculating the overlap between the charge and analyte spawned from parent droplets to determine the amount of analyte charged. This overlap was then graphed as a function of analyte concentration. Differences in the amount of analyte charged during droplet fission were predicted for analytes of varying surface affinities. The issue of analyte partitioning between the surface and interior phases of the ESI droplet was also included in the discussion. This was accomplished by applying the equilibrium partitioning model to a set of offspring droplets to determine the amount of analyte on their surfaces and then calculating the overlap between fissioning analyte and excess charge. Experimental response curves resembled theoretical ones, and S values predicted from theory were in excellent agreement with those predicted on the basis of the structural characteristics of the analytes.     

Microfluidic separation and gateable fraction collection for mass-limited samples

Integrating multiple analytical processes into microfluidic devices is an important research area required for a variety of microchip-based analyses. A microfluidic system is described that achieves preparative separations by intelligent fraction collection of attomole quantities of sample. The device consists of a main microfluidic channel used to perform electrophoresis, which is interconnected at 90 degrees to two vertically displaced channels via a nanocapillary array membrane. The membrane interconnect contains nanometer-diameter pores that provide fluidic communication between the channels. Sample injection and analyte collection are controlled by application of an electrical bias between the microfluidic channels across the nanocapillary array. After the separation, the automated transfer of the FITC-labeled Arg, Gln, and Gly bands occurs; a fluorescence detector located at the separation/collection channel interconnect is used to generate a triggering signal that initiates suitable voltages to allow near-quantitative transfer of analyte from the separation channel to the second fluidic layer. The ability to achieve such sample manipulations from mass-limited samples enables a variety of postseparation processing events.     

Fluorescence correlation spectroscopy excited with a stationary interference pattern for capillary electrophoresis

Using a combination of capillary electrophoresis (CE) and patterned fluorescence correlation spectroscopy (patterned FCS), we have developed a new technique for performing electrophoretic analysis independently of the initial length of injected analyte plugs. In t histechnique, which is abbreviated as CE/patterned FCS, fluorescent analyte molecules dispersed continuously in a capillary migrate through a stationary interference pattern created by two intersecting excitation laser beams, and their fluorescence emission is monitored. We prove theoretically that the power spectrum of fluctuations in the fluorescence intensity gives a virtual electropherogram. The profile of the electropherogram and the number of theoretical plates are in general obtained by using analytical methods. Characterizing the capillary length within the excitation beams as the effective length, we compare CE/ patterned FCS with conventional CE. Numerical simulations on capillary gel electrophoresis of DNA predict that the optimized CE/patterned FCS is superior to conventional CE when the effective length is shorter than 1 cm. The experimental feasibility of this technique is demonstrated in the fluorometry of TOTO-1-stained DNA. For an effective length of 740 microm, a maximum number of plates of 7400, and a resolution of 1.0 were obtained with a one-component injection of pUC18 DNA and a two-component injection of pUC 18 DNA and lambda DNA, respectively.     

Multianalyte on-chip native Western blotting

We introduce and characterize multiplexed native Western blotting in an automated and unified microfluidic format. While slab gel Western blotting is slow and laborious, conventional multiplexed blotting ("reblotting": probing one sample with multiple antibodies) requires even more resources. Here we detail three key advances that enable an automated and rapid microfluidic alternative to slab gel reblotting. First, we introduce both assay and microdevice designs that integrate protein blotting against multiple antibody blotting regions with native polyacrylamide gel electrophoresis. This microfluidic integration strategy overcomes nonspecific material losses inherent to harsh antibody stripping steps typically needed for conventional reblotting; said conditions can severely limit analyte quantitation. Second, to inform rational design of the multiplexed microfluidic device we develop an analytical model for analyte capture on the blotting regions. Comparison to empirical observations is reported, with capture efficiencies of >85%. Third, we introduce label free detection that makes simultaneous and quantitative multiplexed measurements possible without the need for prelabeling of sample. Assay linear dynamic range spans 8-800 nM with assay completion in 5 min. Owing to the speed, automation, enhanced quantitation capability, and the difficulty of conventional slab gel Western reblotting, microfluidic multiplexed native Western blotting should find use in systems biology, in particular in analyses of protein isoforms and multimeric protein complexes.     

Fluorescence assay based on preconcentration by a self-ordered ring using berberine as a model analyte

A novel assay for trace amounts of fluorescent analytes is proposed based on the assembly of a self-ordered ring (SOR) through capillary flow in a sessile droplet on a glass slide support. After solvent evaporation of the sessile droplet containing a fluorescent analyte on a hydrophobic-treated glass slide, an outward capillary flow of the solvent from the interior of the droplet occurs. The resultant outward capillary flow then carries the analyte to the perimeter of the droplet spot where the analyte deposits and forms a fluorescent SOR. For the model analyte of berberine, SORs with outer diameter less than 1.2 mm and ring belt width less than 19 microm can be obtained depending on the droplet volume of the berberine solution. Data analysis for the digitally imaged SOR by using a CCD camera showed that the berberine molecules across the SOR belt section follow a Gaussian distribution, and the maximum fluorescent intensity (Imax) was found to be proportional to berberine content at the femtomole level. With the proposed technique, the content in tablets and the average excretion rates of berberine through human urine after oral administration could be satisfactorily monitored.     

A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry

Most cellular functions are performed by multi-protein complexes. The identity of the members of such complexes can now be determined by mass spectrometry. Here we show that mass spectrometry can also be used in order to define the spatial organization of these complexes. In this approach, components of a protein complex are purified via molecular interactions using an affinity tagged member and the purified complex is then partially cross-linked. The products are separated by gel electrophoresis and their constituent components identified by mass spectrometry yielding nearest-neighbor relationships. In this study, a member of the yeast nuclear pore complex (Nup85p) was tagged and a six-member sub-complex of the pore was cross-linked and analyzed by 1D SDS-PAGE. Cross-linking reactions were optimized for yield and number of products. Analysis by MALDI mass spectrometry resulted in the identification of protein constituents in the cross-linked bands even at a level of a few hundred femtomoles. Based on these results, a model of the spatial organization of the complex was derived that was later supported by biological experiments. This work demonstrates, that the use of mass spectrometry is the method of choice for analyzing cross-linking experiments aiming on nearest neighbor relationships.     

Nanoliter solvent extraction combined with microspot MALDI TOF mass spectrometry for the analysis of hydrophobic biomolecules

A nanoliter solvent extraction technique combined with microspot matrix-assisted laser desorption/ionization (MALDI) mass spectrometry is presented. This method involves the use of a nanoliter droplet containing organic solvents at the tip of a small capillary for extraction. The droplet is formed inside a microliter aqueous sample containing the analyte of interest. After extraction, the droplet is deposited onto a MALDI target precoated with a thin matrix layer. Since the nanoliter droplet never touches the sample container wall, any possible extraction of contaminants adsorbed on the plastic or glassware is avoided. In addition, there is no need to concentrate the organic phase after the extraction, thus avoiding any possible loss during the concentration step. The nanoliter volume can be readily deposited onto a MALDI target, producing a high analyte concentration within a microspot. Combined with microspot MALDI, this technique allows for very sensitive analysis of the extracted analyte. The performance of this technique is illustrated in several applications involving the detection of hydrophobic peptides or phospholipids. It is shown that very hydrophobic analytes can be extracted from small-volume samples containing a large amount of salts and/or more hydrophilic analytes, which tend to give dominant signals in conventional MALDI experiments. Nanoliter extraction of analyte from samples containing less than 100 nM hydrophobic analyte and over 1 microM easily ionized hydrophilic species is demonstrated. Finally, using the analysis of the ionophore valinomycin as an example, it is demonstrated that the technique is a more reliable tool for probing metal-peptide complexes than regular MALDI sample preparations.     

Attomole amino acid determination by capillary zone electrophoresis with thermooptical absorbance detection

Attomole quantities of 4-(dimethylamino)azobenzene-4'-sulfonyl chloride derivatized amino acids are separated by using capillary zone electrophoresis in a mixed acetonitrile/aqueous buffer system. Detection is performed with an on-column thermooptical absorbance detection technique based on a 130-mW argon ion pump laser. Detection limits for the concentration of analyte injected onto the column range from 5 x 10(-8) M for methionine to 5 x 10(-7) M for aspartic acid. Only 37 amol of methionine and 450 amol of aspartic acid are contained within the subnanoliter injection volume. It is interesting to note that these limits are a factor of 4 superior to the best fluorescence detection limit reported for chromatographic separation of amino acids. A subnanoliter sample of derivatized human urine was analyzed with this technique; quantities of amino acids contained within the sample are 3 orders of magnitude greater than the detection limit.