Fast separation of oligonucleotide and triplet repeat DNA on a microfabricated capillary electrophoresis device and capillary electrophoresis

Analysis of oligonucleotides by ion-pairing hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry

RATIONALE

Hydrophilic interaction liquid chromatography/electrospray ionization mass spectrometry (HILIC-LC/ESI-MS) has been proved to be useful for the quality control of oligonucleotides. However, the lack of separation for some oligonucleotides using HILIC-LC/MS has proved problematic. This study aimed to improve the resolving ability of HILIC-LC/MS.

METHODS

The study was performed on a Waters UPLC® system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer using a Zorbax® RRHD HILIC column (2.1 mm × 100 mm, 1.8 μm). Buffer systems contained triethylammonium acetate (TEAA) and acetonitrile. The effects of the concentration of TEAA and the type of organic modifiers on the separation of oligonucleotides were investigated.

RESULTS

The results showed that the optimum concentration of TEAA is 10 mM and acetonitrile is a better organic solvent than methanol. The addition of TEAA in the HILIC mobile phase improved the separation of N from N + A significantly compared to the HILIC method buffered with ammonium acetate. The IP-HILIC chromatography has demonstrated that the separation of oligonucleotides is sequence dependent. In addition, the IP-HILIC method produces a much simpler mass spectrum of an oligonucleotide with very efficient desalting.

CONCLUSIONS

The HILIC-LC/MS method with the addition of TEAA at a MS-compatible concentration has improved the separation of oligonucleotides. The IP-HILIC-LC/MS method also produces very simple mass spectra with high desalting efficiency.

Comparing ion-pairing reagents and sample dissolution solvents for ion-pairing reversed-phase liquid chromatography/electrospray ionization mass spectrometry analysis of oligonucleotides

RATIONALE

A sensitive and selective liquid chromatography/mass spectrometry (LC/MS) method is essential for quality control of synthetic oligonucleotides. However, researchers are still searching for improvements to ion-pairing reagents for ion-pairing reversed-phase LC/MS. This study performed a comprehensive comparison of six ion-pairing reagents to determine their performance as mobile phase modifiers for oligonucleotide LC/MS.

METHODS

The study was performed using a Waters ultra-performance liquid chromatography (UPLC®) system coupled to a Waters LCT premier XE ESI-TOF mass spectrometer by using a UPLC® OST column (2.1 mm × 100 mm, 1.7 µm). Buffer systems containing ion-pairing reagents (triethylamine, tripropylamine, hexylamine, N,N-dimethylbutylamine, dibutylamine, N,N-diisopropylethylamine) and hexafluoro-2-propanol were compared by measuring the adduct ion formation, chromatographic separation, and MS signal intensity of four oligonucleotides (10mer to 40mer). The effect of dissolution solvents on MS signal intensity and adduct ion formation was also investigated.

RESULTS

Results showed that the type of dissolution solvent can have a signficiant impact on adduct ion formation with oligonucleotides. Results also showed that the maximum separation for small, medium and large oligonucleotides occured when using tripropylamine, N,N-dimethylbutylamine, and dibutylamine, respectively. However, on average 15 mM hexylamine and 50 mM hexafluoro-2-propanol provided the best chromtatographic performance (resolution values: 14.1 ± 0.34, 11.0 ± 0.17, and 6.4 ± 0.11 for the pairs of oligonucleotides T10 & T15, T15 & T25, and T25 & T40, respectively (3 replicates)).

CONCLUSIONS

The impact of dissolution solvent on the MS signal of oligonucleotides depends on the type of ion-pairing reagent. Buffer combining 15 mM hexylamine and 50 mM hexafluoro-2-propanol produced the highest overall performance for oligonucleotides (10mer to 40mer) with respect to chromatographic resolution and mass detection.

Colocalization of quantum dots by reactive molecules carried by motor proteins on polarized microtubule arrays

The field of microfluidics has drastically contributed to downscale the size of benchtop experiments to the dimensions of a chip without compromising results. However, further miniaturization and the ability to directly manipulate individual molecules require a platform that permits organized molecular transport. The motor proteins and microtubules that carry out orderly intracellular transport are ideal for driving in vitro nanotransport. Here, we demonstrate that a reconstruction of the cellular kinesin/dynein-microtubule system in nanotracks provides a molecular total analysis system (MTAS) to control massively parallel chemical reactions. The mobility of kinesin and a microtubule dissociation method enable orientation of a microtubule in an array for directed transport of reactive molecules carried by kinesin or dynein. The binding of glutathione S-transferase (GST) to glutathione (GSH) and the binding of streptavidin to biotin are visualized as colocalizations of quantum dots (Q-dots) when motor motilities bring them into contact. The organized nanotransport demonstrated here suggests the feasibility of using our platform to perform parallel biochemical reactions focused at the molecular level.

Millimeter scale separation of DNA with a replaceable polymer matrix

Electrophoresis is a powerful method that has seen a wide range of applications, often in automated genetic diagnostic instruments that require the use of a replaceable sieving matrix. The power and simplicity of electrophoresis as an analysis technique would be ideal for highly integrated and low-cost analysis systems if the method could be implemented in microfluidics on the scale of several mm. We demonstrate the electrophoretic analysis of DNA with separation lengths as small as 2 mm and with a resolution adequate for the analysis of PCR products, i.e. resolutions of 10-20 base pairs. Such small-scale separations enable analysis systems consisting of microfluidics and microelectronics integrated into a single inexpensive package, thereby overcoming a key challenge facing the development of the lab on chip technologies.

Preparation of methacrylate-based anion-exchange monolithic microbore column for chromatographic separation of DNA fragments and oligonucleotides

In this paper, we report on the preparation of a microbore-scale (1 mm i.d.) anion-exchange monolithic column suitable not only for analytical purposes but also for potentially preparative applications. In order to meet the conflicting requirements of high permeability and good mechanical strength, the following two-step procedure was applied. First, an epoxy-containing monolith was synthesized by in situ copolymerization of glycidyl methacrylate (GMA) and ethylene dimethacrylate (EDMA) within the confines of a silicosteel tubing of 1.02 mm i.d. and 1/16" o.d. in the presence of a ternary porogenic mixture of 1-propanol, 1,4-butanediol, and water. The monolithic matrix was subsequently converted into weak anion-exchanger via the ring-opening reaction of epoxy group with diethyl amine. The dynamic binding capacity was 21.4 mg mL(-1) for bovine serum albumin (BSA) at 10% breakthrough. The morphology and porous structure of this monolith were assessed by scanning electron microscope (SEM) and inverse size exclusion chromatography (ISEC). To optimize the separation efficiency, the effects of various chromatographic parameters upon the separation of DNA fragments were investigated. The resulting monolithic anion exchanger demonstrated good potential for the separation of both single- and double-stranded DNA molecules using a gradient elution with NaCl in Tris-HCl buffer (20 mM). Oligodeoxythymidylic acids (dT(12)-dT(18)) were successfully resolved at pH 8, while the fragments of 20 bp DNA ladder, 100 bp DNA ladder, and pBR322-HaeIII digest were efficiently separated at pH 9.

Highly sensitive detection of monosaccharides on microchip electrophoresis using pH discontinuous solution system

We improved the detection sensitivity of neutral and amino monosaccharides labeled with 2-aminoacridone by a factor of 19.6-48.7 and 44.4-65.9, respectively, with no deterioration in separation resolution, using a pH discontinuous solution system instead of the conventional solution system. The pH discontinuous solution system is simple, using only a borate solution at pH 6.0 as a sample solution and a Tris-borate solution at pH 9.3 as a separation solution, enabling an enhancement of the sensitivity by monosaccharide stacking. This technique is fully compatible with conventional microchip electrophoresis, thereby allowing us to develop efficient tools for highly sensitive and resolved detection of monosaccharides.

Nanostructured polymer matrix for oligonucleotide separation

A nanostructured copolymer matrix has successfully separated oligonucleotides with high resolution by CE using a very short separation channel which simulates the real microchip condition for the first time. The triblock copolymer, E(45)B(14)E(45) (B20-5000) with E, B, and subscript denoting oxyethylene, oxybutylene, and segment length, respectively, has a unique temperature-dependent viscosity-adjustable property and a dynamic coating ability in 1xTBE buffer (89 mM Tris, 89 mM boric acid, 2 mM EDTA in Milli-Q water). The B-block is hydrophilic at low temperatures, e.g., 4 degrees C, and the polymer solution has a very low viscosity of about 100 cP in a 32.5% w/v solution. At room temperatures, the B-block becomes hydrophobic due to a breakdown of hydrogen bonds between B-blocks and water, and the polymer matrix forms a body-centered cubic structure at high concentrations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated with one-base resolution in a 1.5 cm long separation channel by E(45)B(14)E(45) in its gel-like state.

Designing polymer matrix for microchip-based double-stranded DNA capillary electrophoresis

Polyacrylamide (PAM) was used as a model polymer to build up an empirical model that relates polymer molecular weight, polymer concentration and solution viscosity. The desired random copolymers of acrylamide (AM) and N,N-dimethylacrylamide (DMA) used as DNA separation media for different specifications were synthesized under the guidance of the empirical model. The separation performances of rationally designed copolymers were tested in a 1.2 cm long separation channel, simulating microchip-based capillary electrophoresis. pBR322/HaeIII digest was successfully separated with good separation resolution and fast speed. Validation of the sieving ability of our polymers was performed in the Agilent 2,100 Bioanalyzer. The results of the 10 bp (base pair) DNA ladder separation demonstrate the potential of our approach for the sieving matrix in microchip-based electrophoresis.

Reversible thermo-responsive sieving matrix for oligonucleotide separation

A reversible thermo-responsive gel system, consisting of Pluronic copolymer mixture of F87 and F127, has been used to successfully carry out the separation of oligonucleotides, for the first time, by microchip-based capillary electrophoresis. Pluronic triblock copolymers F87 (E(61)P(40)E(61)) and F127 (E(99)P(69)E(99)), with E, P, and subscript denoting oxyethylene, oxypropylene, and segment length respectively, have a unique temperature dependent viscosity-adjustable property and a dynamic coating ability in aqueous solution, including 1 x TBE buffer. The mixture solution has a reversible thermo-responsive property and its sol-gel transition temperature can be adjusted ranging from about 17 degrees C to 38 degrees C by varying the relative weight ratio of F87 and F127 at an optimized concentration of approximately 30% (w/v) for oligonucleotide separations. Oligonucleotide sizing markers ranging from 8 to 32 base could be successfully separated in a 1.5 cm long separation channel by the mixture solution in its gel-like state. A 30% (w/v) with a F87/F127 weight ratio of 1 ratio 2 which has a "sol-gel" transition point of about 26 degrees C shows the best sieving ability. The sieving ability of the mixture solution was further confirmed in an Agilent Bioanalyzer 2100 system. Fast separation of oligonucleotides has been achieved within 40 s with one base resolution.

Fast separation of single-stranded oligonucleotides by capillary electrophoresis using OliGreen as fluorescence inducing agent

The fast separation of oligonucleotide (oligos) sizing marker by CE using OliGreen and including effects due to the concentration of separation medium and urea denaturant is presented. OliGreen dye is found to be more sensitive than ethidium bromide (by a factor of about 6 based on S/N considerations) for the oligos' separations. Higher concentration of F127 in 1xTris-boricacid-EDTA (TBE) up to 30% w/v leads to better resolution of oligos separations. The addition of urea into the separation medium decreases the sensitivity. With an optimized running condition, the oligos sizing marker could be successfully separated with 1-base resolution within 1.3 min by using 30% w/v F127/1xTBE solution as the separation medium at an applied electric field of 800 V/cm in a 3 cm long capillary, the fastest capillary gel electrophoresis separation with high resolution reported to date for oligos in the similar size range.

Applications of capillary electrophoresis on microchip

CE on microchip is an emerging separation technique that has attracted wide attention and gained considerable popularity. Because of miniaturization of the separation format, CE on chip typically offers shorter analysis time and lower reagent consumption with potential development of portable analytical instrumentation. This review with 143 references is focused on proteins and peptides analysis, DNA separation including fragment sizing, genotyping, mutation detection and sequencing, and also the analysis of low-molecular-weight compounds, namely explosive residues and warfare agents, pharmaceuticals and drugs of abuse, and various small molecules in body fluids.

Rapid and Reversible Generation of a Microscale pH Gradient Using Surface Electric Fields

We report a method for the rapid and reversible generation of microscale pH gradients using a spatially varied electric field. A linear gradient in electrochemical potential is produced on an electrode surface consisting of a platinum catalyst layer on indium-tin oxide-coated glass by the application of two different potential values at spatially distinct surface locations. The resulting potential gradient drives the oxidation and reduction of water at different rates along the surface, as dictated by the local applied potential. A nonuniform distribution of pH in the neighboring solution results due to the variation in surface reaction rates. The extent and magnitude of the pH gradient can be controlled by the appropriate selection of applied potential values. In addition, the gradient can be rapidly turned on or off and reversibly switched between various profiles. The size of the pH gradient can be readily modified by changing the dimensions of the electrode and contact pads to allow integration into chip-scale devices. Characteristics of the pH gradient are described, including experimental and theoretical evidence of significant improvement in time response over competing methods for the generation of microscale pH gradients.

Modification of poly(methyl methacrylate) microchannels for highly efficient and reproducible electrophoretic separations of double-stranded DNA

This paper deals with dynamic coating of the microchannels fabricated on poly(methyl methacrylate) (PMMA) chips and DNA separation by microchip electrophoresis (MCE). After testing a number of polymers, including 2-hydroxyethyl cellulose, hydroxypropylmethyl cellulose, different sizes of poly(ethylene oxide) (PEO), and poly(vinyl pyrrolidone) (PVP), we found that coating of the PMMA microchannels with PEO(Mr = 6.0 x 10(5) g/mol) on the first layer is essential to minimize the interaction of DNA with PMMA surface. To achieve high efficiency, multilayer coating of PMMA chips with PEO, PVP, and PEO containing gold nanoparticles [PEO(GNP)] is important. A 2-(PEO-PVP)-PEO(GNP) PMMA chip, which was repeatedly coated with 1.0% PEO and 5.0% PVP twice, and then coated with 0.75% PEO(GNP) each for 30 min, provided a high efficiency (up to 1.7 x 10(6) plates/m) for the separation of DNA markers V (pBR 322/HaeIII digest) and VI (pBR 328/BgiI digest and pBR 328/HinfI digest) when using 0.75% PEO(GNP). With such a high efficiency, we demonstrated the separation of hsp65 gene fragments of Mycobacterium HaeIII digests by MCE within 90 s. The advantages of this approach to DNA analysis include ease of filling the microchannel with 0.75% PEO(GNP), rapidity, and reproducibility.

Cytometry and Velocimetry on a Microfluidic Chip Using Polyelectrolytic Salt Bridges

This paper reports a polyelectrolytic salt bridge-based electrode (PSBE), which is a key embedded unit in a microchip device that can size-selectively count microparticles and measure their velocities. The construction of salt bridges at specific locations within a microfluidic chip enables dc-driven electrical detection to be performed successfully. This is expected to be a competitive alternative to the optical methods currently used in conventional cell sorters. The PSBEs were fabricated by irradiating ultraviolet light over a patterned mask on the parts of interest, which were filled with an aqueous monomer solution containing diallyldimethylammonium chloride. A pair of such PSBEs was easily formed at the two lateral branches perpendicular to the main microchannel and was found to be very useful for dc impedometry. The human blood cells as well as the fluorescent microbeads passing between the two PSBEs produced impedance signals in proportional to their size. The information about the velocity of a microparticle was extracted from a doublet of the dc impedance signals, which were generated when cells or microbeads sequentially passed through two PSBE pairs separated from each other by a fixed distance. The plot of peak amplitude versus velocity of the moving microbeads and cells indicated only a slight correlation between the size and the velocity, which means that the peak amplitude of the dc impedance signals alone can provide information about the size of the cells in a mixture. The experimental results showed a screening rate of over 1000 cells s(-1) and a velocity of the cells of over 100 mm s(-1). Compared with the previously suggested electrical detection system based on metal electrodes, the sensitivity and selectivity in cell detection were remarkably improved. In addition, the detection unit including the operating circuit became innovatively simple and the whole device could be miniaturized.

Rapid heteroduplex analysis by capillary electrophoresis

The very important parameters for mutation screening are short time of analysis and high throughput. The analytical platform which fulfills these criteria most satisfactorily is capillary electrophoresis. Here we show the influence of several parameters such as temperature, presence of glycerol, capillary length and polymer concentration on the electrophoretic properties of DNA duplexes and evaluate their contribution to the overall time of analysis. The careful optimization of analyzed conditions allowed us to significantly decrease the time required for the detection of the 185delAG and 4153delA mutations by heteroduplex analysis. It enabled us to analyze these typical BRCA1 gene deleterious mutations in several minutes only by using very popular and widely accessible capillary electrophoresis instrumentation.

Short-capillary electrophoresis with electrochemiluminescence detection using porous etched joint for fast analysis of lidocaine and ofloxacin

Fast analysis of ofloxacin and lidocaine, as bactericide and analgesic or anesthetics, is of clinic importance for understanding the patient's medical process. This paper presented a high throughput, simple analysis method of lidocaine and ofloxacin by capillary electrophoresis coupled with electrochemiluminescence (ECL) using porous etched joint. To shorten the analysis time and to improve the analytical performance, a capillary with 10 cm in length was used as the separation channel. The cyclic voltammograms of Ru(bpy)3(2+) with different capillary length at same field strength showed that the porous etched joint eliminated the effect of electrophoretic current on the ECL detection. Following micro total analysis systems (microTAS), some advantages of which this approach has, the fabrication of channel in chip was not needed. Compared with capillary electrophoresis with 40-cm-long capillary, the high sample throughput and low zone broadening may be the main advantage of the present system. Under optimal condition, the detection limits of lidocaine and ofloxacin based on peak height were 3.0 x 10(-8) and 5.0 x 10(-7) molL(-1) and a 60 h(-1) of sampling frequency was obtained. The precision (R.S.D.) of the migration time and the peak height for five replicate injections of a mixture of lidocaine (1.0 x 10(-6) molL(-1)) and ofloxacin (4.0 x 10(-6) molL(-1)) were 3.2-3.9% and 4.7-5.3%, respectively.

Microfabricated electrophoresis systems for DNA sequencing and genotyping applications: current technology and future directions

Many routine genomic-analysis assays rely on gel electrophoresis to perform size-selective fractionation of DNA fragments in the size range below 1 kb in length. Over the past decade, impressive progress has been made towards the development of microfabricated electrophoresis systems to conduct these assays in a microfluidic lab-on-a-chip format. Since these devices are inexpensive, require only nanolitre sample volumes, and do not rely on the availability of a pre-existing laboratory infrastructure, they are readily deployable in remote field locations for use in a variety of medical and biosensing applications. The design and construction of microfabricated electrophoresis devices poses a variety of challenges, including the need to achieve high-resolution separations over distances of a few centimetres or less, and the need to easily interface with additional microfluidic components to produce self-contained integrated DNA-analysis systems. In this paper, we review recent efforts to develop devices to satisfy these requirements and live up to the promise of fulfilling the growing need for inexpensive portable genomic-analysis equipment.

Microfluidic chips for clinical and forensic analysis

This review gives an overview of developments in the field of microchip analysis for clinical diagnostic and forensic applications. The approach chosen to review the literature is different from that in most microchip reviews to date, in that the information is presented in terms of analytes tested rather than microchip method. Analyte categories for which examples are presented include (i) drugs (quality control, seizures) and explosives residues, (ii) drugs and endogenous small molecules and ions in biofluids, (iii) proteins and peptides, and (iv) analysis of nucleic acids and oligonucleotides. Few cases of microchip analysis of physiological samples or other "real-world" matrices were found. However, many of the examples presented have potential application for these samples, especially with ongoing parallel developments involving integration of sample pretreatment onto chips and the use of fluid propulsion mechanisms other than electrokinetic pumping.

High-performance genetic analysis using microfabricated capillary array electrophoresis microplates

This review focuses on some recent advances in realizing microfabricated capillary array electrophoresis (microCAE). In particular, the development of a novel rotary scanning confocal fluorescence detector has facilitated the high-speed collection of sequencing and genotyping data from radially formatted microCAE devices. The concomitant development of a convenient energy-transfer cassette labeling chemistry allows sensitive multicolor labeling of any DNA genotyping or sequencing analyte. High-performance hereditary haemochromatosis and short tandem repeat genotyping assays are demonstrated on these devices along with rapid mitochondrial DNA sequence polymorphism analysis. Progress in supporting technology such as robotic fluid dispensing and batched data analysis is also presented. The ultimate goal is to develop a parallel analysis platform capable of integrated sample preparation and automated electrophoretic analysis with a throughput 10-100 times that of current technology.

Microchips, microarrays, biochips and nanochips: personal laboratories for the 21st century

Micro miniaturization of analytical procedures is having significant impact on diagnostic testing, and will enable highly complex clinical testing to be miniaturized and permit testing to move from the central laboratory into non-laboratory settings. The diverse range of micro analytical devices includes microchips, gene chips, bioelectronic chips. They have been applied to several clinically important assays (e.g., PCR, immunoassay). The main advantages of the new devices are integration of multiple steps in complex analytical procedures, diversity of application, sub-microliter consumption of reagents and sample, and portability. These devices form the basis of new and smaller analyzers (e.g., capillary electrophoresis) and may ultimately be used in even smaller devices useful in decentralized testing (lab-on-a-chip, personal laboratories). The impact of microchips on healthcare costs could be significant via timely intervention and monitoring, combined with improved treatments (e.g., microchip-based pharmacogenomic tests). Empowerment of health consumers to perform self-testing is limited, but microchips could accelerate this process and so produce a level of self-awareness of biochemical and genetic information hitherto unimaginable. The next level of miniaturization is the nanochip (nanometer-sized features) and the technological foundation for these futuristic devices is discernable in nanotubes and self-assembling molecular structures.

Field-inversion electrophoresis on a microchip device

We have proposed a field-inversion electrophoresis on a microchip for a shorter effective length, and investigated the external frequency for the DNA analysis based on the field-inversion electrophoresis device. By using the optimized frequency, we demonstrated that the field-inversion electrophoresis has great potentials for the separation of DNA fragments with shorter effective length.

Recent developments in electrokinetically driven analysis on microfabricated devices

This review is devoted to the rapid developments in the field of microfluidic separation devices in which the flow is electrokinetically driven, and where the separation element forms the heart of the system, in order to give an overview of the trends of the last three years. Examples of microchip layouts that were designed for various application areas are given. Optimization of mixing and injection strategies, designs for the handling of multiple samples, and capillary array systems show the enormous progress made since the first proof-of-concept papers about lab-on-a-chip devices. Examples of functional elements for on-chip preconcentration, filtering, DNA amplification and on-chip detection indicate that the real integration of various analytical tasks on a single microchip is coming into reach. The use of materials other than glass, such as poly(dimethylsiloxane) and polymethylmethacrylate, for chip fabrication and detection methods other than laser-induced fluorescence (LIF) detection, such as mass spectrometry and electrochemical detection, are described. Furthermore, it can be observed that the separation modes known from capillary electrophoresis (CE) in fused-silica capillaries can be easily transferred to the microchip platform. The review concludes with an overview of applications of microchip CE and with a brief outlook.