Preparative concentration of nucleic acids fragments by capillary isotachophoretic analyzer

On-line dual-stage enrichment via magneto-extraction and electrokinetic preconcentration: A new concept and instrumentation for capillary electrophoresis

This study reports on the development of a new concept of on-line dual preconcentration stages for capillary electrophoresis (CE), in which two completely different preconcentration approaches can be realized in the same capillary. In the first stage, a dynamic magneto-extraction of target analytes on circulating magnetic beads is implemented within the capillary. In the second one, electrokinetic preconcentration of eluted analytes via large volume sample stacking is carried out to focus them into a nano band, prior to CE separation of enriched analytes. To implement the dual-stage preconcentration operation, a purpose-made instrument was designed, combining electrophoretic and microfluidic modules to allow precise control of the movement of magnetic beads and analyte's flow. The potential of this new enrichment principle and its associated instrument was demonstrated for CE separation with light-emitting-diode-induced fluorescent (LEDIF) detection of target double-stranded DNA (ds-DNA). The workflow consists of purification and preconcentration of a target DNA fragment (300 bp) on negatively charged magnetic beads, followed by in-capillary elution and fluorescent labelling of the enriched DNA. Large volume sample stacking of the DNA eluent was then triggered to further preconcentrate the labelled DNA before its analysis by CE-LEDIF. An enrichment factor of 125 was achieved for the target DNA fragment. With our new approach, dual-stage sample pretreatment and CE separation can now be performed in-capillary without any mismatch of working volumes, nor any waste of pretreated samples.

Dynamic computer simulations of electrophoresis: 2010-2020

The transport of components in liquid media under the influence of an applied electric field can be described with the continuity equation. It represents a nonlinear conservation law that is based upon the balance laws of continuous transport processes and can be solved in time and space numerically. This procedure is referred to as dynamic computer simulation. Since its inception four decades ago, the state of dynamic computer simulation software and its use has progressed significantly. Dynamic models are the most versatile tools to explore the fundamentals of electrokinetic separations and provide insights into the behavior of buffer systems and sample components of all electrophoretic separation methods, including moving boundary electrophoresis, CZE, CGE, ITP, IEF, EKC, ACE, and CEC. This article is a continuation of previous reviews (Electrophoresis 2009, 30, S16–S26 and Electrophoresis 2010, 31, 726–754) and summarizes the progress and achievements made during the 2010 to 2020 time period in which some of the existing dynamic simulators were extended and new simulation packages were developed. This review presents the basics and extensions of the three most used one‐dimensional simulators, provides a survey of new one‐dimensional simulators, outlines an overview of multi‐dimensional models, and mentions models that were briefly reported in the literature. A comprehensive discussion of simulation applications and achievements of the 2010 to 2020 time period is also included.

3D printed device for epitachophoresis

Polyacrylamide or agarose gels are the most frequently used sieving and stabilizing media in slab gel electrophoresis. Recently, we have introduced a new electrophoretic technique for concentration/separation of milliliter sample volumes. In this technique, the gel is used primarily as an anticonvection media eliminating liquid flow during the electromigration. While serving well for the liquid stabilization, the gels can undergo deformation when exposed to a discontinuous electrolyte buffer system used in epitachophoresis. In this work, we have explored 3D printing to form rigid stabilizing manifolds to minimize liquid flow during the epitachophoresis run. The whole device was printed using the stereolithography technique from a low water-absorbing resin. The stabilizing manifold, serving as the gel substitute, was printed as a replaceable composite structure preventing electrolyte mixing during the separation. Different geometries of the 3D printed stabilizing manifolds were tested for use in concentrating ionic sample components without spatial separation. The presented device can focus analytes from 3 or 4 mL of the sample to 150 μL or less, depending on the collection cup size. With the 150 μL collection cup, this represents the enrichment factor from 20 to 27. The time of concentration was from 15 to 25 min, depending on stabilization media and power used.

DNA purification and concentration by isotachophoresis in nonwoven fabric strip

We present a novel method for concentration and purification of DNA from biological samples. The method is based on isotachophoretic separation of DNA strands in a separation bed made of a disposable nonwoven fabric strip. Application of oxalate as the leading ion prevented corrosion of the carbon anode and also the leading ion was continually removed from the system due to its decomposition into CO₂ at the anode. The fractions were marked by three colored markers of electrophoretic mobility closely surrounding the mobility of DNA. The fraction collection was realized by a centrifugal drain of cut out strip segments. The method was evaluated using two purified salmon sperm DNA fragments of lengths 200 bp and 2000 bp. The results confirmed the high DNA concentrating effect of the method (34-fold increase of the original DNA concentration). The composition of running solutions and voltage program were optimized in order to finish the analysis within 30 min. The optimized method was used to extract, concentrate and purify DNA from a crude yeast cell lysate. The maximum DNA enrichment factor decreased to 12 due to the stretching of DNA zones caused by low-molecular contaminants present in the original lysate. The average recovery determined for yeast DNA was 71 ± 11% (n = 3). The connected elimination of the proteins from DNA zones resulted in the purification factor value of 582 for DNA vs proteins. This demonstrates that the presented method is capable to concentrate DNA from the bulk volume and to further purify it from crude cell lysates using a simple instrumentation and low-cost disposable separation bed.

Purification of anionic fluorescent probes through precise fraction collection with a two-point detection system using multiple-stacking preparative capillary transient isotachophoresis

A novel combination of CE-based separation techniques was used for the precise fractionation of ionic compounds from impurities. The combination of on-capillary concentration and separation using transient isotachophoresis, with multiple injections and a two-point detection system provided higher efficiency, and accuracy at a microliter-scale injection volume, than when CE was individually used for purification. In this paper, we present successful applications of the CE fractionation techniques for the purification of fluorescein, fluorescein-4-isothiocyanate, two fluorescent metal ion probes, and a fluorescein-modified DNA aptamer. The purity of the isolated fluorescent probes ranged from 95 to 99%. Such high purity could not be achieved using chromatographic purification techniques. With relatively low dilution factors of 6-9, the purified probe solutions were practical for use as purified stock solutions. In addition, the fluorescein-modified DNA aptamer purified by our method was successfully used in a thrombin binding assay. The method developed was useful for the purification of anionic fluorescent reagents to be of ultratrace analytical grade for use with CE-LIF.

Isolation of enriched small RNA from cell-lysate using on-chip isotachophoresis

In spite of the growing interest in the roles and applications of small RNAs (sRNAs), sRNA isolation methods are inconsistent, tedious, and dependent on the starting number of cells. In this work, we employ ITP to isolate sRNAs from the cell-lysate of K562 (chronic myelogenous leukemia) cells in a polydimethylsiloxane (PDMS) mesofluidic device. Our method specifically purifies sRNA of <60 nucleotides from lysate of a wide range of cell number spanning from 100 to 1 000 000 cells. We measured the amount of sRNA using the Agilent Bioanalyzer and further verified the extraction efficiency by reverse transcription quantitative PCR. Our method was shown to be more efficient in sRNA extraction than commercial sRNA isolation kits, especially when using smaller numbers of starting cells. Our assay presents a simple and rapid sRNA extraction method with 20 min assay time and no intermediate transfer steps.