Microsystem for Field-Amplified Electrokinetic Trapping Preconcentration of DNA at Poly(ethylene terephthalate) Membranes

Circulating miRNA and circulating tumor DNA application as liquid biopsy markers in gastric cancer

Liquid biopsy has been investigated as a novel method to overcome the numerous challenges in gastric cancer (GC) management. This non-invasive, feasible, and easy-to-repeat method has been shown to be cost-effective and capable of increasing diagnostic sensitivity and prognostic assessment. Additionally, it is potentially accurate to aid decision-making and personalized treatment planning. MicroRNA (miRNA) and circulating tumor DNA (ctDNA) markers can enhance GC management in various aspects, including diagnosis (mainly earlier diagnosis and the ability to perform population-based screening), prognosis (more precise stratification of prognosis), and treatment (including more accurate prediction of treatment response and earlier detection of resistance to the treatment). Concerning the treatment-related application, miRNAs' mimics and antagonists (by using two main strategies of restoring tumor suppressor miRNAs and inhibiting oncogene miRNAs) have been shown to be effective therapeutic agents. However, these need to be further validated in clinical trials. Furthermore, novel delivery systems, such as lipid-based vectors, polymeric-based vectors, and exosome-based delivery, have been developed to enhance the performance of these agents. Moreover, this paper explores the current detection and measuring methods for these markers. These approaches are categorized into direct methods (e.g., Chem-NAT, HTG EdgeSeq, and Multiplex Circulating Fireplex) and indirect methods (e.g., Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), qPCR, microarray, and NGS) for miRNA detection. For ctDNA measurement, main core technologies like NGS, digital PCR, real-time PCR, and mass spectrometry are suggested.

Transverse migration and microfluidic concentration of DNA using Newtonian buffers

We present experimental evidence that DNA can be concentrated due to an electrohydrodynamic coupling between a pressure-driven flow and a parallel electric field. The effects of buffer properties on the process were measured in a microfluidic channel. The concentration rates and the efficiency of trapping DNA were quantified as functions of the ion and polymer concentrations of the buffer solution. Buffers with large ion concentrations hindered the ability to trap DNA, reducing the short-time efficiency of the concentration process from nearly 100% to zero. Importantly, DNA was trapped in the microfluidic channel even when the buffer solution lacked any measurable viscoelastic response. These observations indicate that electrohydrodynamic migration drives the concentration of DNA. We found no evidence of viscoelastic migration in these experiments.

Microfluidic Techniques for Analytes Concentration

Microfluidics has been undergoing fast development in the past two decades due to its promising applications in biotechnology, medicine, and chemistry. Towards these applications, enhancing concentration sensitivity and detection resolution are indispensable to meet the detection limits because of the dilute sample concentrations, ultra-small sample volumes and short detection lengths in microfluidic devices. A variety of microfluidic techniques for concentrating analytes have been developed. This article presents an overview of analyte concentration techniques in microfluidics. We focus on discussing the physical mechanism of each concentration technique with its representative advancements and applications. Finally, the article is concluded by highlighting and discussing advantages and disadvantages of the reviewed techniques.

Rapid concentration of deoxyribonucleic acid via Joule heating induced temperature gradient focusing in poly-dimethylsiloxane microfluidic channel

This paper reports rapid microfluidic electrokinetic concentration of deoxyribonucleic acid (DNA) with the Joule heating induced temperature gradient focusing (TGF) by using our proposed combined AC and DC electric field technique. A peak of 480-fold concentration enhancement of DNA sample is achieved within 40s in a simple poly-dimethylsiloxane (PDMS) microfluidic channel of a sudden expansion in cross-section. Compared to a sole DC field, the introduction of an AC field can reduce DC field induced back-pressure and produce sufficient Joule heating effects, resulting in higher concentration enhancement. Within such microfluidic channel structure, negative charged DNA analytes can be concentrated at a location where the DNA electrophoretic motion is balanced with the bulk flow driven by DC electroosmosis under an appropriate temperature gradient field. A numerical model accounting for a combined AC and DC field and back-pressure driven flow effects is developed to describe the complex Joule heating induced TGF processes. The experimental observation of DNA concentration phenomena can be explained by the numerical model.

Nanofracture on fused silica microchannel for Donnan exclusion based electrokinetic stacking of biomolecules

Due to Donnan exclusion, charged molecules are prohibited from passing through a channel of electrical double layer scale (nanometers), even though the molecules are smaller than the lowest dimension of the channel. To employ this effect for on-chip pre-concentration, an ion channel of nanometer scale has to be introduced. Here we introduced a simple method of generating a fracture (11-250 nm) directly on the commercially available open tubular fused silica capillary, and a chip comprised of the capillary with the nanofracture was prepared. A ring-disk model of the fracture was derived with which the fracture width can be easily characterized online without any damage to the chip, and the result was validated by a scanning electron microscope (SEM). The fractures can be used directly as a nanofluidic interface exhibiting an obvious ion concentration polarization effect with high current flux. On-chip electrokinetic stacking of SYBR Green I labeled λDNA inside the capillary was successfully demonstrated, and a concentration factor close to the amplification rate of the polymerase chain reaction (PCR) was achieved within 7 min. The chip is inexpensive and easy to prepare in common chemistry and biochemistry laboratories without limitations in expensive microfabrication facilities and sophisticated expertise. More applications of this interface could be found for enhancing the detectability of capillary based microfluidic analytical systems for the analysis of low concentrated charged species.

Recent progress of on-line sample preconcentration techniques in microchip electrophoresis

This review highlights recent developments and applications of on-line sample preconcentration techniques to enhance the detection sensitivity in microchip electrophoresis (MCE); references are mainly from 2008 and later. Among various developed techniques, we focus on the sample preconcentration based on the changes in the migration velocity of analytes in two or three discontinuous solutions system, since they can provide the sensitivity enhancement with relatively easy experimental procedures and short analysis times. The characteristic features of the on-line sample preconcentration applied to microchip electrophoresis (MCE) are presented, categorized on the basis of "field strength-" or "chemically" induced changes in the migration velocity. The preconcentration techniques utilizing field strength-induced changes in the velocity include field-amplified sample stacking, isotachophoresis and transient-isotachophoresis, whereas those based on chemically induced changes in the velocity are sweeping, transient-trapping and dynamic pH junction.

Concentration and size separation of DNA samples at liquid-liquid interfaces

This report introduces a new analytical concept utilizing the mass transfer resistance of a liquid-liquid interface to concentrate and separate DNA samples. DNA molecules can be electrophoretically accumulated at a liquid-liquid interface of an aqueous two-phase system (ATPS) of poly(ethylene glycol) (PEG) and dextran, two polymers that form two immiscible phases in aqueous electrolyte solutions. The detachment of DNA from the interface into the other phase can be triggered by increasing the applied electric field. We experimentally study the size dependence of the detachment process for a broad spectrum of DNA fragments. In a regime where the coiling of the chains does not play a significant role, the process shows a linear dependence on the diffusion coefficient, with shorter DNA chains detaching at lower electric field strengths than larger ones. The concept may enable novel separation protocols for preparative and analytical purposes.

Optofluidic in situ maskless lithography of charge selective nanoporous hydrogel for DNA preconcentration

An optofluidic maskless photopolymerization process was developed for in situ negatively charged nanoporous hydrogel [poly-AMPS (2-acrylamido-2-methyl-1-propanesulfonic acid)] fabrication. The optofluidic maskless lithography system, which combines a high power UV source and digital mirror device, enables fast polymerization of arbitrary shaped hydrogels in a microfluidic device. The poly-AMPS hydrogel structures were positioned near the intersections of two microchannels, and were used as a cation-selective filter for biological sample preconcentration. Preconcentration dynamics as well as the fabricated polymer shape were analyzed in three-dimensions using fluorescein sample and a confocal microscope. Finally, single-stranded DNA preconcentration was demonstrated for polymerase chain reaction-free signal enhancement.

Recent advances in enhancing the sensitivity of electrophoresis and electrochromatography in capillaries and microchips (2008-2010)

Capillary electrophoresis has been alive for over two decades now; yet, its sensitivity is still regarded as being inferior to that of more traditional methods of separation such as HPLC. As such, it is unsurprising that overcoming this issue still generates much scientific interest. This review continues to update this series of reviews, first published in Electrophoresis in 2007, with an update published in 2009 and covers material published through to June 2010. It includes developments in the fields of stacking, covering all methods from field-amplified sample stacking and large volume sample stacking, through to ITP, dynamic pH junction and sweeping. Attention is also given to on-line or in-line extraction methods that have been used for electrophoresis.

Microsystem for Isolation of Fetal DNA from Maternal Plasma by Preparative Size Separation

Background: Routine prenatal diagnosis of chromosomal anomalies is based on invasive procedures, which carry a risk of approximately 1%–2% for loss of pregnancy. An alternative to these inherently invasive techniques is to isolate fetal DNA circulating in the pregnant mother’s plasma. Free fetal DNA circulates in maternal plasma primarily as fragments of lengths <500 bp, with a majority being <300 bp. Separating these fragments by size facilitates an increase in the ratio of fetal to maternal DNA.

Methods: We describe our development of a microsystem for the enrichment and isolation of cell-free fetal DNA from maternal plasma. The first step involves a high-volume extraction from large samples of maternal plasma. The resulting 80-μL eluate is introduced into a polymeric microsystem within which DNA is trapped and preconcentrated. This step is followed by a transient isotachophoresis step in which the sample stacks within a neighboring channel for subsequent size separation and is recovered via an outlet at the end of the channel.

Results: Recovered fractions of fetal DNA were concentrated 4–8 times over those in preconcentration samples. With plasma samples from pregnant women, we detected the fetal SRY gene (sex determining region Y) exclusively in the fragment fraction of <500 bp, whereas a LEP gene (leptin) fragment was detected in both the shorter and longer recovery fractions.

Conclusions: The microdevice we have described has the potential to open new perspectives in noninvasive prenatal diagnosis by facilitating the isolation of fetal DNA from maternal plasma in an integrated, inexpensive, and easy-to-use microsystem.