Enhancing the speed of morpholino-DNA biosensor by electrokinetic concentration of DNA in a microfluidic chip

Microfluidic Paper-Based Preconcentration and Retrieval for Rapid Ribonucleic Acid Biomarker Detection and Visualization

Microfluidic paper-based analytical devices (μPADs) have attracted significant attention in the field of point-of-care (POC) diagnostics. However, the heterogeneous structure of the paper often impairs the limit of detection (LOD) for low-abundance targets when those targets are directly analyzed. One viable solution to bypass this limitation is to elevate the target concentration above the LOD on-site to reach a valid readout. Here, we developed a 3D μPADs preconcentrator (3D-μP²) to increase sample concentration by electrokinetic trapping and demonstrated its application in increasing the LOD of a downstream colorimetric assay. The three-dimensional (3D) structure of this device was composed of a loading pad, a vertical fluid path formed by stacked absorbent pads, and an ion-selective membrane of PEDOT:PSS. This novel design facilitates fast preconcentration, high capacity in sample processing, and easy target retrieval. The concentration of an exemplary target, a single-stranded DNA sequence, was increased up to 170-fold within 80 s. The LOD of the colorimetric assay to verify the DNA target was increased 3 orders of magnitude with a preconcentrated sample compared to the control. The device and its analysis equipment used in this study were all cheap and portable. Thus, the 3D-μP² can be a powerful POC tool for sample pretreatment in resource-limited areas.

Recent Advancements in the Technologies Detecting Food Spoiling Agents

To match the current life-style, there is a huge demand and market for the processed food whose manufacturing requires multiple steps. The mounting demand increases the pressure on the producers and the regulatory bodies to provide sensitive, facile, and cost-effective methods to safeguard consumers' health. In the multistep process of food processing, there are several chances that the food-spoiling microbes or contaminants could enter the supply chain. In this contest, there is a dire necessity to comprehend, implement, and monitor the levels of contaminants by utilizing various available methods, such as single-cell droplet microfluidic system, DNA biosensor, nanobiosensor, smartphone-based biosensor, aptasensor, and DNA microarray-based methods. The current review focuses on the advancements in these methods for the detection of food-borne contaminants and pathogens.

One-Step Nucleic Acid Purification and Noise-Resistant Polymerase Chain Reaction by Electrokinetic Concentration for Ultralow-Abundance Nucleic Acid Detection

Nucleic acid amplification tests (NAATs)integrated on a chip hold great promise for point-of-care diagnostics. Currently, nucleic acid (NA) purification remains time-consuming and labor-intensive, and it takes extensive efforts to optimize the amplification chemistry. Using selective electrokinetic concentration, we report one-step, liquid-phase NA purification that is simpler and faster than conventional solid-phase extraction. By further re-concentrating NAs and performing polymerase chain reaction (PCR) in a microfluidic chamber, our platform suppresses non-specific amplification caused by non-optimal PCR designs. We achieved the detection of 5 copies of M. tuberculosis genomic DNA (equaling 0.3 cell) in real biofluids using both optimized and non-optimal PCR designs, which is 10- and 1000-fold fewer than those of the standard bench-top method, respectively. By simplifying the workflow and shortening the development cycle of NAATs, our platform may find use in point-of-care diagnosis.

Electrode-Free Concentration and Recovery of DNA at Physiologically Relevant Ionic Concentrations

Advances in microanalytical and microfluidic technologies have enabled rapid and amplification-free detection of DNA with a high signal-to-noise ratio. The low sample volume, however, poses a limit in the DNA detection sensitivity, which can be challenging for analyzing rare DNA in physiological samples. One way to improve the sensitivity is to concentrate the DNA in the sample prior to the analysis. The most common DNA concentration techniques are based on electrokinetics, which require an external electric field and generally become ineffective in high ionic concentration conditions. In this work, we present a facile method termed high-salt molecular rheotaxis (HiSMRT) to concentrate and recover DNA from samples with physiologically relevant ionic concentrations without any external electric field. HiSMRT requires only pressure-driven flow and ion concentration gradient to induce a stable local electric field and achieve DNA concentration, making it impervious to high ionic concentrations. We demonstrate that HiSMRT performs robustly at ionic concentrations equivalent to 2%-20% of the ionic concentration in blood serum. HiSMRT can concentrate DNA by up to 960-fold and recover an average of 96.4% of the DNA fragments from 2.0 to 23 kbp uniformly. The concentration process using HiSMRT takes as little as 7.5 min. Moreover, we show that this technique can be easily integrated to perform DNA concentration, size separation, and single-molecule detection all in one platform. We anticipate that this technique will be applicable to a wide range of biological samples and will help to improve the sensitivity of nucleic acid detection for low-abundance DNA biomarkers.

Pressure-Modulated Selective Electrokinetic Trapping for Direct Enrichment, Purification, and Detection of Nucleic Acids in Human Serum

Micro total-analysis systems (μTAS) have been extensively developed for the detection of nucleic acids (NAs) in resource-limited settings in recent years, yet the sample-preparation steps that interface real-world samples with on-chip analytics remain as the technical bottleneck. We report pressure-modulated selective electrokinetic trapping (PM-SET) for the direct enrichment, purification, and detection of NAs in human serum in one step without involving tedious solid-phase extraction, chemical amplification, and surface-hybridization-based assays. Under appropriately modulated hydrostatic pressures, NAs in human serum were selectively enriched in an electrokinetic concentrator with the majority of background proteins removed, achieving an enrichment factor of >4800 in 15 min. A sequence-specific NA was detected simultaneously during the enrichment process using a complementary morpholino (MO) probe, realizing a limit of detection of 3 pM in 15 min. PM-SET greatly reduces the cost, time, and complexity of sample preparation for NA detection and could be easily interfaced with existing NA-detection devices to achieve true sample-to-answer biomolecular analytics.

A Multiwell-Based Detection Platform with Integrated PDMS Concentrators for Rapid Multiplexed Enzymatic Assays

We report an integrated system for accelerating assays with concentrators in a standard 12-well plate (ISAAC-12) and demonstrate its versatility for rapid detection of matrix metalloproteinase (MMP)-9 expression in the cell culture supernatant of breast cancer cell line MDA-MB-231 by accelerating the enzymatic reaction and end-point signal intensity via electrokinetic preconcentration. Using direct printing of a conductive ion-permselective polymer on a polydimethylsiloxane (PDMS) channel, the new microfluidic concentrator chip can be built without modifying the underlying substrate. Through this decoupling fabrication strategy, our microfluidic concentrator chip can easily be integrated with a standard multiwell plate, the de facto laboratory standard platform for high-throughput assays, simply by reversible bonding on the bottom of each well. It increases the reaction rate of enzymatic assays by concentrating the enzyme and the reaction product inside each well simultaneously for rapid multiplexed detection.

Rapid Detection and Trapping of Extracellular Vesicles by Electrokinetic Concentration for Liquid Biopsy on Chip

Exosomes have gained immense importance since their proteomic and genetic contents could potentially be used for disease diagnostics, monitoring of cancer progression, metastasis, and drug efficacy. However, establishing the clinical utility of exosomes has been restricted due to small sizes and high sample loss from extensive sample preparation. Sample loss is particularly critical for body fluids limited in volume and difficult to access, e.g., cerebrospinal fluid. We present a microfluidic technique that locally enhances the concentration of extracellular vesicles extracted from MDA-MB-231 human breast cancer cell lines by using an ion concentration polarization (ICP)-based electrokinetic concentrator. Our design incorporates a trapping mechanism near the conductive polymer membrane; therefore, we can preconcentrate and capture extracellular vesicles simultaneously. Compared with standard fluorescence detection, our method increased the limit of detection (LOD) of extracellular vesicles by two orders of magnitude in 30 min. Our concentrator increased the extracellular vesicle concentration for 5.0 × 10⁷ particles/1 mL (LOD), 5.0 × 10⁸ particles/1 mL, and 5.0 × 10⁸ particles/1 mL by ~100-fold each within 30 min using 45 V. This study demonstrates an alternative platform to simultaneously preconcentrate and capture extracellular vesicles that can be incorporated as part of a liquid biopsy-on-a-chip system for the detection of exosomal biomarkers and analysis of their contents for early cancer diagnosis.

Amplification-free detection of DNA in a paper-based microfluidic device using electroosmotically balanced isotachophoresis

We present a novel microfluidic paper-based analytical device (μPAD) which utilizes the native high electroosmotic flow (EOF) in nitrocellulose to achieve stationary isotachophoresis (ITP) focusing. This approach decouples sample accumulation from the length of the channel, resulting in significant focusing over short channel lengths. We provide a brief theory for EOF-balanced ITP focusing under continuous injection from a depleting reservoir and present the design of a short (7 mm) paper-based microfluidic channel, which allows a 200 μL sample to be processed in approximately 6 min, resulting in a 20 000-fold increase in concentration - a full order of magnitude improvement compared to previous paper-based ITP devices. We show the stability of the assay over longer (40 min) durations of time, and using Morpholino probes, we present the applicability of the device for amplification-free detection of nucleic acids, with a limit-of-detection (LoD) of 5 pM in 10 min. Finally, we utilize the small footprint of the channel and show a multiplexed platform in which 12 assays operate in parallel in a 24-well plate format.

Diagnostic Applications of Morpholinos and Label-Free Electrochemical Detection of Nucleic Acids

Diagnostic applications of morpholinos take advantage of their unique properties including backbone charge neutrality, a weak impact of ionic strength on their hybridization behavior, and their resistance to enzymatic degradation. This chapter overviews how these properties have advanced transduction and other capabilities useful for the analysis of nucleic acids. In many cases, the benefits stem from electrostatic mechanisms; for example, use of low ionic strengths improves sensitivity of detection while decreasing background signals because only the nucleic acid analyte is charged. While most literature reports focus on in vitro assays in buffer, morpholinos have been also used for biodistribution measurements of species such as fungal rRNA and miRNA. After reviewing the diagnostic applications of morpholinos, the chapter describes preparation of morpholino monolayers on metal supports for electrochemical diagnostics and the procedure for performing label-free detection of DNA from changes in surface capacitance.

Detection of Zika virus using reverse-transcription LAMP coupled with reverse dot blot analysis in saliva

In recent years, there have been increasing numbers of infectious disease outbreaks that spread rapidly to population centers resulting from global travel, population vulnerabilities, environmental factors, and ecological disasters such as floods and earthquakes. Some examples of the recent outbreaks are the Ebola epidemic in West Africa, Middle East respiratory syndrome coronavirus (MERS-Co) in the Middle East, and the Zika outbreak through the Americas. We have created a generic protocol for detection of pathogen RNA and/or DNA using loop-mediated isothermal amplification (LAMP) and reverse dot-blot for detection (RDB) and processed automatically in a microfluidic device. In particular, we describe how a microfluidic assay to detect HIV viral RNA was converted to detect Zika virus (ZIKV) RNA. We first optimized the RT-LAMP assay to detect ZIKV RNA using a benchtop isothermal amplification device. Then we implemented the assay in a microfluidic device that will allow analyzing 24 samples simultaneously and automatically from sample introduction to detection by RDB technique. Preliminary data using saliva samples spiked with ZIKV showed that our diagnostic system detects ZIKV RNA in saliva. These results will be validated in further experiments with well-characterized ZIKV human specimens of saliva. The described strategy and methodology to convert the HIV diagnostic assay and platform to a ZIKV RNA detection assay provides a model that can be readily utilized for detection of the next emerging or re-emerging infectious disease.

Rapid detection of exosomal microRNA biomarkers by electrokinetic concentration for liquid biopsy on chip

An ion concentration polarization (ICP)-based electrokinetic concentration device is used for accelerating the surface hybridization reaction between exosomal microRNAs (miRNAs) and morpholinos (MOs) as a synthetic oligo capture probe in the nanomolar concentration range in a microfluidic channel. Compared with standard hybridization at the same concentration, the hybridization time of the miRNA target on MO capture probes could be reduced from ∼24 h to 30 min, with an increase in detection speed by 48 times. This ICP-enhanced hybridization method not only significantly decreases the detection time but also makes workflow simple to use, circumventing use of quantitative reverse transcription polymerase chain reaction or other conventional enzyme-based amplification methods that can cause artifacts.

Electrostatic Cycling of Hybridization Using Nonionic DNA Mimics

This study demonstrates efficient electrostatic control of surface hybridization through use of morpholinos, a charge-neutral DNA mimic, as the immobilized "probes". In addition to being compatible with low ionic strengths, use of uncharged probes renders the field interaction specific to the nucleic acid analyte. In contrast to DNA probes, morpholino probes enable facile cycling between hybridized and dehybridized states within minutes. Impact of ionic strength and temperature on the effectiveness of electrostatics to direct progress of hybridization is evaluated. Optimal electrostatic control is found when stability of probe-analyte duplexes is set so that electrostatics can efficiently switch between the forward (hybridization) and reverse (dehybridization) directions.

Microfluidic cytometers with integrated on-chip optical systems for red blood cell and platelet counting

A microfluidic cytometer with integrated on-chip optical systems was designed for red blood cell (RBC) and platelet (PLT) counting. The design, fabrication, and characterization of the microfluidic cytometer with on-chip optical signal detection were described. With process using only a single mask, the device that integrates optical fibers and on-chip microlens with microfluidic channels on a polydimethylsiloxane layer by standard soft photolithography. This compact structure increased the sensitivity of the device and eliminated time-consuming free-space optical alignments. The microfluidic cytometer was used to count red blood cells and platelets. Forward scatter and extinction were collected simultaneously for each cell. Experimental results indicated that the microfluidic cytometer exhibited comparable performance with a conventional cytometer and demonstrated superior capacity to detect on-chip optical signals in a highly compact, simple, truly portable, and low-cost format that is well suitable for point-of-care clinical diagnostics.

Integration of Multiplexed Microfluidic Electrokinetic Concentrators with a Morpholino Microarray via Reversible Surface Bonding for Enhanced DNA Hybridization

We describe a microfluidic concentration device to accelerate the surface hybridization reaction between DNA and morpholinos (MOs) for enhanced detection. The microfluidic concentrator comprises a single polydimethylsiloxane (PDMS) microchannel onto which an ion-selective layer of conductive polymer poly(3,4-ethylenedioxythiophene)-poly(styrenesulfonate) (

PEDOT

PSS) was directly printed and then reversibly surface bonded onto a morpholino microarray for hybridization. Using this electrokinetic trapping concentrator, we could achieve a maximum concentration factor of ∼800 for DNA and a limit of detection of 10 nM within 15 min. In terms of the detection speed, it enabled faster hybridization by around 10-fold when compared to conventional diffusion-based hybridization. A significant advantage of our approach is that the fabrication of the microfluidic concentrator is completely decoupled from the microarray; by eliminating the need to deposit an ion-selective layer on the microarray surface prior to device integration, interfacing between both modules, the PDMS chip for electrokinetic concentration and the substrate for DNA sensing are easier and applicable to any microarray platform. Furthermore, this fabrication strategy facilitates a multiplexing of concentrators. We have demonstrated the proof-of-concept for multiplexing by building a device with 5 parallel concentrators connected to a single inlet/outlet and applying it to parallel concentration and hybridization. Such device yielded similar concentration and hybridization efficiency compared to that of a single-channel device without adding any complexity to the fabrication and setup. These results demonstrate that our concentrator concept can be applied to the development of a highly multiplexed concentrator-enhanced microarray detection system for either genetic analysis or other diagnostic assays.