Rapid DNA hybridization in microfluidics

Graphene Oxide-Functionalized Thread-Based Electrofluidic Approach for DNA Hybridization

A novel, low-cost, and disposable thread-based electrofluidic analytical method employing isotachophoresis (ITP) was developed for demonstrating surface DNA hybridization. This approach was based on graphene oxide (GO) surface-functionalized zones on nylon threads as a binding platform to trap a fluorescently labeled isotachophoretically focused single-stranded DNA (ssDNA) band, resulting in quenching of the fluorescence, which signaled quantitative trapping. In the event of an isotachophoretically focused complementary DNA (cDNA) band passing over the GO-trapped ssDNA zone, surface hybridization of the ssDNA and cDNA to form double-stranded DNA (dsDNA) band occurred, which is released from the GO-coated zones, resulting in restoration of the fluorescent signal as it exits the GO band and migrates further along the thread. This controllable process demonstrates the potential of the GO-functionalized thread-based microfluidic analytical approach for DNA hybridization and its visualization, which could be adapted into point-of-care (POC) diagnostic devices for real-world applications.

Nucleic acid amplification-free detection of DNA and RNA at ultralow concentration

The broad spectrum of approaches for nucleic acid amplification-free detection of DNA and RNA at single-digit attomolar (10^-18 M) concentration and lower is reviewed. These low concentrations correspond roughly to the most clinically desirable detection range for pathogen-specific nucleic acid as well as the detection limits of commercially available, nucleic acid amplification tests based primarily on polymerase chain reaction (PCR). The need for more rapid and inexpensive, yet still highly accurate tests, has become evident during the pandemic. It is expected that publication of reports describing improved tests will accelerate soon, and this review covers the wide variety of detection methods based on both optical and electrical measurements that have been conceived over recent years, enabled generally by the advent of nanotechnology.

Uncertainties in synthetic DNA-based data storage

Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.

Active bioparticle manipulation in microfluidic systems

The motion of bioparticles in a microfluidic environment can be actively controlled using several tuneable mechanisms, including hydrodynamic, electrophoresis, dielectrophoresis, magnetophoresis, acoustophoresis, thermophoresis and optical forces.

Spin-coated Au-nanohole arrays engineered by nanosphere lithography for a Staphylococcus aureus 16S rRNA electrochemical sensor

The nanopatterning of gold nanoparticle (AuNP) arrays on an indium tin oxide (ITO) electrode using efficient and low-cost methods is described. This process used nanosphere lithography (NSL) encompassing the deposition of monolayered Polystyrene (PS) followed by a convective self-assembly drop coating protocol onto the ITO substrate that further acted as the mask after the AuNP assembly. The results showed that spin-coating allowed AuNPs to follow the contour and adhere to the PS nanospheres. The final products, after etching the PS, generated a highly ordered Au-nanohole array on an ITO substrate. The Au-nanohole arrays on the ITO electrode provided a greater surface area and successfully enhanced the peak current of electrochemical measurements by 82% compared with bare ITO and was used to detect Staphylococcus aureus 16S rRNA hybridization. In contrast to non-templated AuNP structures, the Au-nanohole arrays on the ITO electrode contributed to an optimum sensitivity improvement in DNA hybridization detection by 23%, along with an impressive limit of detection (LOD) of 10 pM. The high specificity of this distinguished structure was also achieved in the hybridization measurements of multi-analyte pathogens. These findings indicate that the combination of PS nanosphere lithography, followed by the spin-coating of AuNPs, leads to an inexpensive and simple engineering process that effectively generates uniform Au-nanohole arrays on ITO, which provides a greater surface area to optimize the electrochemical performance of the DNA biosensor.

A controlled microfluidic electrochemical lab-on-a-chip for label-free diffusion-restricted DNA hybridization analysis

Lab-on-a-chip (LOC) devices for electrochemical analysis of DNA hybridization events offer a technology for real-time and label-free assessment of biomarkers at the point-of-care. Here, we present a microfluidic LOC, with 3 × 3 arrayed electrochemical sensors for the analysis of DNA hybridization events. A new dual layer microfluidic valved manipulation system is integrated providing controlled and automated capabilities for high throughput analysis. This feature improves the repeatability, accuracy, and overall sensing performance (Fig. 1). The electrochemical activity of the fabricated microfluidic device is validated and demonstrated repeatable and reversible Nernstian characteristics. System design required detailed analysis of energy storage and dissipation as our sensing modeling involves diffusion-related electrochemical impedance spectroscopy. The effect of DNA hybridization on the calculated charge transfer resistance and the diffusional resistance components is evaluated. We demonstrate a specific device with an average cross-reactivity value of 27.5%. The device yields semilogarithmic dose response and enables a theoretical detection limit of 1 nM of complementary ssDNA target. This limit is lower than our previously reported non-valved device by 74% due to on-chip valve integration providing controlled and accurate assay capabilities.

Industrial lab-on-a-chip: design, applications and scale-up for drug discovery and delivery

Microfluidics is an emerging and promising interdisciplinary technology which offers powerful platforms for precise production of novel functional materials (e.g., emulsion droplets, microcapsules, and nanoparticles as drug delivery vehicles- and drug molecules) as well as high-throughput analyses (e.g., bioassays, detection, and diagnostics). In particular, multiphase microfluidics is a rapidly growing technology and has beneficial applications in various fields including biomedicals, chemicals, and foods. In this review, we first describe the fundamentals and latest developments in multiphase microfluidics for producing biocompatible materials that are precisely controlled in size, shape, internal morphology and composition. We next describe some microfluidic applications that synthesize drug molecules, handle biological substances and biological units, and imitate biological organs. We also highlight and discuss design, applications and scale up of droplet- and flow-based microfluidic devices used for drug discovery and delivery.

Label-free DNA biosensor based on SERS Molecular Sentinel on Nanowave chip

Development of a rapid, cost-effective, label-free biosensor for DNA detection is important for many applications in clinical diagnosis, homeland defense, and environment monitoring. A unique label-free DNA biosensor based on Molecular Sentinel (MS) immobilized on a plasmonic 'Nanowave' chip, which is also referred to as a metal film over nanosphere (MFON), is presented. Its sensing mechanism is based upon the decrease of the surface-enhanced Raman scattering (SERS) intensity when Raman label tagged at one end of MS is physically separated from the MFON's surface upon DNA hybridization. This method is label-free as the target does not have to be labeled. The MFON fabrication is relatively simple and low-cost with high reproducibility based on depositing a thin shell of gold over close-packed arrays of nanospheres. The sensing process involves a single hybridization step between the DNA target sequences and the complementary MS probes on the Nanowave chip without requiring secondary hybridization or posthybridization washing, thus resulting in rapid assay time and low reagent usage. The usefulness and potential application of the biosensor for medical diagnostics is demonstrated by detecting the human radical S-adenosyl methionine domain containing 2 (RSAD2) gene, a common inflammation biomarker.

Numerical modeling of DNA-chip hybridization with chaotic advection

We present numerical simulations of DNA-chip hybridization, both in the "static" and "dynamical" cases. In the static case, transport of free targets is limited by molecular diffusion; in the dynamical case, an efficient mixing is achieved by chaotic advection, with a periodic protocol using pumps in a rectangular chamber. This protocol has been shown to achieve rapid and homogeneous mixing. We suppose in our model that all free targets are identical; the chip has different spots on which the probes are fixed, also all identical, and complementary to the targets. The reaction model is an infinite sink potential of width dh , i.e., a target is captured as soon as it comes close enough to a probe, at a distance lower than dh . Our results prove that mixing with chaotic advection enables much more rapid hybridization than the static case. We show and explain why the potential width dh does not play an important role in the final results, and we discuss the role of molecular diffusion. We also recover realistic reaction rates in the static case.