Multiplexed detection of nucleic acids in a combinatorial screening chip

Fully Integrated Microfluidic Digital Chip for Simple and Highly Quantitative Detection of Norovirus

The prevalence of foodborne illnesses is a significant global concern, resulting in numerous illnesses, deaths, and substantial economic losses annually. Traditional detection methods for foodborne pathogens are often slow, limited, and impractical for field use, underscoring the need for rapid, sensitive, and portable assays. Microfluidic technology has emerged as a promising solution for sample preparation, reaction, and detection on a small scale. Our study introduces a novel microfluidic digital loop-mediated isothermal amplification (LAMP) assay platform, which employs digital microfluidic chips for absolute quantitative analysis of nucleic acids. This portable chip utilizes LAMP technology to achieve ultrasensitive detection of target nucleic acids within 30 min and reduces the detection limit to 1 fM without the need for complex instrumentation. By digitizing amplification signals directly from the target sample, our platform offers simplicity, affordability, portability, and quantitative molecular readouts. This innovation represents a crucial step toward the on-site detection of foodborne pathogens, thereby enhancing food safety and mitigating disease outbreaks.

Advanced technologies towards improved HPV diagnostics

Persistent infection with high-risk types of human papillomaviruses (HPV) is a major cause of cervical cancer, and an important factor in other malignancies, for example, head and neck cancer. Despite recent progress in screening and vaccination, the incidence and mortality are still relatively high, especially in low-income countries. The mortality and financial burden associated with the treatment could be decreased if a simple, rapid, and inexpensive technology for HPV testing becomes available, targeting individuals for further monitoring with increased risk of developing cancer. Commercial HPV tests available in the market are often relatively expensive, time-consuming, and require sophisticated instrumentation, which limits their more widespread utilization. To address these challenges, novel technologies are being implemented also for HPV diagnostics that include for example, isothermal amplification techniques, lateral flow assays, CRISPR-Cas-based systems, as well as microfluidics, paperfluidics and lab-on-a-chip devices, ideal for point-of-care testing in decentralized settings. In this review, we first evaluate current commercial HPV tests, followed by a description of advanced technologies, explanation of their principles, critical evaluation of their strengths and weaknesses, and suggestions for their possible implementation into medical diagnostics.

Femtomolar detection of SARS-CoV-2 via peptide beacons integrated on a miniaturized TIRF microscope

The novel coronavirus SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) continues to pose a substantial global health threat. Along with vaccines and targeted therapeutics, there is a critical need for rapid diagnostic solutions. In this work, we use computational protein modeling tools to suggest molecular beacon architectures that function as conformational switches for high-sensitivity detection of the SARS-CoV-2 spike protein receptor binding domain (S-RBD). Integrating these beacons on a miniaturized total internal reflection fluorescence (mini-TIRF) microscope, we detect the S-RBD and pseudotyped SARS-CoV-2 with limits of detection in the femtomolar range. We envision that our designed mini-TIRF platform will serve as a robust platform for point-of-care diagnostics for SARS-CoV-2 and future emergent viral threats.

Responsive polymers for medical diagnostics

Stimulus-responsive polymers have been used in improving the efficacy of medical diagnostics through different approaches including enhancing the contrast in imaging techniques and promoting the molecular recognition in diagnostic assays. This review overviews the mechanisms of stimulus-responsive polymers in response to external stimuli including temperature, pH, ion, light, etc. The applications of responsive polymers in magnetic resonance imaging, capture and purification of biomolecules through protein-ligand recognition and lab-on-a-chip technology are discussed.

Electrokinetic Scanning Probe

The theoretical analysis and experimental demonstration of a new concept are presented for a non-contact scanning probe, in which transport of fluid and molecules is controlled by electric fields. The electrokinetic scanning probe (ESP) enables local chemical and biochemical interactions with surfaces in liquid environments. The physical mechanism and design criteria for such a probe are presented, and its compatibility with a wide range of processing solutions and pH values are demonstrated. The applicability of the probe is shown for surface patterning in conjunction with localized heating and 250-fold analyte stacking.

A Solution to the Common Problem of the Synthesis and Applications of Hexachlorofluorescein Labeled Oligonucleotides

A common problem of the preparation of hexachlorofluorescein labeled oligonucleotides is the transformation of the fluorophore to an arylacridine derivative under standard ammonolysis conditions. We show here that the arylacridine byproduct with distinct optical characteristics cannot be efficiently separated from the major product by HPLC or electrophoretic methods, which hampers precise physicochemical experiments with the labeled oligonucleotides. Studies of the transformation mechanism allowed us to select optimal conditions for avoiding the side reaction. The novel method for the post-synthetic deblocking of hexachlorofluorescein-labeled oligodeoxyribonucleotides described in this paper prevents the formation of the arylacridine derivative, enhances the yield of target oligomers, and allows them to be proper real-time PCR probes.

Structured oligonucleotides for target indexing to allow single-vessel PCR amplification and solid support microarray hybridization

The combination of molecular diagnostic technologies is increasingly used to overcome limitations on sensitivity, specificity or multiplexing capabilities, and provide efficient lab-on-chip devices. Two such techniques, PCR amplification and microarray hybridization are used serially to take advantage of the high sensitivity and specificity of the former combined with high multiplexing capacities of the latter. These methods are usually performed in different buffers and reaction chambers. However, these elaborate methods have high complexity and cost related to reagent requirements, liquid storage and the number of reaction chambers to integrate into automated devices. Furthermore, microarray hybridizations have a sequence dependent efficiency not always predictable. In this work, we have developed the concept of a structured oligonucleotide probe which is activated by cleavage from polymerase exonuclease activity. This technology is called SCISSOHR for Structured Cleavage Induced Single-Stranded Oligonucleotide Hybridization Reaction. The SCISSOHR probes enable indexing the target sequence to a tag sequence. The SCISSOHR technology also allows the combination of nucleic acid amplification and microarray hybridization in a single vessel in presence of the PCR buffer only. The SCISSOHR technology uses an amplification probe that is irreversibly modified in presence of the target, releasing a single-stranded DNA tag for microarray hybridization. Each tag is composed of a 3-nucleotide sequence-dependent segment and a unique "target sequence-independent" 14-nucleotide segment allowing for optimal hybridization with minimal cross-hybridization. We evaluated the performance of five (5) PCR buffers to support microarray hybridization, compared to a conventional hybridization buffer. Finally, as a proof of concept, we developed a multiplexed assay for the amplification, detection, and identification of three (3) DNA targets. This new technology will facilitate the design of lab-on-chip microfluidic devices, while also reducing consumable costs. At term, it will allow the cost-effective automation of highly multiplexed assays for detection and identification of genetic targets.

Electrophoresis of two spheres: Influence of double layer and van der Waals interactions

Considering recent applications of electrophoresis conduced in nanoscaled devices, where particle-particle interaction can play a role, we studied for the first time the electrophoresis of two rigid spheres along their center line, taking account of the hydrodynamic, electric, and van der Waals interactions between them. Under the conditions of constant surface potential and surface charge density, the influences of the level of surface potential/charge density, the bulk salt concentration, and the particle-particle distance on their electrokinetic behaviors are examined. Numerical simulation reveals that these behaviors are much more complicated and interesting than those of isolated particles. In particular, we show that care must be taken in choosing an appropriate particle concentration in relevant experiment to avoid obtaining unreliable mobility data.

Centrifugal LabTube platform for fully automated DNA purification and LAMP amplification based on an integrated, low-cost heating system

This paper introduces a disposable battery-driven heating system for loop-mediated isothermal DNA amplification (LAMP) inside a centrifugally-driven DNA purification platform (LabTube). We demonstrate LabTube-based fully automated DNA purification of as low as 100 cell-equivalents of verotoxin-producing Escherichia coli (VTEC) in water, milk and apple juice in a laboratory centrifuge, followed by integrated and automated LAMP amplification with a reduction of hands-on time from 45 to 1 min. The heating system consists of two parallel SMD thick film resistors and a NTC as heating and temperature sensing elements. They are driven by a 3 V battery and controlled by a microcontroller. The LAMP reagents are stored in the elution chamber and the amplification starts immediately after the eluate is purged into the chamber. The LabTube, including a microcontroller-based heating system, demonstrates contamination-free and automated sample-to-answer nucleic acid testing within a laboratory centrifuge. The heating system can be easily parallelized within one LabTube and it is deployable for a variety of heating and electrical applications.

Multiplex detection of nucleic acids using a low cost microfluidic chip and a personal glucose meter at the point-of-care

A simple assay for multiplex DNA detection has been developed using a low cost microfluidic chip and a personal glucose meter.

PDMS bonding to a bio-friendly photoresist via self-polymerized poly(dopamine) adhesive for complex protein micropatterning inside microfluidic channels

Protein micropatterned surfaces integrated with microfluidics are useful in numerous bioanalytical and biological applications. In this study, we demonstrated the fabrication of complex protein micropatterned surfaces within poly(dimethylsiloxane) (PDMS) microfluidic channels by attaching the PDMS channels to bio-friendly photoresist films and subsequently performing microscope projection photolithography (MPP). A muscle-inspired poly(dopamine) (PDA) coating was employed to mediate the bonding between the PDMS and the bio-friendly photoresist poly(2,2-dimethoxy nitrobenzyl methacrylate-r-methyl methacrylate-r-poly(ethylene glycol) methacrylate) (PDMP). By adjusting the dip-coating time for the PDA coating, we could successfully introduce sufficient amounts of functional groups on the PDMP surfaces to mediate strong bonding between the PDMS channels and the PDA-coated PDMP thin films with minimal alteration of the surface properties of the PDMP thin films that are critical for protein micropatterning. Using this novel bonding strategy, we successfully fabricated multiple protein micropatterns and gradient micropatterns of proteins within microfluidic channels. The technique developed in this study will be useful for the fabrication of complex biochips for multiplex bioassays and fundamental cell biological studies.

Fabrication of X-ray compatible microfluidic platforms for protein crystallization

This paper reports a method for fabricating multilayer microfluidic protein crystallization platforms using different materials to achieve X-ray transparency and compatibility with crystallization reagents. To validate this approach, three soluble proteins, lysozyme, thaumatin, and ribonuclease A were crystallized on-chip, followed by on-chip diffraction data collection. We also report a chip with an array of wells for screening different conditions that consume a minimal amount of protein solution as compared to traditional screening methods. A large number of high quality isomorphous protein crystals can be grown in the wells, after which slices of X-ray data can be collected from many crystals still residing within the wells. Complete protein structures can be obtained by merging these slices of data followed by further processing with crystallography software. This approach of using an x-ray transparent chip for screening, crystal growth, and X-ray data collection enables room temperature data collection from many crystals mounted in parallel, which thus eliminates crystal handling and minimizes radiation damage to the crystals.

Rapid hybridization of nucleic acids using isotachophoresis

We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.

Linear conversion of pressure into concentration, rapid switching of concentration, and generation of linear ramps of concentration in a microfluidic device

Mixing of liquids to produce solutions with different concentrations is one of the basic functionalities of microfluidic devices. Generation of specific temporal patterns of concentration in microfluidic devices is an important technique to study responses of cells and model organisms to variations in the chemical composition of their environment. Here, we present a simple microfluidic network that linearly converts pressure at an inlet into concentration of a soluble reagent in an observation region and also enables independent concurrent linear control of concentrations of two reagents. The microfluidic device has an integrated mixer channel with chaotic three-dimensional flow that facilitates rapid switching of concentrations in a continuous range. A simple pneumatic setup generating linear ramps of pressure is used to produce smooth linear ramps and triangular waves of concentration with different slopes. The use of chaotic vs. laminar mixers is discussed in the context of microfluidic devices providing rapid switching and generating temporal waves of concentration.

Design considerations for electrostatic microvalves with applications in poly(dimethylsiloxane)-based microfluidics

Microvalves are critical in the operation of integrated microfluidic chips for a wide range of applications. In this paper, we present an analytical model to guide the design of electrostatic microvalves that can be integrated into microfluidic chips using standard fabrication processes and can reliably operate at low actuation potentials (<250 V). Based on the analytical model, we identify design guidelines and operational considerations for elastomeric electrostatic microvalves and formulate strategies to minimize their actuation potentials, while maintaining the feasibility of fabrication and integration. We specifically explore the application of the model to design microfluidic microvalves fabricated in poly(dimethylsiloxane), using only soft-lithographic techniques. We discuss the electrostatic actuation in terms of several microscale phenomena, including squeeze-film damping and adhesion-driven microvalve collapse. The actuation potentials predicted by the model are in good agreement with experimental data obtained with a microfabricated array of electrostatic microvalves actuated in air and oil. The model can also be extended to the design of peristaltic pumps for microfluidics and to the prediction of actuation potentials of microvalves in viscous liquid environments. Additionally, due to the compact ancillaries required to generate low potentials, these electrostatic microvalves can potentially be used in portable microfluidic chips.

A ceramic microreactor for the synthesis of water soluble CdS and CdS/ZnS nanocrystals with on-line optical characterization

In this paper, a computer controlled microreactor to synthesize water soluble CdS and CdS/ZnS nanocrystals with in situ monitoring of the reaction progress is developed. It is based on ceramic tapes and the Low-Temperature Co-fired Ceramics technology (LTCC). As well the microsystem set-up, the microreactor fluidic design has also been thoroughly optimized. The final device is based on a hydrodynamic focusing of the reagents followed by a three-dimensional micromixer. This generates monodispersed and stable CdS and core-shell CdS/ZnS nanocrystals of 4.5 and 4.2 nm, respectively, with reproducible optical properties in terms of fluorescence emission wavelengths, bandwidth, and quantum yields, which is a key requirement for their future analytical applications. The synthetic process is also controlled in real time with the integration of an optical detection system for absorbance and fluorescence measurements based on commercial miniaturized optical components. This makes possible the efficient managing of the hydrodynamic variables to obtain the desired colloidal suspension. As a result, a simple, economic, robust and portable microsystem for the well controlled synthesis of CdS and CdS/ZnS nanocrystals is presented. Moreover, the reaction takes place in aqueous medium, thus allowing the direct modular integration of this microreactor in specific analytical microsystems, which require the use of such quantum dots as labels.