Lab-on-a-chip technologies for single-molecule studies

Trends in Single-Molecule Total Internal Reflection Fluorescence Imaging and Their Biological Applications with Lab-on-a-Chip Technology

Single-molecule imaging technologies, especially those based on fluorescence, have been developed to probe both the equilibrium and dynamic properties of biomolecules at the single-molecular and quantitative levels. In this review, we provide an overview of the state-of-the-art advancements in single-molecule fluorescence imaging techniques. We systematically explore the advanced implementations of in vitro single-molecule imaging techniques using total internal reflection fluorescence (TIRF) microscopy, which is widely accessible. This includes discussions on sample preparation, passivation techniques, data collection and analysis, and biological applications. Furthermore, we delve into the compatibility of microfluidic technology for single-molecule fluorescence imaging, highlighting its potential benefits and challenges. Finally, we summarize the current challenges and prospects of fluorescence-based single-molecule imaging techniques, paving the way for further advancements in this rapidly evolving field.

Water-in-water droplet microfluidics: A design manual

Droplet microfluidics is utilized in a wide range of applications in biomedicine and biology. Applications include rapid biochemical analysis, materials generation, biochemical assays, and point-of-care medicine. The integration of aqueous two-phase systems (ATPSs) into droplet microfluidic platforms has potential utility in oil-free biological and biomedical applications, namely, reducing cytotoxicity and preserving the native form and function of costly biomolecular reagents. In this review, we present a design manual for the chemist, biologist, and engineer to design experiments in the context of their biological applications using all-in-water droplet microfluidic systems. We describe the studies achievable using these systems and the corresponding fabrication and stabilization methods. With this information, readers may apply the fundamental principles and recent advancements in ATPS droplet microfluidics to their research. Finally, we propose a development roadmap of opportunities to utilize ATPS droplet microfluidics in applications that remain underexplored.

Recent Advances in Single-Molecule Sensors Based on STM Break Junction Measurements

Single-molecule recognition and detection with the highest resolution measurement has been one of the ultimate goals in science and engineering. Break junction techniques, originally developed to measure single-molecule conductance, recently have also been proven to have the capacity for the label-free exploration of single-molecule physics and chemistry, which paves a new way for single-molecule detection with high temporal resolution. In this review, we outline the primary advances and potential of the STM break junction technique for qualitative identification and quantitative detection at a single-molecule level. The principles of operation of these single-molecule electrical sensing mainly in three regimes, ion, environmental pH and genetic material detection, are summarized. It clearly proves that the single-molecule electrical measurements with break junction techniques show a promising perspective for designing a simple, label-free and nondestructive electrical sensor with ultrahigh sensitivity and excellent selectivity.

A Critical Review on the Sensing, Control, and Manipulation of Single Molecules on Optofluidic Devices

Single-molecule techniques have shifted the paradigm of biological measurements from ensemble measurements to probing individual molecules and propelled a rapid revolution in related fields. Compared to ensemble measurements of biomolecules, single-molecule techniques provide a breadth of information with a high spatial and temporal resolution at the molecular level. Usually, optical and electrical methods are two commonly employed methods for probing single molecules, and some platforms even offer the integration of these two methods such as optofluidics. The recent spark in technological advancement and the tremendous leap in fabrication techniques, microfluidics, and integrated optofluidics are paving the way toward low cost, chip-scale, portable, and point-of-care diagnostic and single-molecule analysis tools. This review provides the fundamentals and overview of commonly employed single-molecule methods including optical methods, electrical methods, force-based methods, combinatorial integrated methods, etc. In most single-molecule experiments, the ability to manipulate and exercise precise control over individual molecules plays a vital role, which sometimes defines the capabilities and limits of the operation. This review discusses different manipulation techniques including sorting and trapping individual particles. An insight into the control of single molecules is provided that mainly discusses the recent development of electrical control over single molecules. Overall, this review is designed to provide the fundamentals and recent advancements in different single-molecule techniques and their applications, with a special focus on the detection, manipulation, and control of single molecules on chip-scale devices.

Active matter dynamics in confined microfluidic environments

The field of active matter is a nascent area of research in soft condensed matter physics, which is drawing on the expertise of researchers from diverse disciplines. Small scale active particles-both inorganic and biological-display non-trivial emergent dynamics and interactions that could help us understand complex biological processes and phenomena. Recently, using microfluidic technologies, several research groups have performed important experimental and theoretical studies to understand the behavior of self-propelled particles and molecular active matter within confined environments-to glean a fundamental understanding of the cellular processes occurring under ultra-low Reynolds number conditions. In this chapter, we would like to review applications of microfluidics in active matter research, highlighting a few important theoretical and experimental investigations. We will conclude the discussion with a note on the future of this field mentioning a few open questions that are at the forefront of our minds.

Optofluidic ptychography on a chip

We report the implementation of a fully on-chip, lensless microscopy technique termed optofluidic ptychography. This imaging modality complements the miniaturization provided by microfluidics and allows the integration of ptychographic microscopy into various lab-on-a-chip devices. In our prototype, we place a microfluidic channel on the top surface of a coverslip and coat the bottom surface with a scattering layer. The channel and the coated coverslip substrate are then placed on top of an image sensor for diffraction data acquisition. Similar to the operation of a flow cytometer, the device utilizes microfluidic flow to deliver specimens across the channel. The diffracted light from the flowing objects is modulated by the scattering layer and recorded by the image sensor for ptychographic reconstruction, where high-resolution quantitative complex images are recovered from the diffraction measurements. By using an image sensor with a 1.85 μm pixel size, our device can resolve the 550 nm linewidth on the resolution target. We validate the device by imaging different types of biospecimens, including C. elegans, yeast cells, paramecium, and closterium sp. We also demonstrate a high-resolution ptychographic reconstruction at a video framerate of 30 frames per second. The reported technique can address a wide range of biomedical needs and engenders new ptychographic imaging innovations in a flow cytometer configuration.

Capture and elongation of single chromosomal DNA molecules using optically driven microchopsticks

DNA analysis based on the observation of single DNA molecules has been a key technology in molecular biology. Several techniques for manipulating single DNA molecules have been proposed for this purpose; however, these techniques have limits on the manipulatable DNA. To overcome this, we demonstrate a method of DNA manipulation using microstructures captured by optical tweezers that allow the manipulation of a chromosomal DNA molecule. For proper DNA handling, we developed microstructures analogous to chopsticks to capture and elongate single DNA molecules under an optical microscope. Two microstructures (i.e., microchopsticks) were captured by two focused laser beams to pinch a single yeast chromosomal DNA molecule between them and thereby manipulate it. The experiments demonstrated successful DNA manipulation and revealed that the size and geometry of the microchopsticks are important factors for effective DNA handling. This technique allows a high degree of freedom in handling single DNA molecules, potentially leading to applications in the study of chromosomal DNA.

High-throughput single-molecule imaging system using nanofabricated trenches and fluorescent DNA-binding proteins

DNA curtain is a high-throughput system, integrating a lipid bilayer, fluorescence imaging, and microfluidics to probe protein-DNA interactions in real-time and has provided in-depth understanding of DNA metabolism. Especially, the microfluidic platform of a DNA curtain is highly suitable for a biochip. In the DNA curtain, DNA molecules are aligned along chromium nanobarriers, which are fabricated on a slide surface, and visualized using an intercalating dye, YOYO-1. Although the chromium barriers confer precise geometric alignment of DNA, reuse of the slides is limited by wear of the barriers during cleaning. YOYO-1 is rapidly photobleached and causes photocleavage of DNA under continuous laser illumination, restricting DNA observation to a brief time window. To address these challenges, we developed a new nanopatterned slide, upon which carved nanotrenches serve as diffusion barriers. The nanotrenches were robust under harsh cleaning conditions, facilitating the maintenance of surface cleanliness that is essential to slide reuse. We also stained DNA with a fluorescent protein with a DNA-binding motif, fluorescent protein-DNA binding peptide (FP-DBP). FP-DBP was slowly photobleached and did not cause DNA photocleavage. This new DNA curtain system enables a more stable and repeatable investigation of real-time protein-DNA interactions and will serve as a good platform for lab-on-a-chip.

Single-molecule biosensors: Recent advances and applications

Single-molecule biosensors serve the unmet need for real time detection of individual biological molecules in the molecular crowd with high specificity and accuracy, uncovering unique properties of individual molecules which are hidden when measured using ensemble averaging methods. Measuring a signal generated by an individual molecule or its interaction with biological partners is not only crucial for early diagnosis of various diseases such as cancer and to follow medical treatments but also offers a great potential for future point-of-care devices and personalized medicine. This review summarizes and discusses recent advances in nanosensors for both in vitro and in vivo detection of biological molecules offering single-molecule sensitivity. In the first part, we focus on label-free platforms, including electrochemical, plasmonic, SERS-based and spectroelectrochemical biosensors. We review fluorescent single-molecule biosensors in the second part, highlighting nanoparticle-amplified assays, digital platforms and the utilization of CRISPR technology. We finally discuss recent advances in the emerging nanosensor technology of important biological species as well as future perspectives of these sensors.

Metallic photonic crystal-based sensor for cryogenic environments

We investigate the design, characterization, and application of metallic photonic crystal (MPC) structures, consisting of plasmonic gold nanogratings on top of a photonic waveguide, as transducers for lab-on-chip biosensing in cryogenic environments. The compact design offers a promising approach to sensitive, in situ biosensing platforms for astrobiology applications (e.g., on the "icy moons" of the outer solar system). We fabricated and experimentally characterized three MPC sensor geometries, with variable nanograting width, at temperatures ranging from 300 K to 180 K. Sensors with wider nanogratings were more sensitive to changes in the local dielectric environment. Temperature-dependent experiments revealed an increase in plasmonic resonance intensity of around 13% at 180 K (compared with 300 K), while the coupled plasmonic-photonic resonance was less sensitive to temperature, varying by less than 5%. Simulation results confirm the relative temperature stability of the plasmonic-photonic mode and, combined with its high sensitivity, suggest a novel application of this mode as the sensing transduction mechanism over wide temperature ranges. To our knowledge, this is among the first reports of the design and characterization of a nanoplasmonic sensor specifically for low-temperature sensing operation.

Tweezing of Magnetic and Non-Magnetic Objects with Magnetic Fields

Although strong magnetic fields cannot be conveniently "focused" like light, modern microfabrication techniques enable preparation of microstructures with which the field gradients - and resulting magnetic forces - can be localized to very small dimensions. This ability provides the foundation for magnetic tweezers which in their classical variant can address magnetic targets. More recently, the so-called negative magnetophoretic tweezers have also been developed which enable trapping and manipulations of completely nonmagnetic particles provided that they are suspended in a high-magnetic-susceptibility liquid. These two modes of magnetic tweezing are complimentary techniques tailorable for different types of applications. This Progress Report provides the theoretical basis for both modalities and illustrates their specific uses ranging from the manipulation of colloids in 2D and 3D, to trapping of living cells, control of cell function, experiments with single molecules, and more.

Evolvable Smartphone-Based Platforms for Point-of-Care In-Vitro Diagnostics Applications

The association of smart mobile devices and lab-on-chip technologies offers unprecedented opportunities for the emergence of direct-to-consumer in vitro medical diagnostics applications. Despite their clear transformative potential, obstacles remain to the large-scale disruption and long-lasting success of these systems in the consumer market. For instance, the increasing level of complexity of instrumented lab-on-chip devices, coupled to the sporadic nature of point-of-care testing, threatens the viability of a business model mainly relying on disposable/consumable lab-on-chips. We argued recently that system evolvability, defined as the design characteristic that facilitates more manageable transitions between system generations via the modification of an inherited design, can help remedy these limitations. In this paper, we discuss how platform-based design can constitute a formal entry point to the design and implementation of evolvable smart device/lab-on-chip systems. We present both a hardware/software design framework and the implementation details of a platform prototype enabling at this stage the interfacing of several lab-on-chip variants relying on current- or impedance-based biosensors. Our findings suggest that several change-enabling mechanisms implemented in the higher abstraction software layers of the system can promote evolvability, together with the design of change-absorbing hardware/software interfaces. Our platform architecture is based on a mobile software application programming interface coupled to a modular hardware accessory. It allows the specification of lab-on-chip operation and post-analytic functions at the mobile software layer. We demonstrate its potential by operating a simple lab-on-chip to carry out the detection of dopamine using various electroanalytical methods.

Biophysics in drug discovery: impact, challenges and opportunities

Over the past 25 years, biophysical technologies such as X-ray crystallography, nuclear magnetic resonance spectroscopy, surface plasmon resonance spectroscopy and isothermal titration calorimetry have become key components of drug discovery platforms in many pharmaceutical companies and academic laboratories. There have been great improvements in the speed, sensitivity and range of possible measurements, providing high-resolution mechanistic, kinetic, thermodynamic and structural information on compound-target interactions. This Review provides a framework to understand this evolution by describing the key biophysical methods, the information they can provide and the ways in which they can be applied at different stages of the drug discovery process. We also discuss the challenges for current technologies and future opportunities to use biophysical methods to solve drug discovery problems.

Lab-on-chip systems for integrated bioanalyses

Biomolecular detection systems based on microfluidics are often called lab-on-chip systems. To fully benefit from the miniaturization resulting from microfluidics, one aims to develop 'from sample-to-answer' analytical systems, in which the input is a raw or minimally processed biological, food/feed or environmental sample and the output is a quantitative or qualitative assessment of one or more analytes of interest. In general, such systems will require the integration of several steps or operations to perform their function. This review will discuss these stages of operation, including fluidic handling, which assures that the desired fluid arrives at a specific location at the right time and under the appropriate flow conditions; molecular recognition, which allows the capture of specific analytes at precise locations on the chip; transduction of the molecular recognition event into a measurable signal; sample preparation upstream from analyte capture; and signal amplification procedures to increase sensitivity. Seamless integration of the different stages is required to achieve a point-of-care/point-of-use lab-on-chip device that allows analyte detection at the relevant sensitivity ranges, with a competitive analysis time and cost.

Tuning the Music: Acoustic Force Spectroscopy (AFS) 2.0

AFS is a recently introduced high-throughput single-molecule technique that allows studying structural and mechanochemical properties of many biomolecules in parallel. To further improve the method, we developed a modelling tool to optimize the layer thicknesses, and a calibration method to experimentally validate the modelled force profiles. After optimization, we are able to apply 350pN on 4.5μm polystyrene beads, without the use of an amplifier, at the coverslip side of the AFS chip. Furthermore, we present the use of a transparent piezo to generate the acoustic force and we show that AFS can be combined with high-NA oil or water-immersion objectives. With this set of developments AFS will be applicable to a broad range of single-molecule experiments.

Optofluidic wavelength division multiplexing for single-virus detection

Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context--the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine.

Optofluidic wavelength division multiplexing for single-virus detection

Optical waveguides simultaneously transport light at different colors, forming the basis of fiber-optic telecommunication networks that shuttle data in dozens of spectrally separated channels. Here, we reimagine this wavelength division multiplexing (WDM) paradigm in a novel context--the differentiated detection and identification of single influenza viruses on a chip. We use a single multimode interference (MMI) waveguide to create wavelength-dependent spot patterns across the entire visible spectrum and enable multiplexed single biomolecule detection on an optofluidic chip. Each target is identified by its time-dependent fluorescence signal without the need for spectral demultiplexing upon detection. We demonstrate detection of individual fluorescently labeled virus particles of three influenza A subtypes in two implementations: labeling of each virus using three different colors and two-color combinatorial labeling. By extending combinatorial multiplexing to three or more colors, MMI-based WDM provides the multiplexing power required for differentiated clinical tests and the growing field of personalized medicine.

Rapid single-molecule imaging in cyclic olefin copolymer channels

Rapid preparation of high quality capture surfaces is a major challenge for surface-based single-molecule protein binding assays. Here we introduce a simple method to activate microfluidic chambers made from cyclic olefin copolymer for single-molecule imaging with total internal reflection fluorescence microscopy. We describe a surface coating protocol and demonstrate single-molecule imaging in off-the-shelf microfluidic parts that can be activated for binding assays within a few minutes. As the first example, biotinylated protein directly captured on the neutravidin-coated surface was detected using fluorescently labeled antibody. We then showed detection of a fusion construct containing green fluorescence protein and verified its single fluorophore behavior by observing stepwise photobleaching events. Finally, a target protein was identified in the crude cell lysate using antibody-sandwich complex formation. In all experiments, controls were completed to ensure that nonspecific binding to the surface was minimal. Based on our results, we conclude that the simple surface preparation described in this paper enables single-molecule imaging assays without time-consuming coating procedures.

Playing the notes of DNA with light: extremely high frequency nanomechanical oscillations

We use a double nanohole (DNH) optical tweezer with two trapping lasers beating to excite the vibrational modes of single-stranded DNA (ssDNA) fragments in the extremely high frequency range. We find the resonant vibration frequency of a 20 base ssDNA to be 40 GHz. We show that the change in the resonant frequency for different lengths of the DNA strand is in good agreement with one dimensional lattice vibration theory. Thus the DNH tweezer system could distinguish between different lengths of DNA strands with resolution down to a few bases. By varying the base sequence and length, it is possible to adjust the resonance frequency vibration spectrum. The technique shows the potential for use in sequencing applications if we can improve the resolution of the present system to detect changes in resonant frequency for a single base change in a given sequence. The technique is single-molecule and label-free as compared to the existing methods used for DNA characterization like gel electrophoresis.

Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging

Single-molecule imaging and manipulation of biochemical reactions continues to reveal numerous biological insights. To facilitate these studies, we have developed and implemented a high-throughput approach to organize and image hundreds of individual DNA molecules at aligned diffusion barriers. Nonetheless, obtaining statistically relevant data sets under a variety of reaction conditions remains challenging. Here, we present a method for integrating high-throughput single-molecule "DNA curtain" imaging with poly(dimethylsiloxane) (PDMS)-based microfluidics. Our benchtop fabrication method can be accomplished in minutes with common tools found in all molecular biology laboratories. We demonstrate the utility of this approach by simultaneous imaging of two independent biochemical reaction conditions in a laminar flow device. In addition, five different reaction conditions can be observed concurrently in a passive linear gradient generator. Combining rapid microfluidic fabrication with high-throughput DNA curtains greatly expands our capability to interrogate complex biological reactions.

Dark-field illumination on zero-mode waveguide/microfluidic hybrid chip reveals T4 replisomal protein interactions

The ability of zero-mode waveguides (ZMWs) to guide light energy into subwavelength-diameter cylindrical nanoapertures has been exploited for single-molecule fluorescence studies of biomolecules at micromolar concentrations, the typical dissociation constants for biomolecular interactions. Although epi-fluorescence microscopy is now adopted for ZMW-based imaging as an alternative to the commercialized ZMW imaging platform, its suitability and performance awaits rigorous examination. Here, we present conical lens-based dark-field fluorescence microscopy in combination with a ZMW/microfluidic chip for single-molecule fluorescence imaging. We demonstrate that compared to epi-illumination, the dark-field configuration displayed diminished background and noise and enhanced signal-to-noise ratios. This signal-to-noise ratio for imaging using the dark-field setup remains essentially unperturbed by the presence of background fluorescent molecules at micromolar concentration. Our design allowed single-molecule FRET studies that revealed weak DNA-protein and protein-protein interactions found with T4 replisomal proteins.

A highly sensitive microfluidics system for multiplexed surface-enhanced Raman scattering (SERS) detection based on Ag nanodot arrays

We present a microfluidics system with Ag nanodot arrays as the enhancement substrate for multiplexed SERS detection of low-concentration mixtures of thiram and adenine.

Accelerating drug discovery via organs-on-chips

Considerable advances have been made in the development of micro-physiological systems that seek to faithfully replicate the complexity and functionality of animal and human physiology in research laboratories. Sometimes referred to as "organs-on-chips", these systems provide key insights into physiological or pathological processes associated with health maintenance and disease control, and serve as powerful platforms for new drug development and toxicity screening. In this Focus article, we review the state-of-the-art designs and examples for developing multiple "organs-on-chips", and discuss the potential of this emerging technology to enhance our understanding of human physiology, and to transform and accelerate the drug discovery and preclinical testing process. This Focus article highlights some of the recent technological advances in this field, along with the challenges that must be addressed for these technologies to fully realize their potential.

Fabrication and functionalization of periodically aligned metallic nanocup arrays using colloidal lithography with a sinusoidally wrinkled substrate

We propose a general strategy for fabricating ultrasmall attoliter-sized (10(-18) L) one-dimensional (1D) aligned nanocup arrays embedded in poly(dimethylsiloxane) (PDMS) films based on a combination of colloidal soft-lithography and wrinkle processing. The nanocup consists of a metallic shell (silver-single or double-layer silver/gold type) with a thickness of several tens of nanometers and whose diameter was ca. 500 nm and cavity depth was ca. 250 nm. First, monodisperse polystyrene (PS) colloids (d = 500 nm) were arranged onto a sinusoidally wrinkled PDMS substrate. Then, the colloid particle arrays were transferred onto another flat PDMS substrate, and a metal film was vacuum deposited over the array to form a nanostructured surface consisting of half-shell metal-coated colloid particle arrays. After the metal-coated PS array was gently transferred onto another soft PDMS substrate prepared by nonthermal curing, the attached films were thermally cured. After that, both films were carefully separated to selectively transfer the metal-coated PS particle arrays, since the metallic shell on the PS surface can adhere to the soft PDMS. Finally, the PS colloids were removed by plasma etching, leaving behind the 1D hemispherical metallic shells, called here the "metallic nanocup array structure". This structure was evaluated by performing atomic force microscopy, scanning electron microscopy, and X-ray photoelectron spectroscopy measurements. We further demonstrate chemical modification of the inner nanocup surface through construction of a self-assembled monolayer, and we also fill them with nanomaterials (silica nanoparticles) to demonstrate their application to size-selecting devices. The obtained metallic nanocup arrays could be components in a new class of chemical and/or biological nanoreactors with small reaction vessels, surface-enhanced Raman scattering (SERS)-based sensors, and size separators for nanoparticles.