Highly sensitive restriction enzyme assay and analysis: a review

Biological assays at the single molecule level are crucial to fundamental studies of DNA-protein mechanisms. In order to cater for high throughput applications, one area of immense research potential is single-molecule bioassays where miniaturized devices are developed to perform rapid and effective biological reactions and analyses. With the success of various emerging technologies for engineering miniaturized structures down to the nanoscale level, supported by specialized equipment for detection, many investigations in the field of life science that were once thought impossible can now be actively explored. In this review, the significance of downscaling to the single-molecule level is firstly presented in selected examples, with the focus placed on restriction enzyme assays. To determine the effectiveness of single-molecule restriction enzyme reactions, simple and direct analytical methods based on DNA stretching have often been reliably employed. DNA stretching can be realized based on a number of working principles related to the physical forces exerted on the DNA samples. We then discuss two examples of a nanochannel system and a microchamber system where single-molecule restriction enzyme digestion and DNA stretching have been integrated, which possess prospective capabilities of developing into highly sensitive and high-throughput restriction enzyme assays. Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels. Figure Minaturization of Restriction Enzyme Assays and DNA Stretching     

Combining microchip and cell technology for creation of novel biodevices

Microchip technology has matured over the years into an important field in which novel technologies are being constantly invented, and down-sizing and incorporation of already existing methodologies into the microscale is increasing assay performance and bearing the promise of future total integration for simple, widespread use. One rapidly growing sub-discipline of the microchip research field is focused around the integration of microchip technology and cell biology. In this review, we recapitulate progress here at the Kitamori laboratory in direct relation to cell and microchip technologies, and show some examples of successful integration of the two, going from controlled patterning of cells, on-chip cell culture stimulation, and cardiovascular systems on a chip, to bio-microdevices integrating cardiovascular cells and microtechnology to create novel biodevices such as biocompatible, miniature pumps.     

Organocatalytic Desymmetrization Reactions for the Synthesis of Axially Chiral Compounds

The enantioselective synthesis of atropisomers is an emerging field, that in recent years reached fundamental results and put the bases for innovative applications. Organocatalysis is playing a central role in the realization of original synthesis for novel atropisomeric scaffolds.^[1] In this short review, we would like to highlight the results obtained by our group and others in the field of axially enantioselective desymmetrization reactions using organocatalysis as main strategy.     

基于裂结技术的单分子尺度化学反应研究进展

分子电子学是研究单分子器件的构筑、性质以及功能调控的一门新兴学科。其中,金属/分子/金属结的构筑和表征是现阶段分子电子学的主要研究内容。裂结技术是当前分子电子学研究的主要实验方法,主要包括机械可控裂结技术和扫描隧道显微镜裂结技术。本文对裂结技术进行了介绍,并对近年来利用这些技术,在单分子尺度化学反应的检测和动力学研究,以及将这些技术与溶液环境、静电场、电化学门控等方法相结合,调控单分子器件的电输运性质等方面所取得的进展进行了概述。     

Recent developments in optical detection methods for microchip separations

This paper summarizes the features and performances of optical detection systems currently applied in order to monitor separations on microchip devices. Fluorescence detection, which delivers very high sensitivity and selectivity, is still the most widely applied method of detection. Instruments utilizing laser-induced fluorescence (LIF) and lamp-based fluorescence along with recent applications of light-emitting diodes (LED) as excitation sources are also covered in this paper. Since chemiluminescence detection can be achieved using extremely simple devices which no longer require light sources and optical components for focusing and collimation, interesting approaches based on this technique are presented, too. Although UV/vis absorbance is a detection method that is commonly used in standard desktop electrophoresis and liquid chromatography instruments, it has not yet reached the same level of popularity for microchip applications. Current applications of UV/vis absorbance detection to microchip separations and innovative approaches that increase sensitivity are described. This article, which contains 85 references, focuses on developments and applications published within the last three years, points out exciting new approaches, and provides future perspectives on this field.     

Single-molecule, single-particle approaches for exploring the structure and kinetics of nanocatalysts

In this Article, we focus on the in situ observation of photochemical reactions on individual nanoobjects of solid catalysts using single-molecule, single-particle fluorescence spectroscopy. The use of high-resolution imaging techniques with suitable fluorogenic probes enables us to determine the location of the catalytically active sites that are related to the structural heterogeneities on the surface of the solid catalyst and the temporal fluctuation of photochemical reactivity. Furthermore, we present the real-time observation of metastable gold nanoclusters in polymer matrices at the single-cluster level. This Article encourages readers to explore the nanoworld in terms of practical applications in many fields such as fundamental physics and chemistry.     

Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials

Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors are gaining widespread attention as non-destructive tools, visible to the human eye, that are capable of a real-time and in-situ response. Optical “visual” sensors are expanding researchers’ interests in many chemical contexts and are routinely used for biological, environmental, and medical applications. In this review we provide an overview of trending colorimetric, fluorescent, or dual-mode responsive visual pH sensors. These sensors include molecular synthetic organic sensors, metal organic frameworks (MOF), engineered sensing nanomaterials, and bioengineered sensors. We review different typological chemical entities of visual pH sensors, three-dimensional structures, and signaling mechanisms for pH sensing and applications; developed in the past five years. The progression of this review from simple organic molecules to biological macromolecules seeks to benefit beginners and scientists embarking on a project of pH sensing development, who needs background information and a quick update on advances in the field. Lessons learned from these tools will aid pH determination projects and provide new ways of thinking for cell bioimaging or other cutting-edge in vivo applications.     

Single-molecule detection in exploring nanoenvironments: an overview

In the last one decade or so, a variety of optical experiments have been designed and performed that are capable of exploring down to the regime of single-molecule detection and measurements in all different environments, including solids, surfaces, and liquids. Single-molecule detection in condensed phases has many important chemical and biological applications. A few to list are: rapid DNA sequencing, DNA fragment sizing, medical diagnosis, forensic analysis, understanding of chemical dynamics and mechanisms, etc. Single-molecule spectroscopy allows us to observe the individual molecules hidden in a condensed phase sample, by using a tunable laser light. This technique has the ability to detect and monitor systems with an ultimate sensitivity level of ∼1.66 × 10⁻²⁴ moles (1/N₀). Measurement at the single-molecule level can completely remove the complicacy associated with ensemble-averaged macroscopic measurements. It allows us to construct a frequency histogram of the distribution of values for a parameter of interest following a large number of measurements on many individual molecules. Such a distribution carries much more information than the average value of the parameter obtained from a macroscopic measurement. As there is no ensemble averaging involved, only measurements at the single-molecule level can give an appropriate test for microscopic dynamical theories. Using single-molecule spectroscopy one can, in principle, follow the temporal evolution of any complex reaction path. As the field is still emerging, with newer methodologies of detecting single molecules with improved signal-to-noise ratios, it is expected that many new physical and chemical phenomena will certainly be explored using this technique. In the present article, our endeavor is to give an overview of the different aspects of single-molecule detection, along with some of its important applications in the areas of bioscience and chemical physics.     

Nanofluidics for sub-single cellular studies: Nascent progress,critical technologies,and future perspectives

In the field of cell studies, there is a burgeoning trend to further downscale the investigation from a single-cell level to a sub-single-cell level. Subcellular matter is the basic content in cells and correlates with cell heterogeneity. Sub-single cellular studies focus on the subcellular matter in single cells and aim to understand the details and heterogeneity of individual cells in terms of the subcellular matter or even at the single component/vesicle/molecule level. Hence, sub-single cell...     

Development of individual semiconductor nanowire for bioelectrochemical device at low overpotential conditions

In this work we report the bioelectrochemical study using an individual indium tin oxide (ITO) nanowire (ITO-NW) electrode modified with glucose oxidase enzyme (GOx), in which the enzymatic activity and the biocatalytic activity was evaluated. The main objective is to show that at low overpotential condition, semiconductor NW can be used as an electron donor during biocatalytic process. We demonstrate the possibility of immobilizing an ITO-NW electrode on gold contacts deposited on top of a microchip (oxidized Si wafer). A protective polymer layer containing an aperture over the sample area was photolithographically deposited over the microchip to isolate the metallic contacts. For H₂O₂ reduction during the biocatalysis at ITO-NWs surface, with η  50 mV, normal linear behavior is not observed and an exponential current is evident, similar to n–p semiconductor junction behavior. These results can open new tools for studying redox enzymes at the single-molecule level, and the device described here is very promising as a candidate for further exploration in bioelectrochemical devices, such as biofuel cells and biosensors.     

Skin‐worn Soft Microfluidic Potentiometric Detection System

A flexible skin‐mounted microfluidic potentiometric device for simultaneous electrochemical monitoring of sodium and potassium in sweat is presented. The wearable device allows efficient natural sweat pumping to the potentiometric detection chamber, containing solid‐contact ion‐selective Na⁺ and K⁺ electrodes, during exercise activity. The fabricated microchip electrolyte‐sensing device displays good analytical performance and addresses sweat mixing and carry‐over issues of early epidermal potentiometric sensors. Such soft skin‐worn microchip platform integrates potentiometric measurement, microfluidic technologies with flexible electronics for real‐time wireless data transmission to mobile devices. The new fully integrated microfluidic electrolyte‐detection device paves the way for practical fitness and health monitoring applications.     

Lighting Up the Plasma Membrane: Development and Applications of Fluorescent Ligands for Transmembrane Proteins

Despite the fact that transmembrane proteins represent the main therapeutic targets for decades, complete and in-depth knowledge about their biochemical and pharmacological profiling is not fully available. In this regard, target-tailored small-molecule fluorescent ligands are a viable approach to fill in the missing pieces of the puzzle. Such tools, coupled with the ability of high-precision optical techniques to image with an unprecedented resolution at a single-molecule level, helped unraveling many of the conundrums related to plasma proteins’ life-cycle and druggability. Herein, we review the recent progress made during the last two decades in fluorescent ligand design and potential applications in fluorescence microscopy of voltage-gated ion channels, ligand-gated ion channels and G-coupled protein receptors.     

Nanomanipulation using near field photonics

In this article we review the use of near-field photonics for trapping, transport and handling of nanomaterials. While the advantages of traditional optical tweezing are well known at the microscale, direct application of these techniques to the handling of nanoscale materials has proven difficult due to unfavourable scaling of the fundamental physics. Recently a number of research groups have demonstrated how the evanescent fields surrounding photonic structures like photonic waveguides, optical resonators, and plasmonic nanoparticles can be used to greatly enhance optical forces. Here, we introduce some of the most common implementations of these techniques, focusing on those which have relevance to microfluidic or optofluidic applications. Since the field is still relatively nascent, we spend much of the article laying out the fundamental and practical advantages that near field optical manipulation offers over both traditional optical tweezing and other particle handling techniques. In addition we highlight three application areas where these techniques namely could be of interest to the lab-on-a-chip community, namely: single molecule analysis, nanoassembly, and optical chromatography.     

Single-molecule spectroscopy of fluorescent proteins

The discovery and use of fluorescent proteins has revolutionized cellular biology. Despite the widespread use of visible fluorescent proteins as reporters and sensors in cellular environments the versatile photophysics of fluorescent proteins is still subject to intense research. Understanding the details of the photophysics of these reporters is essential for accurate interpretation of the biological and biochemical processes illuminated by fluorescent proteins. Some aspects of the complex photophysics of fluorescent proteins can only be observed and understood at the single-molecule level, which removes averaging inherent to ensemble studies. In this paper we review how single-molecule emission detection has helped understanding of the complex photophysics of fluorescent proteins.

Frontiers of optofluidics in synthetic biology

The development of optofluidic-based technology has ushered in a new era of lab-on-a-chip functionality, including miniaturization of biomedical devices, enhanced sensitivity for molecular detection, and multiplexing of optical measurements. While having great potential, optofluidic devices have only begun to be exploited in many biotechnological applications. Here, we highlight the potential of integrating optofluidic devices with synthetic biological systems, which is a field focusing on creating novel cellular systems by engineering synthetic gene and protein networks. First, we review the development of synthetic biology at different length scales, ranging from single-molecule, single-cell, to cellular population. We emphasize light-sensitive synthetic biological systems that would be relevant for the integration with optofluidic devices. Next, we propose several areas for potential applications of optofluidics in synthetic biology. The integration of optofluidics and synthetic biology would have a broad impact on point-of-care diagnostics and biotechnology.     

Multifunctional Helicene-Based Ytterbium Coordination Polymer Displaying Circularly Polarized Luminescence,Slow Magnetic Relaxation and Room Temperature Magneto-Chiral Dichroism**

The combination of physical properties sensitive to molecular chirality in a single system allows the observation of fascinating phenomena such as magneto-chiral dichroism (MChD) and circularly polarized luminescence (CPL) having potential applications for optical data readout and display technology. Homochiral monodimensional coordination polymers of Yb^III were designed from a 2,15-bis-ethynyl-hexahelicenic scaffold decorated with two terminal 4-pyridyl units. Thanks to the coordination of the chiral organic chromophore to Yb(hfac)₃ units (hfac⁻=1,1,1,5,5,5-hexafluoroacetylaconate), efficient NIR-CPL activity is observed. Moreover, the specific crystal field around the Yb^III induces a strong magnetic anisotropy which leads to a single-molecule magnet (SMM) behaviour and a remarkable room temperature MChD. The MChD-structural correlation is supported by computational investigations.     

Combining nanosurface chemistry and microfluidics for molecular analysis and cell biology

Development of new tools catalyzes progress in biochemical sciences [G.M. Whitesides, E. Ostuni, S. Takayama, X.Y. Jiang, D.E. Ingber, Annual Review of Biomedical Engineering 3 (2001) 335]. Recent advances in micro-/nano-technology have resulted in an explosion of the number of new tools available for biochemical sciences. We have used surface chemistry, nano-structures and microfluidics to create a set of tools applicable for problems ranging from molecular to cellular analysis. These tools will promote the understanding of fundamental problems in cell biology, development and neurobiology, and become useful for real-world applications such as molecular diagnostics, food analysis and environmental monitoring.     

Label-free fluorescence detection in capillary and microchip electrophoresis

Herein, we summarize the current status of native fluorescence detection in microchannel electrophoresis, with a strong focus on chip-based systems. Fluorescence detection is a powerful technique with unsurpassed sensitivity down to the single-molecule level. Accordingly fluorescence detection is attractive in combination with miniaturised separation techniques. A drawback is, however, the need to derivatize most analytes prior to analysis. This can often be circumvented by utilising excitation light in the UV spectral range in order to excite intrinsic fluorescence. As sensitive absorbance detection is challenging in chip-based systems, deep-UV fluorescence detection is currently one of the most general optical detection techniques in microchip electrophoresis, which is especially attractive for the detection of unlabelled proteins. This review gives an overview of research on native fluorescence detection in capillary (CE) and microchip electrophoresis (MCE) between 1998 and 2008. It discusses material aspects of native fluorescence detection and the instrumentation used, with particular focus on the detector design. Newer developments, featured techniques, and their prospects in the future are also included. In the last section, applications in bioanalysis, drug determination, and environmental analysis are reviewed with regard to limits of detection.     

Integration of chemical and biochemical analysis systems into a glass microchip.

This review focuses on the integration of chemical and biochemical analysis systems into glass microchips for general use. By combining multiphase laminar flow driven by pressure and micro unit operations, such as mixing, reaction, extraction and separation, continuous-flow chemical processing systems can be realized in the microchip format, while the application of electrophoresis-based chip technology is limited. The performances of several analysis systems were greatly improved by microchip integration because of some characteristics of microspace, i.e., a large specific interface area, a short molecular diffusion time, a small heat capacity and so on. By applying these concepts, several different analysis systems, i.e., wet analysis of cobalt ion, multi-ion sensor, immunoassay, and cellular analysis, were successfully integrated on a microchip. These microchip technologies are promising for meeting the future demands of high-throughput chemical processing.     

The potential of microelectrode arrays and microelectronics for biomedical research and diagnostics

Planar microelectrode arrays (MEAs) are devices that can be used in biomedical and basic in vitro research to provide extracellular electrophysiological information about biological systems at high spatial and temporal resolution. Complementary metal oxide semiconductor (CMOS) is a technology with which MEAs can be produced on a microscale featuring high spatial resolution and excellent signal-to-noise characteristics. CMOS MEAs are specialized for the analysis of complete electrogenic cellular networks at the cellular or subcellular level in dissociated cultures, organotypic cultures, and acute tissue slices; they can also function as biosensors to detect biochemical events. Models of disease or the response of cellular networks to pharmacological compounds can be studied in vitro, allowing one to investigate pathologies, such as cardiac arrhythmias, memory impairment due to Alzheimer’s disease, or vision impairment caused by ganglion cell degeneration in the retina.