Amplification and Quantification of an Antisense Oligonucleotide from Target microRNA Using Programmable DNA and a Biological Nanopore

Lipid vesicle-based molecular robots

A molecular robot, which is a system comprised of one or more molecular machines and computers, can execute sophisticated tasks in many fields that span from nanomedicine to green nanotechnology. The core parts of molecular robots are fairly consistent from system to system and always include (i) a body to encapsulate molecular machines, (ii) sensors to capture signals, (iii) computers to make decisions, and (iv) actuators to perform tasks. This review aims to provide an overview of approaches and considerations to develop molecular robots. We first introduce the basic technologies required for constructing the core parts of molecular robots, describe the recent progress towards achieving higher functionality, and subsequently discuss the current challenges and outlook. We also highlight the applications of molecular robots in sensing biomarkers, signal communications with living cells, and conversion of energy. Although molecular robots are still in their infancy, they will unquestionably initiate massive change in biomedical and environmental technology in the not too distant future.

Nanopore Filter: A Method for Counting and Extracting Single DNA Molecules Using a Biological Nanopore

This paper describes a method for the real-time counting and extraction of DNA molecules at the single-molecule level by nanopore technology. As a powerful tool for electrochemical single-molecule detection, nanopore technology eliminates the need for labeling or partitioning sample solutions at the femtoliter level. Here, we attempt to develop a DNA filtering system utilizing an α-hemolysin (αHL) nanopore. This system comprises two droplets, one filling with and one emptying DNA molecules, separated by a planar lipid bilayer containing αHL nanopores. The translocation of DNA through the nanopores is observed by measuring the channel current, and the number of translocated molecules can also be verified by quantitative polymerase chain reaction (qPCR). However, we found that the issue of contamination seems to be an almost insolvable problem in single-molecule counting. To tackle this problem, we tried to optimize the experimental environment, reduce the volume of solution containing the target molecule, and use the PCR clamp method. Although further efforts are still needed to achieve a single-molecule filter with electrical counting, our proposed method shows a linear relationship between the electrical counting and qPCR estimation of the number of DNA molecules.

Cell-Free Expression of De Novo Designed Peptides That Form β-Barrel Nanopores

Nanopore sensing has attracted much attention as a rapid, simple, and label-free single-molecule detection technology. To apply nanopore sensing to extensive targets including polypeptides, nanopores are required to have a size and structure suitable for the target. We recently designed a de novo β-barrel peptide nanopore (SVG28) that constructs a stable and monodispersely sized nanopore. To develop the sizes and functionality of peptide nanopores, systematic exploration is required. Here we attempt to use a cell-free synthesis system that can readily express peptides using transcription and translation. Hydrophilic variants of SVG28 were designed and expressed by the PURE system. The peptides form a monodispersely sized nanopore, with a diameter 1.1 or 1.5 nm smaller than that of SVG28. Such cell-free synthesizable peptide nanopores have the potential to enable the systematic custom design of nanopores and comprehensive sequence screening of nanopore-forming peptides.

MicroRNA Detection at Femtomolar Concentrations with Isothermal Amplification and a Biological Nanopore

Nanopore sensing is a powerful tool for the rapid and label-free detection of oligonucleotides, including microRNA. When moving towards actual diagnostic applications, detection of microRNA at low concentrations is one of the significant issues to be addressed. We here describe a method to detect ultra-low concentrations of microRNA using isothermal amplification and nanopore technology. Using this method, the amplified DNA from 1 fM of target microRNA can be measured by a nanopore measurement.

Pattern Recognition of microRNA Expression in Body Fluids Using Nanopore Decoding at Subfemtomolar Concentrations

This paper describes a method for detecting microRNA (miRNA) expression patterns using the nanopore-based DNA computing technology. miRNAs have shown promise as markers for cancer diagnosis due to their cancer type specificity, and therefore simple strategies for miRNA pattern recognition are required. We propose a system for pattern recognition of five types of miRNAs overexpressed in bile duct cancer (BDC). The information of miRNAs from BDC is encoded in diagnostic DNAs (dgDNAs) and decoded electrically by nanopore analysis. With this system, we succeeded in the label-free detection of miRNA expression patterns from the plasma of BDC patients. Moreover, our dgDNA-miRNA complexes can be detected at subfemtomolar concentrations, which is a significant improvement compared to previously reported limits of detection (∼10^-12 M) for similar analytical platforms. Nanopore decoding of dgDNA-encoded information represents a promising tool for simple and early cancer diagnosis.

The application of single molecule nanopore sensing for quantitative analysis

Nanopore-based sensors typically work by monitoring transient pulses in conductance via current-time traces as molecules translocate through the nanopore. The unique property of being able to monitor single molecules gives nanopore sensors the potential as quantitative sensors based on the counting of single molecules. This review provides an overview of the concepts and fabrication of nanopore sensors as well as nanopore sensing with a view toward using nanopore sensors for quantitative analysis. We first introduce the classification of nanopores and highlight their applications in molecular identification with some pioneering studies. The review then shifts focus to recent strategies to extend nanopore sensors to devices that can rapidly and accurately quantify the amount of an analyte of interest. Finally, future prospects are provided and briefly discussed. The aim of this review is to aid in understanding recent advances, challenges, and prospects for nanopore sensors for quantitative analysis.

Single polypeptide detection using a translocon EXP2 nanopore

DNA sequencing using nanopores has already been achieved and commercialized; the next step in advancing nanopore technology is towards protein sequencing. Although trials have been reported for discriminating the 20 amino acids using biological nanopores and short peptide carriers, it remains challenging. The size compatibility between nanopores and peptides is one of the issues to be addressed. Therefore, exploring biological nanopores that are suitable for peptide sensing is key in achieving amino acid sequence determination. Here, we focus on EXP2, the transmembrane protein of a translocon from malaria parasites, and describe its pore-forming properties in the lipid bilayer. EXP2 mainly formed a nanopore with a diameter of 2.5 nm assembled from 7 monomers. Using the EXP2 nanopore allowed us to detect poly-L-lysine (PLL) at a single-molecule level. Furthermore, the EXP2 nanopore has sufficient resolution to distinguish the difference in molecular weight between two individual PLL, long PLL (Mw: 30,000-70,000) and short PLL (Mw: 10,000). Our results contribute to the accumulation of information for peptide-detectable nanopores.

Single-Molecule Frequency Fingerprint for Ion Interaction Networks in a Confined Nanopore

The transport of molecules and ions through biological nanopores is governed by interaction networks among restricted ions, transported molecules, and residue moieties at pore inner walls. However, identification of such weak ion fluctuations from only few tens of ions inside nanopore is hard to achieve owing to electrochemical measurement limitations. Here, we developed an advanced frequency method to achieve qualitative and spectral analysis of ion interaction networks inside a nanopore. The peak frequency f_m reveals the dissociation rate between nanopore and ions; the peak amplitude a_m depicts the amount of combined ions with the nanopore after interaction equilibrium. A mathematical model for single-molecule frequency fingerprint achieved the prediction of interaction characteristics of mutant nanopores. This single-molecule frequency fingerprint is important for classification, characterization, and prediction of synergetic interaction networks inside nanoconfinement.

Nanopore decoding for a Hamiltonian path problem

DNA computing has attracted attention as a tool for solving mathematical problems due to the potential for massive parallelism with low energy consumption. However, decoding the output information to a human-recognizable signal is generally time-consuming owing to the requirement for multiple steps of biological operations. Here, we describe simple and rapid decoding of the DNA-computed output for a directed Hamiltonian path problem (HPP) using nanopore technology. In this approach, the output DNA duplex undergoes unzipping whilst passing through an α-hemolysin nanopore, with information electrically decoded as the unzipping time of the hybridized strands. As a proof of concept, we demonstrate nanopore decoding of the HPP of a small graph encoded in DNA. Our results show the feasibility of nanopore measurement as a rapid and label-free decoding method for mathematical DNA computation using parallel self-assembly.

Recent Advances in Liposome-Based Molecular Robots

A molecular robot is a microorganism-imitating micro robot that is designed from the molecular level and constructed by bottom-up approaches. As with conventional robots, molecular robots consist of three essential robotics elements: control of intelligent systems, sensors, and actuators, all integrated into a single micro compartment. Due to recent developments in microfluidic technologies, DNA nanotechnologies, synthetic biology, and molecular engineering, these individual parts have been developed, with the final picture beginning to come together. In this review, we describe recent developments of these sensors, actuators, and intelligence systems that can be applied to liposome-based molecular robots. First, we explain liposome generation for the compartments of molecular robots. Next, we discuss the emergence of robotics functions by using and functionalizing liposomal membranes. Then, we discuss actuators and intelligence via the encapsulation of chemicals into liposomes. Finally, the future vision and the challenges of molecular robots are described.

Recessed Ag/AgCl Microelectrode-Supported Lipid Bilayer for Nanopore Sensing

Biological nanopores reconstituted into supported lipid bilayer membranes are widely used as a platform for stochastic nanopore sensing with the ability to detect single molecules including, for example, single-stranded DNA (ssDNA) and miRNA. A main thrust in this area of research has been to improve overall bilayer stability and ease of measurements. These improvements are achieved through a variety of clever strategies including droplet-based techniques; however, they typically require specific microfabrication techniques to prepare devices or special manipulation techniques for microdroplets. Here, we describe a new method to prepare lipid bilayers using a recessed-in-glass Ag/AgCl microelectrode as a support structure. The lipid bilayer is formed at the tip of the microelectrode by immersing the microelectrode into a layered bath solution consisting of an oil/lipid mixture and an aqueous electrolyte solution. In this paper, we demonstrate this stable, supported lipid bilayer structure for channel current measurements of pore-forming toxins and single-molecule detection of ssDNA. This Ag/AgCl-supported lipid bilayer can potentially be widely adopted as a lipid membrane platform for nanopore sensing because of its simple and easy procedure needed to prepare lipid bilayers.

Development of Artificial Cell Models Using Microfluidic Technology and Synthetic Biology

Giant lipid vesicles or liposomes are primarily composed of phospholipids and form a lipid bilayer structurally similar to that of the cell membrane. These vesicles, like living cells, are 5-100 μm in diameter and can be easily observed using an optical microscope. As their biophysical and biochemical properties are similar to those of the cell membrane, they serve as model cell membranes for the investigation of the biophysical or biochemical properties of the lipid bilayer, as well as its dynamics and structure. Investigation of membrane protein functions and enzyme reactions has revealed the presence of soluble or membrane proteins integrated in the giant lipid vesicles. Recent developments in microfluidic technologies and synthetic biology have enabled the development of well-defined artificial cell models with complex reactions based on the giant lipid vesicles. In this review, using microfluidics, the formations of giant lipid vesicles with asymmetric lipid membranes or complex structures have been described. Subsequently, the roles of these biomaterials in the creation of artificial cell models including nanopores, ion channels, and other membrane and soluble proteins have been discussed. Finally, the complex biological functions of giant lipid vesicles reconstituted with various types of biomolecules has been communicated. These complex artificial cell models contribute to the production of minimal cells or protocells for generating valuable or rare biomolecules and communicating between living cells and artificial cell models.

DNA nanotechnology assisted nanopore-based analysis

Nanopore technology is a promising label-free detection method. However, challenges exist for its further application in sequencing, clinical diagnostics and ultra-sensitive single molecule detection. The development of DNA nanotechnology nonetheless provides possible solutions to current obstacles hindering nanopore sensing technologies. In this review, we summarize recent relevant research contributing to efforts for developing nanopore methods associated with DNA nanotechnology. For example, DNA carriers can capture specific targets at pre-designed sites and escort them from nanopores at suitable speeds, thereby greatly enhancing capability and resolution for the detection of specific target molecules. In addition, DNA origami structures can be constructed to fulfill various design specifications and one-pot assembly reactions, thus serving as functional nanopores. Moreover, based on DNA strand displacement, nanopores can also be utilized to characterize the outputs of DNA computing and to develop programmable smart diagnostic nanodevices. In summary, DNA assembly-based nanopore research can pave the way for the realization of impactful biological detection and diagnostic platforms via single-biomolecule analysis.

Osmotic-engine-driven liposomes in microfluidic channels

Self-propelled underwater microrobots that locomote without external sources of energy have potential application as drug carriers and probes in narrow spaces. In this study, we focused on an osmotic engine model, which is a migration mechanism, and applied it as a negative chemotaxis mechanism to induce liposome displacement. First, we confirmed the osmotic flow across the lipid bilayer and calculated the osmotic flow velocity to be 8.5 fL min-1 μm-2 when a salt concentration difference was applied to the lipid bilayer. Next, we designed and fabricated a microchannel that can trap a giant liposome and apply a salt concentration difference to the front and rear of the liposome. Then, we demonstrated the movement of the liposome by flowing it to the microchannel. The liposome successfully moved in the direction of the lower ion concentration at a speed of 0.6 μm min-1 owing to the osmotic pressure difference. Finally, we visualized the inner flow in the liposome by encapsulating microbeads in the liposome and observed the movement of the microbeads to verify that an osmotic flow was generated on the liposome. As a result, we observed the circulation of the microbeads in the liposome when the concentration difference was applied to the front and rear of the liposome, suggesting that the movement of the liposome was driven by the osmotic flow generated by the osmotic pressure difference. These results indicate that the osmotic-pressure-based migration mechanism has the potential to be utilized as the actuator of molecular robots.

Spatially Resolved Chemical Detection with a Nanoneedle-Probe-Supported Biological Nanopore

In this article, we describe the quantitative characterization of a gold nanoneedle ion channel probe and demonstrate the utility of this probe for spatially resolved detection of a small molecule using ion channel activity. Our report builds on recent reports of Ide and co-workers, who reported the use of an etched gold wire modified with a poly(ethylene) glycol monolayer as a support for a lipid bilayer and subsequent single ion channel recordings. Although this nanoneedle electrode approach was reported previously, in our report, we investigate the effects of several operational parameters on the performance of the ion channel measurement and electrochemical phenomenon that occur in the nanoconfined space between the supported bilayer and the gold electrode. More specifically, we address the effects of length of the supporting monolayer and the composition of the electrolyte baths on channel current measurements and provide a quantitative description of what carries current at the working electrode (double-layer charging). In addition, we demonstrate the ability to control the direction of protein insertion (tip side vs bath side) with freely diffusing protein, which has not been previously reported, with the former method (tip side) enabling single-molecule detection of β-cyclodextrin (βCD) using a reconstituted α-hemolysin channel. Finally, anticipating future use of a nanoneedle-based biological nanopore probe in a scanned-probe microscopy, we demonstrate the ability to quantify and spatially resolve the concentration of βCD molecules in a microfluidic channel. We believe, in the long term, the described nanoneedle-based biological nanopore probe can be employed in, for example, scanning ion conductance microscopy using ion channels.

Nanopore Decoding of Oligonucleotides in DNA Computing

In conventional DNA-computation methods involving logic gate operations, the output molecules are detected and decoded mainly by gel electrophoresis or fluorescence measurements. To employ rapid and label-free decoding, nanopore technology, an emerging methodology for single-molecule detection or DNA sequencing, is proposed as a candidate for electrical and simple decoding of DNA computations. This review describes recent approaches to decoding DNA computation using label-free and electrical nanopore measurements. Several attempts have been successful in DNA decoding with the nanopore either through enzymatic reactions or in water-in-oil droplets. Additionally, DNA computing combined with nanopore decoding has clinical applications, including microRNA detection for early diagnosis of cancers. Because this decoding methodology is still in development and not yet widely accepted, this review aims to inform the scientific community regarding usefulness.

Nanopore based detection of Bacillus thuringiensis HD-73 spores using aptamers and versatile DNA hairpins

A versatile nanopore sensing platform to detect any aptamer using nanopores by designing DNA hairpins that are complementary to the aptamer is described. This platform can detect the presence of aptamer binding targets regardless of their size, which has been a major hurdle for nanopore detection systems. Moreover, the signal-to-noise ratio is increased by eliminating most of the unwanted substances from the sample via simple sample preparation steps. To detect Bacillus thuringiensis HD-73 spores using this sensing platform, DNA hairpins complementary to the target-specific aptamers were designed, and the hairpins were characterized using alpha-hemolysin nanopores after the reaction of spores and aptamers and subsequent reaction with the complementary DNA hairpins. The platform exhibited a detection limit as low as 1.2 × 101 CFU mL-1 and was compatible with a wide range of spore concentrations from 1.2 × 101 CFU mL-1 to 1.2 × 106 CFU mL-1 while it is still expandable to higher spore concentrations.

Microfluidic Formation of Double-Stacked Planar Bilayer Lipid Membranes by Controlling the Water-Oil Interface

This study reports double-stacked planar bilayer lipid membranes (pBLMs) formed using a droplet contact method (DCM) for microfluidic formation with five-layered microchannels that have four micro guide pillars. pBLMs are valuable for analyzing membrane proteins and modeling cell membranes. Furthermore, multiple-pBLM systems have broadened the field of application such as electronic components, light-sensors, and batteries because of electrical characteristics of pBLMs and membrane proteins. Although multiple-stacked pBLMs have potential, the formation of multiple-pBLMs on a micrometer scale still faces challenges. In this study, we applied a DCM strategy to pBLM formation using microfluidic techniques and attempted to form double-stacked pBLMs in micro-meter scale. First, microchannels with micro pillars were designed via hydrodynamic simulations to form a five-layered flow with aqueous and lipid/oil solutions. Then, pBLMs were successfully formed by controlling the pumping pressure of the solutions and allowing contact between the two lipid monolayers. Finally, pore-forming proteins were reconstituted in the pBLMs, and ion current signals of nanopores were obtained as confirmed by electrical measurements, indicating that double-stacked pBLMs were successfully formed. The strategy for the double-stacked pBLM formation can be applied to highly integrated nanopore-based systems.

Channel current analysis estimates the pore-formation and the penetration of transmembrane peptides

We measured the current signal of the transmembrane model peptides using the barrel-stave, toroidal pore, and penetration models in order to establish a precise assignment of the channel signals.

Rapid and label-free fluorescence bioassay for microRNA based on exonuclease III-assisted cycle amplification

A new assay for the rapid and simple detection of microRNA based on G-quadruplex and Exonuclease III (ExoIII) dual signal amplification was constructed.

Synthetic Ion Channels and DNA Logic Gates as Components of Molecular Robots

A molecular robot is a next-generation biochemical machine that imitates the actions of microorganisms. It is made of biomaterials such as DNA, proteins, and lipids. Three prerequisites have been proposed for the construction of such a robot: sensors, intelligence, and actuators. This Minireview focuses on recent research on synthetic ion channels and DNA computing technologies, which are viewed as potential candidate components of molecular robots. Synthetic ion channels, which are embedded in artificial cell membranes (lipid bilayers), sense ambient ions or chemicals and import them. These artificial sensors are useful components for molecular robots with bodies consisting of a lipid bilayer because they enable the interface between the inside and outside of the molecular robot to function as gates. After the signal molecules arrive inside the molecular robot, they can operate DNA logic gates, which perform computations. These functions will be integrated into the intelligence and sensor sections of molecular robots. Soon, these molecular machines will be able to be assembled to operate as a mass microrobot and play an active role in environmental monitoring and in vivo diagnosis or therapy.

MicroRNA detection at femtomolar concentrations with isothermal amplification and a biological nanopore

One of the greatest challenges faced by chemists and biologists is the detection of molecules at extremely low concentrations. This paper describes a method to detect ultra-low concentrations (1 femtomole) of nucleotides using isothermal amplification and a biological nanopore.

Serial DNA relay in DNA logic gates by electrical fusion and mechanical splitting of droplets

DNA logic circuits utilizing DNA hybridization and/or enzymatic reactions have drawn increasing attention for their potential applications in the diagnosis and treatment of cellular diseases. The compartmentalization of such a system into a microdroplet considerably helps to precisely regulate local interactions and reactions between molecules. In this study, we introduced a relay approach for enabling the transfer of DNA from one droplet to another to implement multi-step sequential logic operations. We proposed electrical fusion and mechanical splitting of droplets to facilitate the DNA flow at the inputs, logic operation, output, and serial connection between two logic gates. We developed Negative-OR operations integrated by a serial connection of the OR gate and NOT gate incorporated in a series of droplets. The four types of input defined by the presence/absence of DNA in the input droplet pair were correctly reflected in the readout at the Negative-OR gate. The proposed approach potentially allows for serial and parallel logic operations that could be used for complex diagnostic applications.