Nanopore decoding for a Hamiltonian path problem

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.

Simultaneous Recognition of Over- and Under-Expressed MicroRNAs Using Nanopore Decoding

This paper describes a strategy for simultaneous recognition of over- and under-expressed microRNAs (miRNAs) using the method of signal classification-based nanopore decoding. MiRNA has attracted attention as a promising biomarker for cancer diagnosis owing to its cancer-type-specific expression patterns. While nanopore technology has emerged as a simple and label-free method to detect miRNAs and their expression patterns, recognizing patterns involving simultaneous over/under-expression is still challenging due to the inherent working principles. Here, inspired by the sequence design for DNA computation with nanopore decoding, we designed diagnostic DNA probes targeting two individual over/under-expressed miRNAs in the serum of oral squamous cell carcinoma. Through nanopore measurements, our designed probes exhibited characteristic current signals depending on the hybridized miRNA species, which were plotted on the scatter plot of duration versus current blocking ratio. The classified signals reflected the relative abundance of target miRNAs, thereby enabling successful pattern recognition of over/under-expressed miRNAs, even when using clinical samples. We believe that our method paves the way for miRNA-targeting simple diagnosis as a liquid biopsy.

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.

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.

Biological nanopores for sensing applications

Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.

Simple Fabrication of Solid-State Nanopores on a Carbon Film

Solid-state nanopores are widely used as a platform for stochastic nanopore sensing because they can provide better robustness, controllable pore size, and higher integrability than biological nanopores. However, the fabrication procedures, including thin film preparation and nanopore formation, require advanced micro-and nano-fabrication techniques. Here, we describe the simple fabrication of solid-state nanopores in a commercially available material: a flat thin carbon film-coated micro-grid for a transmission electron microscope (TEM). We attempted two general methods for nanopore fabrication in the carbon film. The first method was a scanning TEM (STEM) electron beam method. Nanopores were fabricated by irradiating a focused electron beam on the carbon membrane on micro-grids, resulting in the production of nanopores with pore diameters ranging from 2 to 135 nm. The second attempt was a dielectric breakdown method. In this method, nanopores were fabricated by applying a transmembrane voltage of 10 or 30 V through the carbon film on micro-grids. As a result, nanopores with pore diameters ranging from 3.7 to 1345 nm were obtained. Since these nanopores were successfully fabricated in the commercially available carbon thin film using readily available devices, we believe that these solid-state nanopores offer great utility in the field of nanopore research.

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.