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.
Small cogs in a small machine: This Minireview discusses the potential of synthetic ion channels and DNA computing technologies as parts of a “molecular robot.” A molecular robot is a biochemical machine consisting of a microsized lipid body. Its collecting of ambient information and its intelligence will rely on synthetic transmembrane channels and DNA logic operations, respectively. Recent studies conducted in these areas are described.
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.
This review describes recent approaches to decoding DNA computation using label‐free and electrical nanopore measurements. To employ the rapid and label‐free decoding, nanopore technology is proposed as a potent candidate for electrical and simple decoding of DNA computations.
This article is part of an AFOB (Asian Federation of Biotechnology) Special issue. To learn more about the AFOB visit www.afob.org.
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.
Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes are key players of the immune system in shrimps; however, their classification, ...maturation, and differentiation are still under debate. To date, only discrete and inconsistent information on the classification of shrimp hemocytes has been reported, showing that the morphological characteristics are not sufficient to resolve their actual roles. Our present study using single-cell RNA sequencing revealed six types of hemocytes of Marsupenaeus japonicus based on their transcriptional profiles. We identified markers of each subpopulation and predicted the differentiation pathways involved in their maturation. We also predicted cell growth factors that might play crucial roles in hemocyte differentiation. Different immune roles among these subpopulations were suggested from the analysis of differentially expressed immune-related genes. These results provide a unified classification of shrimp hemocytes, which improves the understanding of its immune system.
Asymmetric lipid giant vesicles have been used to model the biochemical reactions in cell membranes. However, methods for producing asymmetric giant vesicles lead to the inclusion of an organic ...solvent layer that affects the mechanical and physical characteristics of the membrane. Here we describe the formation of asymmetric giant vesicles that include little organic solvent, and use them to investigate the dynamic responses of lipid molecules in the vesicle membrane. We formed the giant vesicles via the inhomogeneous break-up of a lipid microtube generated by applying a jet flow to an asymmetric planar lipid bilayer. The asymmetric giant vesicles showed a lipid flip-flop behaviour in the membrane, superficially similar to the lipid flip-flop activity observed in apoptotic cells. In vitro synthesis of membrane proteins into the asymmetric giant vesicles revealed that the lipid asymmetry in bilayer membranes improves the reconstitution ratio of membrane proteins. Our asymmetric giant vesicles will be useful in elucidating lipid-lipid and lipid-membrane protein interactions involved in the regulation of cellular functions.
This study describes the pore-forming properties of magainin 1 in planar lipid bilayers. These bilayers were prepared by the droplet contact method, which was executed on a microfabricated device for ...a high-throughput study. We arrayed four droplet chambers parallelly in the single device, and the current measurements were carried out simultaneously. Using this system, we measured the channel current conductance of magainin 1. We determined the pore size and the number of assembling monomers in magainin pores in mammalian and bacterial model membranes. This system is a powerful tool for analyzing transmembrane peptides and their antimicrobial activities.
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.
This paper describes a strategy for autonomous diagnoses of cancers using microRNA (miRNA) and therapy for tumor cells by DNA computing techniques and nanopore measurement. Theranostics, which ...involves the combination of diagnosis and therapy, has emerged as an approach for personalized medicine or point-of-care cancer diagnostics. DNA computing will become a potent tool for theranostics because it functions completely autonomously without the need for external regulations. However, conventional theranostics using DNA computing involves a one-to-one reaction in which a single input molecule generates a single output molecule; the concentration of the antisense drug is insufficient for the therapy in this type of reaction. Herein we developed an amplification system involving an isothermal reaction in which a large amount of the antisense DNA drug was autonomously generated after detecting miRNA from small cell lung cancer. In addition, we successfully quantified the amount of the generated drug molecule by nanopore measurement with high accuracy, which was more accurate than conventional gel electrophoresis. This autonomous amplification strategy is a potent candidate for a broad range of theranostics using DNA computing.
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