Direct Analysis of Incorporation of an Anticancer Drug into DNA at Single-Molecule Resolution

Sub-5 nm nanogap electrodes towards single-molecular biosensing

Nanogap electrodes (NGEs) with sub-5 nm gap has been widely used in single-molecule sensing and sequencing, with the characteristics of label-free, high sensitivity, rapid detection and low-cost. However, the fabrication of sub-5 nm gap electrodes with high controllability and reproducibility still remains a great challenge that impedes the experimental research and the commercialization of the nanogap device. Here, we review the common currently used fabrication methods of nanogap electrodes, such as gap narrowing deposition, mechanical controllable break junctions and the fabrication methods combined with nanopore or nanochannel. We then highlight the typical applications of nanogap electrodes in biological/chemical sensing fields, including single molecule recognition, single molecule sequencing and chemical kinetics analysis. Finally, the challenges of nanogap electrodes in single molecule sensing/sequencing are outlined and the future directions for sensing perspectives are suggested.

Direct observation of DNA alterations induced by a DNA disruptor

DNA alterations, such as base modifications and mutations, are closely related to the activity of transcription factors and the corresponding cell functions; therefore, detection of DNA alterations is important for understanding their relationships. Particularly, DNA alterations caused by exposure to exogenous molecules, such as nucleic acid analogues for cancer therapy and the corresponding changes in cell functions, are of interest in medicine for drug development and diagnosis purposes. However, detection of comprehensive direct evidence for the relationship of DNA modifications/mutations in genes, their effect on transcription factors, and the corresponding cell functions have been limited. In this study, we utilized a single-molecule electrical detection method for the direct observation of DNA alterations on transcription factor binding motifs upon exposure to a nucleic acid analogue, trifluridine (FTD), and evaluated the effects of the DNA alteration on transcriptional activity in cancer cell line cells. We found ~ 10% FTD incorporation at the transcription factor p53 binding regions in cancer cells exposed to FTD for 5 months. Additionally, through single-molecule analysis of p53-enriched DNA, we found that the FTD incorporation at the p53 DNA binding regions led to less binding, likely due to weaken the binding of p53. This work suggests that single-molecule detection of DNA sequence alterations is a useful methodology for understanding DNA sequence alterations.

Nanodevices for Biological and Medical Applications: Development of Single-Molecule Electrical Measurement Method

A comprehensive detection of a wide variety of diagnostic markers is required for the realization of personalized medicine. As a sensor to realize such personalized medicine, a single molecule electrical measurement method using nanodevices is currently attracting interest for its comprehensive simultaneous detection of various target markers for use in biological and medical application. Single-molecule electrical measurement using nanodevices, such as nanopore, nanogap, or nanopipette devices, has the following features:; high sensitivity, low-cost, high-throughput detection, easy-portability, low-cost availability by mass production technologies, and the possibility of integration of various functions and multiple sensors. In this review, I focus on the medical applications of single- molecule electrical measurement using nanodevices. This review provides information on the current status and future prospects of nanodevice-based single-molecule electrical measurement technology, which is making a full-scale contribution to realizing personalized medicine in the future. Future prospects include some discussion on of the current issues on the expansion of the application requirements for single-mole-cule measurement.

Dynamic surface-enhanced Raman spectroscopy of DNA oligomer with a single hotspot from a gold nanoparticle dimer

Various nanostructures for single-molecule surface-enhanced Raman spectroscopy (SERS) have been fabricated through a random aggregation process using nanoparticles that can stochastically generate multiple hotspots in the laser spot. This leads to multiple molecule detection. In this study, a single gold nanoparticle (AuNP) dimer with a single hotspot was fabricated in a laser spot controlling the position and orientation on a silicon substrate using a nanotrench-guided self-assembly. The Raman peaks of deoxyribonucleic acid (DNA) were dynamically observed, indicating a single DNA oligomer detection composed of adenine, guanine, cytosine, phosphate, and deoxyribose.

Single-molecule RNA sequencing for simultaneous detection of m6A and 5mC

Epitranscriptomics is the study of RNA base modifications involving functionally relevant changes to the transcriptome. In recent years, epitranscriptomics has been an active area of research. However, a major issue has been the development of sequencing methods to map transcriptome-wide RNA base modifications. We have proposed a single-molecule quantum sequencer for mapping RNA base modifications in microRNAs (miRNAs), such as N6-methyladenosine (m6A) or 5-methylcytidine (5mC), which are related to cancer cell propagation and suppression. Here, we investigated 5mC and m6A in hsa-miR-200c-5p extracted from colorectal cancer cells and determined their methylation sites and rates; the data were comparable to those determined by mass spectrometry. Furthermore, we evaluated the methylation ratio of cytidine and adenosine at each site in the sequences and its relationship. These results suggest that the methylation ratio of cytidine and adenosine is facilitated by the presence of vicinal methylation. Our work provides a robust new tool for sequencing various types of RNA base modifications in their RNA context.

Development of Single-Molecule Electrical Identification Method for Cyclic Adenosine Monophosphate Signaling Pathway

Cyclic adenosine monophosphate (cAMP) is an important research target because it activates protein kinases, and its signaling pathway regulates the passage of ions and molecules inside a cell. To detect the chemical reactions related to the cAMP intracellular signaling pathway, cAMP, adenosine triphosphate (ATP), adenosine monophosphate (AMP), and adenosine diphosphate (ADP) should be selectively detected. This study utilized single-molecule quantum measurements of these adenosine family molecules to detect their individual electrical conductance using nanogap devices. As a result, cAMP was electrically detected at the single molecular level, and its signal was successfully discriminated from those of ATP, AMP, and ADP using the developed machine learning method. The discrimination accuracies of a single cAMP signal from AMP, ADP, and ATP were found to be 0.82, 0.70, and 0.72, respectively. These values indicated a 99.9% accuracy when detecting more than ten signals. Based on an analysis of the feature values used for the machine learning analysis, it is suggested that this discrimination was due to the structural difference between the ribose of the phosphate site of cAMP and those of ATP, ADP, and AMP. This method will be of assistance in detecting and understanding the intercellular signaling pathways for small molecular second messengers.

Dynamic electrical measurement of biomolecule behavior via plasmonically-excited nanogap fabricated by electromigration

The dynamic motion of DNA oligomers at the nanoscale gap between nanoelectrodes is measured under plasmonic excitation using laser irradiation. The use of a nanogap enables highly sensitive detection of individual molecules using an electrical readout or an optical readout such as Raman spectroscopy. However, the target molecule must reach the nanogap in order to be detected. This study focuses on the use of plasmonic excitation to trap molecules at the nanogap surface. The nanogap electrode is fabricated by electromigration and is, therefore, a much smaller nanogap than the top-down fabrication in the conventional plasmonic trapping studies. To demonstrate the individual molecule detection and to investigate the molecular behavior, the molecules are monitored using an electrical readout under a bias voltage instead of an optical readout used in the conventional studies. The conductance change due to DNA oligomer penetration to the nanogap is observed with the irradiated light intensity of over 1.23 mW. The single-molecule detection is confirmed irradiating the laser to the nanogap. The results suggest that DNA oligomers are spontaneously attracted and concentrated to the nanogap corresponding to the detection point, resulting in high detection probability and sensitivity.

Length Discrimination of Homo-oligomeric Nucleic Acids with Single-molecule Measurement

Single-molecule DNA/RNA sequencing based on single-molecule measurement is a prominent method for higher throughput sequencing. In a previous report, the single-molecule DNA/RNA sequencing method has applied to detect each base-conductance difference in the tunneling current time profiles, and determined the sequence. However, discrimination of identical base lengths has not yet been achieved. The number of the identical contiguous bases has importance in biology because some homopolymers of nucleic acid control gene expression. In this study, we aimed to develop a method for discriminating the length of homopolymer of nucleic acids of adenosine monophosphate (AMP) using a single-molecule sequencing technique. We carried out single-molecule conductance measurements of adenine pentamer, hexamer and heptamer. The single-molecule signals of the oligomers are not distinguishable from current and duration time histograms. The three oligomers were discriminated by our developed machine learning-based analysis with accuracy of 0.54 for a single signal, and 99% for 40 signals. This method will be applied to the single signals and identify the contiguous bases in the sequence and provide new biological insights.

Detection of an alcohol-associated cancer marker by single-molecule quantum sequencing

Alcoholic beverages are a well-known risk factor for cancer. N²-Ethyl-2'-deoxyguanosine (N²-Et-dG) is a promising biomarker for alcohol-associated cancers. However, the lack of a convenient detection method for N²-Et-dG hinders the development of practical DNA damage markers. Herein, we develop a detection method for N²-Et-dG using a single-molecule quantum sequencing (SMQS) method and machine learning analysis. Our method succeeded in discriminating between N²-Et-dG and dG with an accuracy of 99%, using 20 signals. Our developed method quantified the mixing ratio of N²-Et-dG from a mixed solution of N²-Et-dG and dG. It is shown that our method has the potential to facilitate the development of DNA damage markers, and thus the early detection and prevention of cancers.

Single-Molecule Counting of Nucleotide by Electrophoresis with Nanochannel-Integrated Nano-Gap Devices

We utilized electrophoresis to control the fluidity of sample biomolecules in sample aqueous solutions inside the nanochannel for single-molecule detection by using a nanochannel-integrated nanogap electrode, which is composed of a nano-gap sensing electrode, nanochannel, and tapered focusing channel. In order to suppress electro-osmotic flow and thermal convection inside this nanochannel, we optimized the reduction ratios of the tapered focusing channel, and the ratio of inlet 10 μm to outlet 0.5 μm was found to be high performance of electrophoresis with lower concentration of 0.05 × TBE (Tris/Borate/EDTA) buffer containing a surfactant of 0.1 w/v% polyvinylpyrrolidone (PVP). Under the optimized conditions, single-molecule electrical measurement of deoxyguanosine monophosphate (dGMP) was performed and it was found that the throughput was significantly improved by nearly an order of magnitude compared to that without electrophoresis. In addition, it was also found that the long-duration signals that could interfere with discrimination were significantly reduced. This is because the strong electrophoresis flow inside the nanochannels prevents the molecules’ adsorption near the electrodes. This single-molecule electrical measurement with nanochannel-integrated nano-gap electrodes by electrophoresis significantly improved the throughput of signal detection and identification accuracy.

Significant epitranscriptomes in heterogeneous cancer

Precision medicine places significant emphasis on techniques for the identification of DNA mutations and gene expression by deep sequencing of gene panels to obtain medical data. However, other diverse information that is not easily readable using bioinformatics, including RNA modifications, has emerged as a novel diagnostic and innovative therapy owing to its multifunctional aspects. It is suggested that this breakthrough innovation might open new avenues for the elucidation of uncharacterized cancer cellular functions to develop more precise medical applications. The functional characteristics and regulatory mechanisms of RNA modifications, ie, the epitranscriptome (ETR), which reflects RNA metabolism, remains unclear, mainly due to detection methods being limited. Recent studies have revealed that N6‐methyl adenosine, the most common modification in mRNA in eukaryotes, is affected in various types of cancer and, in some cases, cancer stem cells, but also affects cellular responses to viral infections. The ETR can control cancer cell fate through mRNA splicing, stability, nuclear export, and translation. Here we report on the recent progress of ETR detection methods, and biological findings regarding the significance of ETR in cancer precision medicine.

Paving the way to single-molecule chemistry through molecular electronics

Since our understanding of single-molecule junctions, in which single molecules are connected between nanoelectrodes, has deepened, we have paved the way to single-molecule chemistry. Herein, we review fundamental properties, including the number of molecules connected to the electrode, their structure and type, the bonding force between the single molecule and electrode and the thermopower and quantum interference in single-molecule junctions. Additionally, we review the application of single-molecule junctions to biomolecules. Finally, we explore single-molecule chemical reaction analysis, which is one direction of single-molecule junction research.