Molecular diagnostics for personal medicine using a nanopore

Ångström- and Nano-scale Pore-Based Nucleic Acid Sequencing of Current and Emergent Pathogens

State-of-the-art nanopore sequencing enables rapid and real-time identification of novel pathogens, which has wide application in various research areas and is an emerging diagnostic tool for infectious diseases including COVID-19. Nanopore translocation enables de novo sequencing with long reads (> 10 kb) of novel genomes, which has advantages over existing short-read sequencing technologies. Biological nanopore sequencing has already achieved success as a technology platform but it is sensitive to empirical factors such as pH and temperature. Alternatively, ångström- and nano-scale solid-state nanopores, especially those based on two-dimensional (2D) membranes, are promising next-generation technologies as they can surpass biological nanopores in the variety of membrane materials, ease of defining pore morphology, higher nucleotide detection sensitivity, and facilitation of novel and hybrid sequencing modalities. Since the discovery of graphene, atomically-thin 2D materials have shown immense potential for the fabrication of nanopores with well-defined geometry, rendering them viable candidates for nanopore sequencing membranes. Here, we review recent progress and future development trends of 2D materials and their ångström- and nano-scale pore-based nucleic acid (NA) sequencing including fabrication techniques and current and emerging sequencing modalities. In addition, we discuss the current challenges of translocation-based nanopore sequencing and provide an outlook on promising future research directions.

A pH-independent quiet OmpG pore with enhanced electrostatic repulsion among the extracellular loops

Membrane protein pores have emerged as powerful nanopore sensors for single-molecule detection. OmpG, a monomeric nanopore, is comprised of fourteen β-strands connected by seven flexible extracellular loops. The OmpG nanopore exhibits pH-dependent gating as revealed by planar lipid bilayer studies. Current evidence strongly suggests that the dynamic movement of loop 6 is responsible for the gating mechanism. In this work, we have shown that enhancing the electrostatic repulsion forces between extracellular loops suppressed the pH-dependent gating. Our mutant containing additional negative charges in loop 6 and loop 1 exhibited minimal spontaneous gating and reduced sensitivity to pH changes compared to the wild type OmpG. These results provide new evidence to support the mechanism of OmpG gating controlled by the complex electrostatic network around the gating loop 6. The pH-independent quiet OmpG pores could potentially be used as a sensing platform that operates at a broad range of pH conditions.

Injectable Gel Constructs with Regenerative and Anti-Infective Dual Effects Based on Assembled Chitosan Microspheres

There is increasing demand for biomaterials that both assist with bone regeneration and have anti-infection qualities in clinical applications. To achieve this goal, chitosan microspheres with either positive or negative charges were fabricated and then assembled as a gel for bone healing. The positively charged chitosan microspheres (CSM; ∼35.5 μm) and negatively charged O-carboxymethyl chitosan microspheres (CMCSM; ∼13.5 μm) were loaded, respectively, with bone morphogenetic protein (BMP-2) and berberine (Bbr) via swollen encapsulation and physical adsorption without a significant change in the electric charges. The release kinetics of BMP-2 and Bbr from the microspheres were also studied in vitro. The results showed that the Bbr/CMCSM microsphere group possessed high antibacterial activity against Staphylococcus aureus; the BMP-2/CSM microsphere group also had excellent cytocompatibility and improved osteoinductivity with the assistance of BMP-2. The assembled gel group consisting of Bbr/CMCSM and BMP-2/CSM had a porous structure that allowed biological signal transfer and tissue infiltration and exhibited significantly enhanced bone reconstruction compared with that of the respective microsphere groups, which should result from the osteoconductivity of the porous structure and the osteoinduction of the BMP-2 growth factor. The oppositely charged microspheres and their assembled gel provide a promising prospect for making injectable tissue-engineered constructs with regenerative and anti-infective dual effects for biomedical applications.

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods

Microfluidics based biochemical analysis shows distinctive advantages for fast detection of pathogenic microorganisms. This Feature summarizes the progress in the past decade on microfluidic methods for purification and detection of pathogenic bacteria and viruses as well as their applications in food safety control, environmental monitoring, and clinical diagnosis.

Quantitative estimation of electro-osmosis force on charged particles inside a borosilicate resistive-pulse sensor

Nano and micron-scale pore sensors have been widely used for biomolecular sensing application due to its sensitive, label-free and potentially cost-effective criteria. Electrophoretic and electroosmosis are major forces which play significant roles on the sensor's performance. In this work, we have developed a mathematical model based on experimental and simulation results of negatively charged particles passing through a 2μm diameter solid-state borosilicate pore under a constant applied electric field. The mathematical model has estimated the ratio of electroosmosis force to electrophoretic force on particles to be 77.5%.

Unraveling the DNA methylome of atherosclerosis

PURPOSE OF REVIEW

Epigenetic mechanisms of transcriptional regulation in atherosclerosis have gained an increasing interest in recent years. We focus on the relevance of DNA methylation, a well characterized epigenetic modification of the genome, as a biomarker and underlying mechanism of atherosclerosis.

RECENT FINDINGS

A growing number of loci have been identified, which are good candidate biomarkers for atherosclerosis and provide novel insights into the molecular changes taking place in the diseased vessel. Understanding the global change in DNA methylation during atherosclerosis remains a challenge. Novel unfolding research avenues include the interplay between genetic variants and DNA methylation patterns, and the role of long noncoding RNAs as epigenetic regulators.

SUMMARY

Epigenetics continues to represent a promising area of research in atherosclerosis. The full exploitation of cutting edge epigenomics will be decisive to define whether epigenetics will contribute to lower the burden of cardiovascular diseases.

Size and functional tuning of solid state nanopores by chemical functionalization

We demonstrate the possibility of using a simple functionalization procedure, based on an initial vapour-phase silanization, to control the size and functionality of solid state nanopores. The presented results show that, by varying the silanization time, it is possible to modify the efficiency of probe molecule attachment, thus shrinking the pore to the chosen size, while introducing a specific sensing selectivity. The proposed method allows us to tune the nanopore biosensor adapting it to the specific final application, and it can be efficiently applied when the pore initial diameter does not exceed a limit dimension related to the mean free path of the silane molecules at the working pressure.

Slowing the translocation of double-stranded DNA using a nanopore smaller than the double helix

It is now possible to slow and trap a single molecule of double-stranded DNA (dsDNA), by stretching it using a nanopore, smaller in diameter than the double helix, in a solid-state membrane. By applying an electric force larger than the threshold for stretching, dsDNA can be impelled through the pore. Once a current blockade associated with a translocating molecule is detected, the electric field in the pore is switched in an interval less than the translocation time to a value below the threshold for stretching. According to molecular dynamics (MD) simulations, this leaves the dsDNA stretched in the pore constriction with the base-pairs tilted, while the B-form canonical structure is preserved outside the pore. In this configuration, the translocation velocity is substantially reduced from 1 bp/10 ns to approximately 1 bp/2 ms in the extreme, potentially facilitating high fidelity reads for sequencing, precise sorting, and high resolution (force) spectroscopy.