Preparation of Cytolysin A (ClyA) Nanopores

Nanopores for DNA and biomolecule analysis: Diagnostic, genomic insights, applications in energy conversion and catalysis

Recently, nanopores have emerged as highly significant structures with broad applications in diverse scientific and technological fields. They can naturally occur in biological membranes or be artificially fabricated using advanced techniques. Recent advances in nanopore technology have revolutionized genomics by offering previously unheard-of capacities for deoxyribo nucleic acid (DNA) sequencing and analysis. These tiny pores allow individual molecules to be found more easily, allowing for real-time DNA analysis and providing currently unheard-of insights into genetics and diagnostics. By tracking alterations in electrical or ionic currents as biomolecules traverse the pore, nanopores make possible the real-time recognition of other biomolecules, like proteins, nucleic acids, and small molecules, eliminating the need for labeling. This label-free detection potential holds a huge promise in medical diagnostics, genotyping, environmental monitoring, etc. Nanopores have significantly improved DNA sequencing technology such as increment in read length, enabling researchers to sequence entire genomic regions, accuracy can be improved and recent updates have led to a reported increase in total DNA reads, demonstrating the technology's capacity for high-throughput applications via trapping individual DNA strands and monitoring the variations of ionic current as each nucleotide passes across the pore. Finally, nanopore sequencing is well-known as a novel and highly flexible technique for DNA analyses, which has a huge deal of promise in clinical diagnosis and genomics research. Hence, this review article comprehensively explains nanopores for DNA analysis and other biomolecules, their synthesis, and diverse applications.

Nanopore-Functionalized Hybrid Lipid-Block Copolymer Membranes Allow Efficient Single-Molecule Sampling and Stable Sensing of Human Serum

Biological nanopores are powerful tools for single-molecule detection, with promising potential as next-generation biosensors. A major bottleneck in nanopore analysis is the fragility of the supporting lipid membranes, that easily rupture after exposure to biological samples. Membranes comprising PMOXA-PDMS-PMOXA (poly(2-methyloxazoline-b-dimethylsiloxane-b-2-methyloxazoline)) or PBD-PEO (poly(1,2-butadiene)-b-poly(ethylene oxide)) polymers may form robust alternatives, but their suitability for the reconstitution of a broad range of nanopores has not yet been investigated. Here, PBD-PEO membranes are found to be highly robust toward applied voltages and human serum, while providing a poor environment for nanopore reconstitution. However, hybrid membranes containing a similar molar ratio of PBD11PEO8 polymers and diphytanoyl phosphatidylcholine (DPhPC) lipids show the best of both worlds: highly robust membranes suitable for the reconstitution of a wide variety of nanopores. Molecular dynamics simulations reveal that lipids form ≈12 nm domains interspersed by a polymer matrix. Nanopores partition into these lipid nanodomains and sequester lipids, possibly offering the same binding strength as in a native bilayer. Nanopores reconstituted in hybrid membranes yield efficient sampling of biomolecules and enable sensing of high concentrations of human serum. This work thus shows that hybrid membranes functionalized with nanopores allow single-molecule sensing, while forming robust interfaces, resolving an important bottleneck for novel nanopore-based biosensors.

Sea Anemones, Actinoporins, and Cholesterol

Spanish or Spanish-speaking scientists represent a remarkably populated group within the scientific community studying pore-forming proteins. Some of these scientists, ourselves included, focus on the study of actinoporins, a fascinating group of metamorphic pore-forming proteins produced within the venom of several sea anemones. These toxic proteins can spontaneously transit from a water-soluble fold to an integral membrane ensemble because they specifically recognize sphingomyelin in the membrane. Once they bind to the bilayer, they subsequently oligomerize into a pore that triggers cell-death by osmotic shock. In addition to sphingomyelin, some actinoporins are especially sensible to some other membrane components such as cholesterol. Our group from Universidad Complutense of Madrid has focused greatly on the role played by sterols in this water–membrane transition, a question which still remains only partially solved and constitutes the main core of the article below.

Cytolysin A (ClyA): A Bacterial Virulence Factor with Potential Applications in Nanopore Technology, Vaccine Development, and Tumor Therapy

Cytolysin A (ClyA) is a pore-forming toxin that is produced by some bacteria from the Enterobacteriaceae family. This review provides an overview of the current state of knowledge regarding ClyA, including the prevalence of the encoding gene and its transcriptional regulation, the secretion pathway used by the protein, and the mechanism of protein assembly, and highlights potential applications of ClyA in biotechnology. ClyA expression is regulated at the transcriptional level, primarily in response to environmental stressors, and ClyA can exist stably both as a soluble monomer and as an oligomeric membrane complex. At high concentrations, ClyA induces cytolysis, whereas at low concentrations ClyA can affect intracellular signaling. ClyA is secreted in outer membrane vesicles (OMVs), which has important implications for biotechnology applications. For example, the native pore-forming ability of ClyA suggests that it could be used as a component of nanopore-based technologies, such as sequencing platforms. ClyA has also been exploited in vaccine development owing to its ability to present antigens on the OMV surface and provoke a robust immune response. In addition, ClyA alone or OMVs carrying ClyA fusion proteins have been investigated for their potential use as anti-tumor agents.

Strategies for enzymological studies and measurements of biological molecules with the cytolysin A nanopore

Pore-forming toxins are used in a variety of biotechnological applications. Typically, individual membrane proteins are reconstituted in artificial lipid bilayers where they form water-filled nanoscale apertures (nanopores). When a voltage is applied, the ionic current passing through a nanopore can be used for example to sequence biopolymers, identify molecules, or to study chemical or enzymatic reactions at the single-molecule level. Here we present strategies for studying individual enzymes and measuring molecules, also in highly complex biological samples such as blood.

Biological Nanopores: Engineering on Demand

Nanopore-based sensing is a powerful technique for the detection of diverse organic and inorganic molecules, long-read sequencing of nucleic acids, and single-molecule analyses of enzymatic reactions. Selected from natural sources, protein-based nanopores enable rapid, label-free detection of analytes. Furthermore, these proteins are easy to produce, form pores with defined sizes, and can be easily manipulated with standard molecular biology techniques. The range of possible analytes can be extended by using externally added adapter molecules. Here, we provide an overview of current nanopore applications with a focus on engineering strategies and solutions.