Aerolysin nanopore-based identification of proteinogenic amino acids using a bipolar peptide probe

Nucleic Acid-Based Biological Nanopore Sensing Strategies for Tumor Marker Detection

Cancer, which is characterized by high mortality rates, poses a significant threat to global human health. Early diagnosis is of paramount importance in managing cancer, and tumor markers have emerged as crucial indicators for achieving this goal. The advent of precision medicine has further emphasized the need for the effective detection of these markers. However, traditional detection methods are hampered by numerous limitations. In recent years, nanopore technology has emerged as a promising alternative, due to its unique physical and chemical properties, which facilitate rapid, label-free, and amplification-free detection. This Review focuses on the direct detection of tumor markers through nucleic acid analysis and indirect detection mediated by nucleic acids and facilitated by biological nanopores. Furthermore, it also discusses the challenges and prospects of applying biological nanopore sensing technology in early cancer diagnosis, underscoring its potential to revolutionize tumor marker detection.

Narrowing Signal Distribution by Adamantane Derivatization for Amino Acid Identification Using an α-Hemolysin Nanopore

The rapid progress in nanopore sensing has sparked interest in protein sequencing. Despite recent notable advancements in amino acid recognition using nanopores, chemical modifications usually employed in this process still need further refinements. One of the challenges is to enhance the chemical specificity to avoid downstream misidentification of amino acids. By employing adamantane to label proteinogenic amino acids, we developed an approach to fingerprint individual amino acids using the wild-type α-hemolysin nanopore. The unique structure of adamantane-labeled amino acids (ALAAs) improved the spatial resolution, resulting in distinctive current signals. Various nanopore parameters were explored using a machine-learning algorithm and achieved a validation accuracy of 81.3% for distinguishing nine selected amino acids. Our results not only advance the effort in single-molecule protein characterization using nanopores but also offer a potential platform for studying intrinsic and variant structures of individual molecules.

Engineering Biological Nanopore Approaches toward Protein Sequencing

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.