Bio-nanopore technology for biomolecules detection

Abstract

Bio-nanopore technology holds great promise in biomacromolecule detection, with its high throughput and low cost positioning it as an ideal detection tool. This technology employs a unique detection mechanism that utilizes nanoscale pores to rapidly and sensitively convert biological molecules interactions into electrical signals, enabling real-time, single-molecule detection with exceptional sensitivity. This review focuses on the latest advancements in this technology across various domains, including DNA and RNA sequencing, protein detection, and small molecule identification. Additionally, future trends are explored, providing a comprehensive and in-depth perspective on the role of bio-nanopore technology in biomolecule detection.

Keywords: Bio-nanopore; DNA sequencing; Protein detection; RNA sequencing; Small molecule detection.

Fig. 1

Application of bio-nanopore detection technology in biomolecular detection. DNA: The principle of the MinION Oxford nanopore sequencer involves the unwinding of DNA by an enzyme at the sequencer's center, allowing single-stranded DNA to be fed into a solid-state nanopore (Shivashakarappa, K. et al., 2022). RNA: Individual RNA base recognition in immobilized oligonucleotides using a protein nanopore (Ayub, M. & Bayley, H., 2012). Protein: Peptides were pre-hydrolyzed by specific proteases (e.g. trypsin) and the resulting peptides were measured upon peptide translocation to the nanopore (Lucas, F. L. R. et al., 2021)

Fig. 2

Application of bio-nanopore detection technology in nucleic acids. A The synthetic principles of nanopore DNA sequencing (Fuller, C. W. et al., 2016). B Strategies and tools used for m6A mapping on the direct RNA sequencing platform based on Oxford Nanopore Technologies (Zhong, Z.-D. et al., 2023)

Fig. 3

Application of bio-nanopore detection technology in protein. A Real-time identification of amino acids during peptide hydrolysis. a Schematic representation of the assay. Peptides and Carboxypeptidase A1 are introduced directly into the nanopore. Individual amino acids (excluding arginine (Arg), lysine (Lys), and proline (Pro)) can be cleaved from the peptide chain and detected. b Representative current traces of amino acid signals during peptide hydrolysis. Target amino acids can be accurately identified based on normalized current amplitudes (Zhang, M. et al., 2024). B Enzyme-free nanopore detection of post-translational modifications within long peptides. a Detection of post-translational modifications in protein linkers driven through nanopores using electroosmotic flow technology. b Electroosmotic transport of thioredoxin junction octamers through the nanopore, facilitated by the dissociation solution (Martin-Baniandres, P. et al., 2023). C Reading nanopore proteins using defolding enzymes (Motone, K. et al., 2024)

Fig. 4

Application of bio-nanopore detection technology in small molecule. A Nanopore analysis of salvianolic acid in herbal medicine. a Nanopore workflow for the identification of salvianolic acid directly from natural herbs. b Mechanism of MspA-90PBA nanopore sensing of salvianolic acid (Fan, P., Zhang, S., et al., 2024). B Nanopore analysis of cis-diols in fruits. a Schematic of rapid analysis of natural fruit juices. b Phenylboronic acid-modified nanopore sensor (Fan, P., Cao, Z., et al., 2024)