Designing nanotheranostics with machine learning

Nature Nanotechnology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 3, 2024

Язык: Английский

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Nanopore Discriminates Watson–Crick and Hoogsteen Hydrogen Bonds in Multiple DNA Contexts

Nano Letters, Год журнала: 2025, Номер unknown

Опубликована: Янв. 17, 2025

Watson-Crick and Hoogsteen hydrogen bonds aid the formation of highly ordered structures in genomic DNA that dynamically govern genetic modes such as gene regulation replication. Hence, measuring distinguishing these two types different contexts are essential for understanding architectures. However, due to their transient nature minimal structure differences at sub-nanometer scale, differentiating from is difficult. Relying on nanopore technology, we successfully discriminated multiple presence epigenetic modification, changes structures, proton strength environment. Our results indicate show susceptibilities physicochemical characteristics matter stabilizing bonds. This work provides insight into features nanoscale may benefit profiling complex architectures by subtle structural changes.

Язык: Английский

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Nanopore discrimination of rare earth elements

Nature Nanotechnology, Год журнала: 2025, Номер unknown

Опубликована: Фев. 10, 2025

Язык: Английский

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Direct mapping of tyrosine sulfation states in native peptides by nanopore

Nature Chemical Biology, Год журнала: 2024, Номер unknown

Опубликована: Сен. 25, 2024

Язык: Английский

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Identification and Detection of a Peptide Biomarker and Its Enantiomer by Nanopore

ACS Central Science, Год журнала: 2024, Номер 10(6), С. 1167 - 1178

Опубликована: Май 3, 2024

Until now, no fast, low-cost, and direct technique exists to identify detect protein/peptide enantiomers, because their mass charge are identical. They essential since l- d-protein enantiomers have different biological activities due unique conformations. Enantiomers potential for diagnostic purposes several diseases or normal bodily functions but yet be utilized. This work uses an aerolysin nanopore electrical detection vasopressin l-AVP d-AVP, associated with processes pathologies. We show identification according conformations, in either native reducing conditions, using specific signature. To improve identification, we used a principal component analysis approach define the most relevant parameters identification. Finally, Monte Carlo prediction assign each event type d-AVP enantiomer.

Язык: Английский

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Dynamic Features Driven by Stochastic Collisions in a Nanopore for Precise Single-Molecule Identification

Journal of the American Chemical Society, Год журнала: 2025, Номер unknown

Опубликована: Янв. 2, 2025

Nanopore technology holds great potential for single-molecule identification. However, extracting meaningful features from ionic current signals and understanding the molecular mechanisms underlying specific remain unresolved. In this study, we uncovered a distinctive pattern in K238Q aerolysin nanopore, characterized by transient spikes superimposed on two stable transition states. By employing neural network model, demonstrated that these previously overlooked dynamic spike exhibit superior discriminative power, improving accuracy 44% to 93%. We identified states result simultaneous interactions of ssDNA with sensitive sites nanopore. The proposed stochastic collision model offers mechanistic framework interpreting generation features. This indicates continuous transitions facilitate iterative, comprehensive snapshots nanopores. Our findings introduce new approach optimizing nanopore capture complex substantially improve

Язык: Английский

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Toward a comprehensive profiling of alternative splicing proteoform structures, interactions and functions

Current Opinion in Structural Biology, Год журнала: 2025, Номер 90, С. 102979 - 102979

Опубликована: Янв. 7, 2025

The mRNA splicing machinery has been estimated to generate 100,000 known protein-coding transcripts for 20,000 human genes (Ensembl, Sept. 2024). However, this set is expanding with the massive and rapidly growing data coming from high-throughput technologies, particularly single-cell long-read sequencing. Yet, implications of complexity at protein level remain largely uncharted. In review, we describe current advances toward systematically assessing contribution alternative proteome function diversification. We discuss potential challenges using artificial intelligence-based techniques in identifying proteoforms characterising their structures, interactions, functions.

Язык: Английский

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Pioneering Role of Nanopore Single-Molecule Sensing in Environmental and Food Surveillance

Biosensors, Год журнала: 2025, Номер 15(1), С. 41 - 41

Опубликована: Янв. 13, 2025

In recent years, environmental and food safety have garnered substantial focus due to their intimate connection with human health. Numerous biosensors been developed for identifying deleterious compounds; however, these reveal certain limitations. Nanopore sensors, featuring nano-scaled pore size, demonstrated outstanding performance in terms of rapidity, sensitivity, selectivity as a single-molecule technique surveillance. this review, we present comprehensive overview nanopore applications two fields. To elucidate the pioneering roles nanopores, analytes are categorized into three distinct groups, including metal ions, synthetic contaminants, biotoxins. Moreover, variety strategies involved, such coalescence ligand probes, implementation chemical reactions, functionalization etc. These scientific studies showcase versatility diversity technique, paving way further developments technology safety.

Язык: Английский

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Porous carbon derived from biomass-based polymers: Innovative applications in supercapacitors

Chinese Chemical Letters, Год журнала: 2025, Номер unknown, С. 110860 - 110860

Опубликована: Янв. 1, 2025

Язык: Английский

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Redesign of Translocon EXP2 Nanopore for Detecting Peptide Fragments

Small Methods, Год журнала: 2025, Номер unknown

Опубликована: Фев. 5, 2025

Abstract Nanopore sensing is a rapid, label‐free technique that enables single‐molecule detection and successfully applied to nucleic acid sequencing. Extending this technology the sequencing of peptides proteins key area interest. However, complex structures diverse charge distributions present challenges for extensive using existing nanopores. In study, focus on EXP2 nanopore derived from malaria parasite Plasmodium falciparum address these challenges. Previously, it characterized wild‐type (WT‐EXP2) nanopores demonstrated their ability detect polypeptides, although intrinsic electrical noise pore posed difficulties accurate detection. To overcome limitations, several mutants are designed, including ΔD231 , NC K42D/S46F reduce improve peptide accuracy. The mutant reduced by more than 50% compared WT‐EXP2 improved discrimination accuracy oligoarginine peptides. addition, detected discriminated eight different peptides, ranging in molecular weight small large, previously challenging single type. These results suggest engineered could serve as effective tools protein sequencing, contributing broader application biochemical clinical research.

Язык: Английский

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