Motor protein-assisted glycan translocation and sequencing using nanopores DOI Open Access
Zhaobing Gao, Wenjun Ke, Bingqing Xia

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 29, 2024

The glycan sequencing remains a significant bottleneck in glycoscience. While nanopore platforms have achieved substantial progress single-molecule nucleic acid sequencing, their application to has faced considerable challenges, with limited advancements date. In this study, we propose novel strategy for controlling translocation through the MspA as an initial step toward sequencing. By conjugating target helicase-controlled single-stranded DNA, successfully reads of up eleven glycans. For first time, isolated glycan-associated electrical signals, enabling translocation, stretching, and controlled speed neutral glycans nanopore. This method provides platform obtaining read lengths identifying different modifications, demonstrating capability resolve monosaccharide composition glycosidic linkages. To further improve resolution, engineered M2-MspA reduce pore constriction size enhance precision by minimizing random thermal motion translocating glycan. These modifications are expected increase accuracy reliability. work represents proof-of-concept demonstration chain lays promising foundation development fingerprinting technologies. We anticipate that approach will significantly advance commercialization nanopore-based techniques.

Language: Английский

Highly accurate carbohydrate-binding site prediction with DeepGlycanSite DOI Creative Commons
Xinheng He, Lifen Zhao, Yinping Tian

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 17, 2024

Abstract As the most abundant organic substances in nature, carbohydrates are essential for life. Understanding how regulate proteins physiological and pathological processes presents opportunities to address crucial biological problems develop new therapeutics. However, diversity complexity of pose a challenge experimentally identifying sites where bind act on proteins. Here, we introduce deep learning model, DeepGlycanSite, capable accurately predicting carbohydrate-binding given protein structure. Incorporating geometric evolutionary features into equivariant graph neural network with transformer architecture, DeepGlycanSite remarkably outperforms previous state-of-the-art methods effectively predicts binding diverse carbohydrates. Integrating mutagenesis study, reveals guanosine-5’-diphosphate-sugar-recognition site an important G-protein coupled receptor. These findings demonstrate is invaluable prediction could provide insights molecular mechanisms underlying carbohydrate-regulation therapeutically

Language: Английский

Citations

14
Nanopore-based glycan sequencing: state of the art and future prospects DOI Creative Commons

Guangda Yao,

Wenjun Ke, Bingqing Xia

et al.

Chemical Science, Journal Year: 2024, Volume and Issue: 15(17), P. 6229 - 6243

Published: Jan. 1, 2024

This perspective outlines three potential routes for nanopore-based glycan sequencing, highlighting their applications and offering insights to meet associated challenges. It also introduces the concept of sequencer.

Language: Английский

Citations

9
Pioneering Role of Nanopore Single-Molecule Sensing in Environmental and Food Surveillance DOI Creative Commons

W. W. Tian,

Xu Wang, Yan Zhang

et al.

Biosensors, Journal Year: 2025, Volume and Issue: 15(1), P. 41 - 41

Published: Jan. 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.

Language: Английский

Citations

1
Single-Molecule Identification and Quantification of Steviol Glycosides with a Deep Learning-Powered Nanopore Sensor DOI
Minmin Li, Jing Wang, Chen Zhang

et al.

ACS Nano, Journal Year: 2024, Volume and Issue: 18(36), P. 25155 - 25169

Published: Aug. 27, 2024

Steviol glycosides (SGs) are a class of high-potency noncalorie natural sweeteners made up common diterpenoid core and varying glycans. Thus, the diversity glycans in composition, linkage, isomerism results tremendous structural complexity SG family, which poses challenges for precise identification leads to fact that SGs frequently used mixtures their variances biological activity remain largely unexplored. Here we show wild-type aerolysin nanopore can detect discriminate diverse species through modulable electro-osmotic flow effect at varied applied voltages. At low voltages, neutral molecule was drawn stuck pore entrance due an energy barrier around R220 sites. The ensuing binding events enable majority species. Increasing voltage break cause translocation events, allowing unambiguous several pairs differing by only one hydroxyl group recognition accumulation from multiple sensing regions Based on data 15 SGs, deep learning-based artificial intelligence (AI) model created process individual blockage achieving rapid, automated, single-molecule quantification real samples. This work highlights value analysis complex glycans-containing glycosides, as well potential sensitive rapid quality assurance glycoside products with use AI.

Language: Английский

Citations

5
Recent Progress in Chemoenzymatic Synthesis of Human Glycans DOI Creative Commons

Shengzhou Ma,

Jinhua Gao,

Yinping Tian

et al.

Organic & Biomolecular Chemistry, Journal Year: 2024, Volume and Issue: 22(38), P. 7767 - 7785

Published: Jan. 1, 2024

Glycan is an essential cell component that usually exists in either a free form or glycoconjugated form. Glycosylation affects the regulatory function of glycoconjugates health and disease development, indicating key role glycan organisms. Because complexity diversity structures, it challenging to prepare structurally well-defined glycans, which hinders investigation biological functions at molecular level. Chemoenzymatic synthesis attractive approach for preparing complex because avoids tedious protecting group manipulations chemical ensures high regio- stereo-selectivity glucosides during assembly. Herein, enzymes, such as glycosyltransferases (GTs) glycosidases (GHs), sugar donors involved chemoenzymatic human glycans are initially discussed. Many state-of-the-art methodologies subsequently displayed summarized illustrate development synthetic example,

Language: Английский

Citations

4
Glycan Sequencing Based on Glycosidase-Assisted Nanopore Sensing DOI

Guangda Yao,

Bingqing Xia,

Fangyu Wei

et al.

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Nanopores are promising sensors for glycan analysis with the accurate identification of complex glycans laying foundation nanopore-based sequencing. However, their applicability toward continuous sequencing has not yet been demonstrated. Here, we present a proof-of-concept by combining nanopore technology glycosidase-hydrolyzing reactions. By continuously monitoring changes in characteristic current generated translocation hydrolysis products through nanopore, sequence can be accurately identified based on specificity glycosidases. With machine learning, improved accuracy to over 98%, allowing reliable determination consecutive building blocks and glycosidic linkages chains while reducing need operator expertise. This approach was validated real samples, calibrated using hydrophilic interaction chromatography-high-performance liquid chromatography (HILIC-HPLC) mass spectrometry (MS). We achieved ten units natural chains, which provided first evidence feasibility nanopore-glycosidase-compatible system Compared traditional methods, this strategy enhances efficiency 5-fold. Additionally, introduced concept 'inverse sequencing', focuses electrical signal rather than monosaccharide identification. eliminates reliance fingerprint libraries typically required putative 'forward hydrolysis' strategies. When challenges both inverse strategies' addressed, will pave way establishing at single-molecule level.

Language: Английский

Citations

0
Single-molecule resolution of macromolecules with nanopore devices DOI

Meili Ren,

Daixin Liu,

Fupeng Qin

et al.

Advances in Colloid and Interface Science, Journal Year: 2025, Volume and Issue: unknown, P. 103417 - 103417

Published: Jan. 1, 2025

Language: Английский

Citations

0
DNAzyme-Assisted the Detection of rps27l mRNA in Protein Nanopores DOI
Kang Luo, Xu Wang,

Ling Zheng

et al.

Analytica Chimica Acta, Journal Year: 2025, Volume and Issue: unknown, P. 343711 - 343711

Published: Jan. 1, 2025

Language: Английский

Citations

0
Nanopore toward Genuine Single-Molecule Sensing: Molecular Ping-Pong Technology DOI
Xinjia Zhao, Yahui Zhang, Guangyan Qing

et al.

Nano Letters, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 26, 2025

Nanopore sensing is a so-called label-free, single-molecule technology; however, multiple events of different molecules are recorded to obtain statistically robust data, which can limit both efficiency and sample use. To overcome these challenges, nanopore molecular ping-pong technology enables precise manipulation, reducing systematic stochastic errors by repeatedly measuring the same molecule. This review introduces fundamentals advancements technology, highlighting recent breakthrough achieving over 10,000 recaptures single dsDNA molecule within minutes. innovation not only minimizes requirements, critical for nonamplifiable samples, but also significantly enhances experimental precision. While current applications focus on dsDNA, extending this protein glycan analysis could transform research. Just as revolutionized DNA sequencing, it holds potential drive development nanopore-based sequencers, paving way groundbreaking in biology biomedicine.

Language: Английский

Citations

0
Research Progress on Saccharide Molecule Detection Based on Nanopores DOI Creative Commons
Bohua Yin,

Wanyi Xie,

Shaoxi Fang

et al.

Sensors, Journal Year: 2024, Volume and Issue: 24(16), P. 5442 - 5442

Published: Aug. 22, 2024

Saccharides, being one of the fundamental molecules life, play essential roles in physiological and pathological functions cells. However, their intricate structures pose challenges for detection. Nanopore technology, with its high sensitivity capability single-molecule-level analysis, has revolutionized identification structural analysis saccharide molecules. This review focuses on recent advancements nanopore technology carbohydrate detection, presenting an array methods that leverage molecular complexity saccharides. Biological techniques utilize specific protein binding or pore modifications to trigger typical resistive pulses, enabling high-sensitivity detection monosaccharides oligosaccharides. In solid-state sensing, boronic acid modification pH gating mechanisms are employed recognition quantitative polysaccharides. The integration artificial intelligence algorithms can further enhance accuracy reliability analyses. Serving as a crucial tool we foresee significant potential application disease diagnosis, drug screening, biosensing, fostering innovative progress related research domains.

Language: Английский

Citations

2