---
title: "Nanopore deconvolution of glycosaminoglycans for single-molecule structural analysis"
id: "biorxiv-17-nanopore-based-sequence-deconvolution-of-diverse-glycosaminoglycans"
canonical_url: "https://medichelpline.com/clinical-feed/biorxiv-17-nanopore-based-sequence-deconvolution-of-diverse-glycosaminoglycans"
content_type: "clinical_feed_article"
specialty: "General"
source_name: "bioRxiv (Biomedical Preprints)"
source_url: "https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1?rss=1"
published_at: "2026-08-10T12:00:00.000Z"
evidence_level: "Verified Feed"
license: "CC-BY-NC-4.0 / Informational Use"
---
# Nanopore deconvolution of glycosaminoglycans for single-molecule structural analysis
## Provenance & Clinical Metadata
- **Canonical URL:** https://medichelpline.com/clinical-feed/biorxiv-17-nanopore-based-sequence-deconvolution-of-diverse-glycosaminoglycans
- **Specialty:** [General](https://medichelpline.com/clinical-feed/general.md)
- **Primary Source:** bioRxiv (Biomedical Preprints)
- **Source URL:** [Original Journal Publication](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1?rss=1)
- **Published At:** 2026-08-10T12:00:00.000Z
- **Evidence Rating:** Verified Feed
## Executive GIST (TL;DR)
- The authors present a **nanopore**-based, single-molecule workflow to deconvolute diverse **glycosaminoglycans (GAGs)** without prior fractionation, enabling counting and resolution of di- and oligosaccharides derived from heterogeneous chains. - A modular chemical pre-processing pipeline uses deacylation and an amino-selective ring-contractive reaction to convert aminosugars into electrophilic anhydrosugars bearing aldehydes, which form reversible covalent adducts for nanopore readout. - Distinct clustering of nanopore event amplitudes permits direct sugar sizing (~**10%** amplitude change per residue) and resolves finer features: the number and position of sulfate groups (~**2%** amplitude change per sulfate) and single-atom stereochemistry between epimers (~**0.5%** amplitude change). - Reverse mapping guided by chemical logic maps resolved anhydrosugars back to precursor disaccharides, covering approximately **84–100%** of disaccharides and their eliminative digestion variants in natural **heparan sulfate (HS)**. - The method was applied to a panel of HS polysaccharides representing natural GAG diversity and successfully identified contaminants in pharmaceutical-grade **heparin**, including oversulfated chondroitin sulfate implicated in prior safety incidents. - The approach is operationally simple, requires no fractionation, and is compatible with widely used portable nanopore sequencing devices, suggesting a path toward broader access to glycan analysis. - Competing interest: one author is founder/consultant/shareholder of Oxford Nanopore Technologies and a patent on ring-contractive glycan sensing has been filed. - Funders reported include Oxford Nanopore Technologies, the Gates Foundation, UK Research and Innovation, and the Engineering and Physical Sciences Research Council.
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M. Szeto, Anna Yucknovsky, Daniel P. Cole, Hagan Bayley, Benjamin G. Davis, Yujia Qing doi: https://doi.org/10.64898/2026.08.08.743666 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. Lemuel L. M. Szeto 1 University of Oxford; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Lemuel%2BL.%2BM.%2BSzeto%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Szeto%20LL&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ALemuel%2BL.%2BM.%2BSzeto%2B) * [ORCID record for Lemuel L. M. Szeto](http://orcid.org/0000-0003-3957-1444 "Open in new tab") Anna Yucknovsky 1 University of Oxford; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Anna%2BYucknovsky%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Yucknovsky%20A&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AAnna%2BYucknovsky%2B) Daniel P. Cole 1 University of Oxford; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Daniel%2BP.%2BCole%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Cole%20DP&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ADaniel%2BP.%2BCole%2B) Hagan Bayley 1 University of Oxford; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Hagan%2BBayley%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Bayley%20H&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AHagan%2BBayley%2B) Benjamin G. Davis 2 The Rosalind Franklin Institute * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Benjamin%2BG.%2BDavis%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Davis%20BG&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3ABenjamin%2BG.%2BDavis%2B) Yujia Qing 1 University of Oxford; * [Find this author on Google Scholar](https://www.biorxiv.org/lookup/google-scholar?link_type=googlescholar&gs_type=author&author%5B0%5D=Yujia%2BQing%2B "Open in new tab") * [Find this author on PubMed](https://www.biorxiv.org/lookup/external-ref?access_num=Qing%20Y&link_type=AUTHORSEARCH "Open in new tab") * [Search for this author on this site](https://www.biorxiv.org/search/author1%3AYujia%2BQing%2B) * For correspondence: yujia.qing@chem.ox.ac.uk * [Abstract](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_art/node:5692855/1) * [Info/History](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.article-info)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_info/node:5692855/1) * [Metrics](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.article-metrics)[](https://www.biorxiv.org/panels_ajax_tab/article_tab_metrics/node:5692855/1) * [Supplementary material](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.supplementary-material)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_data/node:5692855/1) * [ Preview PDF](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.full.pdf+html)[](https://www.biorxiv.org/panels_ajax_tab/biorxiv_tab_pdf/node:5692855/1) ![Loading](https://www.biorxiv.org/sites/all/modules/contrib/panels_ajax_tab/images/loading.gif) ## Abstract Glycosaminoglycan (GAG) polysaccharides play vital roles in animal physiology and disease. Their diverse and intricate patterns of sulfation and epimerization endow them with an extensive potential to encode functional information. GAG characterization, however, remains a formidable challenge for state-of-the-art ensemble-based techniques. Single-molecule techniques are uniquely suited for analysing complex mixtures. Here, we report the single-molecule resolution and counting of diverse GAG di- and oligosaccharides derived from longer heterogeneous chains as part of a deconvolutive nanopore-based workflow that requires no fractionation and is operationally simple. Modular chemical deacylation and amino-selective ring-contractive formation of electrophilic aldehydes enable the parsing of libraries of GAG structures into simplified sets of reactive anhydrosugars for nanopore readout via reversible covalent adduct formation. Discrete clustering of event amplitudes enables direct sugar sizing (~10 % step change per residue), which can be coupled to precisely resolved amplitude differences that further reveal sugar fine structure—including the number and position of sulfate groups (~2 % step change per sulfate) alongside single-atom stereochemistry (~0.5 % step change between epimers). Guided by chemical logic, the reverse mapping of resolved anhydrosugars to their precursors covers ~84–100 % of all disaccharides and their eliminative digestion variants in natural heparan sulfate (HS). We demonstrate the practical utility and scope of our approach through the compositional analysis of a panel of HS polysaccharides that together encompass natural GAG structural diversity. Moreover, we detect contaminants in heparin, including oversulfated chondroitin sulfate found in an authentic pharmaceutical heparin sample previously implicated in a global healthcare crisis. Together, our results suggest a general chemo-biophysical framework for the precise and sensitive characterization of GAGs that extends to other aminosugar biopolymers. When adapted for portable, widely used nanopore sequencing devices, our approach may offer a path towards the long-sought ′democratization′ of glycan analysis. ### Competing Interest Statement H.B. is the founder of, a consultant for, and a shareholder of Oxford Nanopore Technologies, a company engaged in the development of nanopore sensing and sequencing technologies. A patent describing ring-contractive glycan sensing has been filed, which may afford the authors royalties if licensed. ## Funder Information Declared Oxford Nanopore Technologies (United Kingdom), https://ror.org/04hyfx005 Gates Foundation, https://ror.org/0456r8d26 UK Research and Innovation, https://ror.org/001aqnf71 Engineering and Physical Sciences Research Council, https://ror.org/0439y7842 Copyright The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a [CC-BY 4.0 International license](http://creativecommons.org/licenses/by/4.0/). bioRxiv and medRxiv thank the following for their generous financial support: > The Chan Zuckerberg Initiative, Cold Spring Harbor Laboratory, the Sergey Brin Family Foundation, California Institute of Technology, Centre National de la Recherche Scientifique, Fred Hutchinson Cancer Center, Imperial College London, Massachusetts Institute of Technology, Stanford University, The University of Edinburgh, University of Washington, and Vrije Universiteit Amsterdam. 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[ Download PDF](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.full.pdf) Print/Save Options [Download PDF](https://www.biorxiv.org/content/biorxiv/early/2026/08/10/2026.08.08.743666.full.pdf)Full Text & In-line FiguresXML [More Info](https://www.biorxiv.org/about/FAQ#PrintOptions "More Information on Print/Save Options") [Supplementary Material ](https://www.biorxiv.org/content/10.64898/2026.08.08.743666v1.supplementary-material) [ Email](https://www.biorxiv.org/ "Email this Article") [ Share](https://www.biorxiv.org/) Nanopore-based sequence deconvolution of diverse glycosaminoglycans Lemuel L. M. Szeto, Anna Yucknovsky, Daniel P. Cole, Hagan Bayley, Benjamin G. Davis, Yujia Qing bioRxiv 2026.08.08.743666; doi: https://doi.org/10.64898/2026.08.08.743666 This article is a preprint and has not been certified by peer review [[what does this mean?](https://www.biorxiv.org/about/FAQ#unrefereed)]. 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