Nanopore-Based Glycan Sequencing via Fragmentation-Reassembly Strategy

Abstract Glycan sequencing remains a major analytical challenge due to the high structural complexity, extensive branching, and isomeric diversity of glycans. Nanopore sensing has emerged as a promising single-molecule platform for glycan analysis, but existing strategies—such as hydrolysis and strand sequencing, face significant limitations when applied to highly branched or non-linear glycans. Here we report the first experimental realization of glycan assembly sequencing, a nanopore-based strategy that reconstructs full glycan structures from individually analyzed fragments. Using a biantennary complex-type N-glycan as a model, we performed controlled enzymatic digestion to generate structurally defined oligosaccharide fragments. An engineered α-HL nanopore was developed for enhanced glycan recognition, enabling the construction of a multidimensional electrical fingerprinting library. Fragment signals from unknown samples were matched to this reference dataset, and full-sequence reconstruction was achieved via fragment reassembly based on set-theoretic integration of structural candidates. This study establishes glycan assembly sequencing as a viable and modular approach to resolve complex glycoforms using nanopore technologies. The method expands the accessible sequence space beyond what is achievable with conventional strategies and provides a foundation for scalable, high-resolution glycomic analysis.