Engineering nanobody-based analytical platforms for molecular sensing and nanoscale characterization

Research conducted at LELS demonstrated internationally visible scientific excellence in the development of engineered nanobody-based systems for molecular sensing, nanoscale imaging and analytical biotechnology. The research combined molecular engineering, nanotechnology and advanced analytical methodologies to establish innovative approaches for selective molecular recognition and high-resolution characterization in complex biological systems.

A major original contribution of this work was the development of nanobody-enabled analytical platforms for the characterization of membrane protein nanoenvironments and receptor organization at nanoscale resolution. Ambrosetti et al. (2021) introduced a DNA-nanoassembly strategy for mapping membrane protein nanoenvironments, while Nieves et al. (2023) established a methodological framework for evaluating single-molecule localization microscopy cluster-analysis algorithms, contributing to improved robustness, reproducibility and analytical sensitivity in super-resolution imaging analyses. The research further demonstrated the applicability of engineered nanobodies in highly sensitive biosensing and diagnostic platforms, including electrochemical sensing systems for biomarkers such as C-reactive protein. Complementary methodological developments in rational protein engineering and machine-learning-supported nanobody optimization strengthened the broader scientific relevance and future applicability of the research.

The achievement strongly supports the university’s strategic priorities in Scientific Excellence, Internationalization and Interdisciplinary Research through the integration of molecular engineering, nanotechnology, analytical biotechnology and advanced imaging methodologies within extensive international research collaborations. The translational relevance of the developed analytical and diagnostic platforms further contributes to the university’s strategic objective of strengthening Societal Relevance and Impact in biomedicine and precision diagnostics.

The achievement resulted from extensive interdisciplinary and international collaboration and produced publications in internationally leading journals, including Nature Nanotechnology, Nature Methods, Nature Communications, ACS Sensors and Biosensors & Bioelectronics. The research achieved international visibility through citations, invited conference presentations, competitive external funding and long-term international research collaborations, including a WEAVE project and support from the Loulou Foundation and the Center for Rare Diseases at the University of Pennsylvania.

The methodological frameworks developed within the programme contributed to improved analytical reproducibility, transparent benchmarking and greater standardization of nanoscale imaging analyses. Future development should focus on further improving methodological standardization, translational scalability and integration of the developed platforms into broader analytical and diagnostic workflows.

• Ambrosetti E, Bernardinelli G, Hoffecker I, Hartmanis L, Kiriako G, de Marco A, Sandberg R, Högberg B, Teixeira AI (2021). A DNA-nanoassembly based approach to map membrane protein nanoenvironments. Nature Nanotechnology 16:85–95.
• Nieves DJ, Pike JA, Levet F, Williamson DJ, Baragilly M, Oloketuyi S, de Marco A, Griffié J, Sage D, Cohen EAK, Sibarita JB, Heilemann M, Owen DM (2023). A framework for evaluating the performance of SMLM cluster analysis algorithms. Nature Methods 20:259–267.
• Boonkaewa S, Szot-Karpińska K, Niedziółka-Jönsson J, de Marco A, Jönsson-Niedziółka M (2024). NFC smartphone-based electrochemical microfluidic device integrated with nanobody recognition for C-reactive protein. ACS Sensors 9:3066–3074.
• Svigelj R, de Marco A (2024). Biological and technical factors affecting point-of-care diagnostics in non-oncological chronic diseases. Biosensors & Bioelectronics 264:116669.