Periodic Reporting for period 1 - SPARXS (High throughput development platform for oligonucleotide aptamers)
Reporting period: 2024-03-01 to 2025-08-31
This project introduces the SPARXS platform, a cutting-edge technology developed to create affinity probes with precise binding kinetics for a variety of applications in therapeutics, microscopy, and assays. Traditional methods for developing affinity probes, such as SELEX, are limited in their ability to tune binding kinetics, often leading to the discovery of probes with suboptimal properties. The SPARXS platform, built on single-molecule fluorescence microscopy combined with high-throughput sequencing, allows for the rapid and precise exploration of aptamers that can bind to targets with defined kinetics, essential for applications like super-resolution microscopy and targeted drug delivery.
The project aims to refine this platform, focusing on aptamers and their customization for specific binding behaviors. The key objective is to bring SPARXS to a higher technological readiness level (TRL5), validating it for commercial applications in biotech industries, including those focused on super-resolution imaging, protein assays, and biopharmaceuticals. The potential market includes a wide range of stakeholders such as imaging users, biotech companies, and pharma developers, with a specific emphasis on clients in need of well-defined kinetic probes.
Through this project, we also intend to assess the feasibility of commercializing the platform by conducting market research, identifying customer needs, and building a business plan for a future spin-off company dedicated to aptamer development. The successful completion of this project will make SPARXS a transformative tool in the field of affinity probe design, offering new opportunities for both research and industry.
The project aims to refine this platform, focusing on aptamers and their customization for specific binding behaviors. The key objective is to bring SPARXS to a higher technological readiness level (TRL5), validating it for commercial applications in biotech industries, including those focused on super-resolution imaging, protein assays, and biopharmaceuticals. The potential market includes a wide range of stakeholders such as imaging users, biotech companies, and pharma developers, with a specific emphasis on clients in need of well-defined kinetic probes.
Through this project, we also intend to assess the feasibility of commercializing the platform by conducting market research, identifying customer needs, and building a business plan for a future spin-off company dedicated to aptamer development. The successful completion of this project will make SPARXS a transformative tool in the field of affinity probe design, offering new opportunities for both research and industry.
Compared to the initial design, we have developed a fully functional SPARXS prototype integrating single-molecule kinetic profiling with high-throughput sequencing.
In WP1, we validated the assay on known aptamer–target pairs, confirming single-molecule rate constants with ensemble benchmarks. We further demonstrated that kinetic traces could be directly linked to DNA barcodes, establishing seamless integration with sequencing workflows.
In WP2, we created structure-guided libraries that reduced sequence redundancy improving analysis efficiency while preserving functional diversity.
In WP3, we performed >10 structured interviews with industrial and academic stakeholders, leading to a business plan outlining two beachhead markets (diagnostics and drug discovery) and a spin-out roadmap.
Together, these achievements advanced SPARXS from TRL2 to TRL5, validated reproducibility across >10^4 single-molecule trajectories and demonstrated scalability for multiplexed kinetic screening.
In WP1, we validated the assay on known aptamer–target pairs, confirming single-molecule rate constants with ensemble benchmarks. We further demonstrated that kinetic traces could be directly linked to DNA barcodes, establishing seamless integration with sequencing workflows.
In WP2, we created structure-guided libraries that reduced sequence redundancy improving analysis efficiency while preserving functional diversity.
In WP3, we performed >10 structured interviews with industrial and academic stakeholders, leading to a business plan outlining two beachhead markets (diagnostics and drug discovery) and a spin-out roadmap.
Together, these achievements advanced SPARXS from TRL2 to TRL5, validated reproducibility across >10^4 single-molecule trajectories and demonstrated scalability for multiplexed kinetic screening.
A draft patent and IP/FTO analysis were completed in collaboration with TU Delft Enterprises.
Summary of results
We established a robust prototype for kinetic selection of aptamers in a high-throughput format and created the foundation for commercial translation via a planned spin-out company.
Summary of results
We established a robust prototype for kinetic selection of aptamers in a high-throughput format and created the foundation for commercial translation via a planned spin-out company.