SPARK-seq: A high-throughput platform for aptamer discovery and kinetic profiling

Cell surface proteins are key disease biomarkers and therapeutic targets, yet high-throughput methods for aptamer discovery targeting these proteins in situ remain limited. We introduce single-cell perturbation-driven aptamer recognition and kinetics sequencing (SPARK-seq), a high-throughput platform integrating single-cell messenger RNA and aptamer sequencing with CRISPR-based surface protein perturbation. In a single experiment, SPARK-seq simultaneously mapped 5535 distinct aptamers to eight surface proteins, capturing interactions across more than two orders of magnitude in protein abundance and spanning diverse biophysical classes. The method discriminated closely related paralogous proteins with no…

• IR
  Innovative Research Team of High-level Local University in Shanghai

  Award: SHSMU-ZLCX20212601
• NN
  National Natural Science Foundation of China

  Awards: T2188102, YQ2022HW01, 22304177, 82503388, 22577133, 22474075, 82372741, 82103287
• NK
  National Key Research and Development Program of China

  Awards: 2024YFC3405600, 2019YFA0905800, 2022YFA1104200, 2023YFF1205905