Theoretical Basis for the Highly Efficient Aptamer Selection Using Unique Molecular Identifiers

Rapid selection methods are crucial for promoting the discovery and application of aptamers across various fields. We previously reported a highly efficient aptamer selection strategy by using unique molecular identifiers (UMIs), enabling the efficient isolation of aptamers from a single cell by only one round. The strategy integrates an ultrasensitive DNA barcoding technology with high-throughput sequencing to accurately quantify aptamer candidates, thereby mitigating issues such as PCR bias and sequence overenrichment that are inherent in traditional multiround selection. Here, we conduct a systematically theoretical analysis of this strategy in the elucidation of the theoretical basis, advantages, and applicability. The feasibility and advantages of isolating aptamers from low-enriched DNA libraries was investigated at a theoretical level, showing that this strategy is effective in reducing nonspecific binding and thus increasing the success of selecting high-affinity aptamers. Our theoretical analysis supports the broad applicability of the strategy for the single-round aptamer selection, paving the way for its widespread adoption in high-efficiency aptamer discovery and aptamer-based cell atlas.