Stem-Engineered Aptamers with Enhanced Stability and Affinity for Tumor-Targeted Imaging

Aptamers, as high-affinity and high-specificity functional nucleic acids obtained through in vitro selection, face significant limitations in clinical applications due to their susceptibility to nuclease-mediated degradation in the bloodstream. To address this challenge, this study introduces a stem-engineered aptamer strategy, which focuses on the rational engineering and chemical modification of the aptamer’s stem region within its stem-loop configuration. Specifically, modifications such as locked nucleic acids (LNA), 2′- O -methyl (2′-OMe), and 3′-inverted deoxythymidine (idT) bases were incorporated, together with optimized structural designs, to enhance nuclease resistance and plasma stability. Through stem-region engineering and secondary-structure analysis, we identified two mismatched base pairs within the extended stem of the c-Met targeting aptamer SL1. Correction of these mismatches followed by stem truncation yielded a 42-nt variant, TSL1. Subsequent LNA stabilization generated MTSL1, which displayed markedly improved c-Met binding affinity and substantially enhanced plasma stability. At the cellular level, MTSL1 displayed improved binding and enhanced cellular association. In animal models, MTSL1 resulted in markedly prolonged circulation time and significantly improved tumor accumulation in nonsmall cell lung cancer xenografts. Collectively, the stem-engineered aptamer strategy may provide a promising framework for the rational design and optimization of aptamers, offering a solid foundation for their clinical translation in precision targeting, diagnostics, and imaging applications.