Programmable Aptamer-Drug Conjugates: Expanding Automated and Modular Platforms for Targeted Therapeutics

Aptamer-drug conjugates (ApDCs) represent a powerful platform for targeted drug delivery, offering the potential to enhance therapeutic efficacy while minimizing systemic toxicity. However, conventional methods for ApDC preparation often involve complex, multistep procedures with limited control over drug loading and site specificity. This protocol describes a modular and automated strategy for the synthesis and structural optimization of ApDCs using custom-designed phosphoramidites that incorporate Anticancer drugs and functional moieties. The customized phosphoramidite is compatible with standard solid-phase oligonucleotide synthesis, enabling the automated and efficient construction of programmable aptamer-drug conjugates (PApDCs) for targeted drug delivery. We also highlight the programmable optimization of aptamer structures to meet clinical needs. The protocol offers a streamlined and versatile platform for the construction of functional ApDCs, facilitating their application in receptor-targeted chemotherapy and nucleic acid-based therapeutics. © 2025 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and purification of phosphoramidites Basic Protocol 2: Automated solid-phase synthesis and characterization of ApDCs.

PApDCs; oligonucleotide; phosphoramidite chemistry; programmable aptamer–drug conjugates; solid‐phase synthesis; targeted drug delivery.