Liquid-Phase Synthesis of DNA Aptamer-Based PROTACs Using the Postsynthesis Conjugation Method

Proteolysis-targeting chimeras (PROTACs) have emerged as a promising strategy for the selective degradation of intracellular proteins by harnessing the ubiquitin-proteasome system. However, the development of PROTACs is often limited by the availability of high-affinity ligands, particularly for targets that are considered difficult to drug, such as transcription factors. In this context, aptamers, which are synthetic nucleic acid molecules capable of high affinity and specificity toward their targets, have attracted increasing attention as alternative binding moieties for PROTAC design. This protocol reports the synthesis of (1) a chimeric molecule in which a nucleic acid aptamer capable of binding to estrogen receptor alpha (ERα) and an E3 ubiquitin ligase ligand is linked via a linker, and (2) a phosphorothioate (PS)-modified analogue to enhance nuclease resistance and cellular uptake. A series of aptamer-PROTACs with various PS modification patterns were synthesized and conjugated to cereblon ligands via copper-catalyzed click chemistry. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Solid-phase synthesis of DNA aptamer Support Protocol 1: Preparation of 5'-hexynyl phosphoramidite Support Protocol 2: Preparation of CuI·P(OEt)₃ Basic Protocol 2: Synthesis of DNA aptamer-based PROTAC Alternate Protocol: Synthesis of phosphorothioate-modified DNA-based PROTAC.