Orthogonal Programming of Ion Recognition and Membrane Anchoring in Sequence-Defined DNA Polymers for Artificial Ion Channels

Sequence-defined polymers provide unique opportunities to encode complex molecular functions through precise sequence control, yet independently programming molecular recognition and membrane interfaces within a single polymer architecture remains challenging. This limitation is particularly evident in artificial ion channels, where ion recognition is intrinsically coupled to channel architecture, requiring redesign of the membrane-spanning structure to target different ions. Here, we establish a sequence-defined DNA polymer platform that orthogonally programs ion recognition and membrane anchoring through independent control of nucleobase sequence and phosphorothioate backbone alkylation. The nucleobase sequence encodes the ion-recognition fold, whereas a fold-matched pattern of phosphorothioate backbone alkylation independently defines the membrane-facing surface. As a stringent demonstration of this design principle, we reprogrammed our previously reported K+-selective DNA channel into a silver ion channel (SIC) by replacing both the recognition chemistry and folding topology from a G-quadruplex to a stem-loop containing Ag+-binding metallo-base pairs, while preserving the orthogonal membrane-anchoring strategy. SIC selectively assembled in response to Ag+, inserted into lipid membranes, and transported Ag+ with no detectable transport of Na+ or K+, producing an Ag+ response more than 240-fold above the detection limit for the competing cations. A Watson–Crick control carrying the identical alkylation pattern but lacking Ag+-coordination sites was inactive, demonstrating that ion conduction proceeds through the sequence-encoded metallo-base-pair recognition axis rather than the alkylated polymer backbone. Together, these results establish orthogonal programming of ion recognition and membrane anchoring as a general molecular design strategy for sequence-defined DNA polymers, enabling programmable artificial ion channels with readily reconfigurable ion selectivity while providing a transferable design framework for future sequence-defined polymer systems.