Enhanced electrochemically-directed oligonucleotide synthesis via porous silica thin-film for DNA data storage

Abstract

DNA-based data storage has emerged as a promising alternative for long-term information archiving and its implementation accelerates the development for on-chip large scale oligonucleotide synthesis. Among various technological routes, electrochemically directed synthesis offers exceptional synthesis-site density thanks to its compatibility with semiconductor microfabrication processes. Yet increasing density typically comes at the expense of reduced per-site oligonucleotide yield, compromising the practical utility of these synthesis platforms for reliable data recovery. Here we report a porous silica thin-film strategy in order to address this fundamental trade-off by substantially increasing the effective on-chip synthesis surface area while preserving spatial confinement during electrochemically generated acid-mediated deblocking. The porous thin-film, fabricated via a sacrificial templating approach, forms an interconnected high-surface-area porous network that enables efficient reagent transport and stable electrochemical control. The presented method enables an areal oligonucleotide yield of more than 1821 pmol/cm², which represents more than 11-fold enhancement compared to a planar silica substrate. Moreover, this platform achieves comparable error statistics of deletion, insertion and substitution compared to other laboratory-built DNA data writing systems. Using this platform, we demonstrated parallel synthesis of 121-nt oligonucleotides and successful encoding, writing and error-corrected recovery of digital information. These results establish a scalable strategy for high-yield on-chip DNA synthesis and provide a practical pathway towards integrated molecular data storage systems.