High-fidelity robotic PCR amplification for DNA data storage

Abstract: Polymerase chain reaction (PCR) is fundamental to molecular biology, yet conventional thermocyclers pose significant challenges for emerging applications such as DNA data storage, where full automation, contamination control, and cost-effectiveness are critical. Here, we introduce a disruptive approach that revisits the original water bath-based PCR method and integrates it with modern robotic liquid-handling technology. Our system performs amplification entirely within sealed pipette tips using automated immersion and withdrawal in a single temperature-controlled oil bath, eliminating the need for sophisticated thermal management while enabling precise temperature control across denaturation, annealing, and extension steps. We demonstrate that this approach achieves amplification efficiency and sequencing fidelity comparable to high-performance thermocyclers when applied to DNA-encoded datasets. The platform minimizes reagent waste, reduces contamination risks through complete tip isolation, and enables full sample recovery. This modular, automation-ready design provides a scalable and cost-effective solution for PCR workflows in DNA data storage, high-throughput diagnostics, and distributed laboratory settings.