PERFECT PCR: Advancing DNA Data Storage to Near-Maximal Density

ABSTRACT DNA-based data storage offers unprecedented storage density and durability compared to traditional media, but it faces challenges in long access latency and limited encoding efficiency. Current DNA storage methods achieve only 8% of the theoretical maximum storage density (TMSD) due to biological constraints and error rates. Here, we demonstrate an approach that improves both synthesis speed and encoding density, bringing DNA data storage closer to practical implementation. We describe Polymerase-Enabled Rapid and Frugal Error Correcting Technology (PERFECT) PCR, which integrates PCR with hyperthermophilic EndoNucS enzymes for efficient DNA mismatch detection and cleavage, enabling accurate and fast DNA synthesis using overlapping oligonucleotides. This approach reduced latency while streamlining the overall DNA synthesis process, achieving significantly lower error rates in amplicons compared to state-of-the-art methods, thereby reducing physical redundancy. Specifically, we achieved a substantially reduced error rate of 0.06 errors per kilobase, with 95% of sequences verified as accurate. As a result, our technique reached 94% TMSD, representing a twelve-fold improvement over current systems and approaching the theoretical limit for existing sequencing technologies. We further validated the versatility of PERFECT PCR by successfully encoding and retrieving digital images, music files, and multilingual text files with near-perfect information recovery. By addressing the core challenges of latency, density, and accuracy, our approach brings DNA-based data storage significantly closer to practical implementation. In addition, the accurate DNA synthesis methods described here may be applied to de novo genome assembly and therefore have broad implications for the synthesis and analysis of biological systems. SUMMARY Low cost, rapid, and error free de novo DNA synthesis for DNA-based data storage and gene synthesis applications.