DNA isothermal amplification for information storage
The synthesized DNA oligomer library has become a powerful information storage medium, and its potential density and duration exceed that of silicon medium. In current hardware systems, DNA polymerase chain reaction (PCR) plays an important role in the manipulation of information writing and sequence reading mediated by oligomeric binding synthesis involving thousands to millions of DNA sequences. However, the huge sequence complexity of a large number of DNA molecules is challenging the ability of PCR to use in repeaters and stable large-scale oligonucleotide amplification, and highly biased amplification seriously damages the reading of information. Here, we prove that due to its inherent molecular mechanism, inefficient start-up, product diffusion trend and complex thermal regulation, it is impossible to completely encode more than DNA strands of synthetic oligomers in stable repetitive information by PCR. In-depth statistical analysis shows that there is a huge amplification deviation in the PCR amplification process, which leads to obvious deletion. In order to solve these problems, we have developed a new biochemical framework for isothermal DNA reading , including oligonucleotide pool standardization and chain replacement amplification in chemometrics. Compared with the current PCR system, isothermal DNA reaction can even achieve very stable low deviation amplification with 10 consecutive deep copies without any quality loss, and reduce the minimum sequencing coverage by at least one order of magnitude for decoding. isothermal DNA reaction has brought us advanced functions, including isothermal amplification, low amplification bias, prevention of error diffusion and no need for primers, which laid the foundation for the development of practical DNA storage hardware. First, we use the basic code system recently developed for DNA's digital distributed file system for storage. The system achieves high information density and low coding redundancy, which is the lowest level reported so far. Most importantly, the special method of amplifying complex oligonucleotides in DNA storage is to design a new method of amplifying oligonucleotides according to the new isothermal reaction of chain replacement ( isothermal DNA reaction). This method drives DNA amplification by a unique mechanism. Due to its nature, isothermal DNA reaction improves key issues related to the number distribution of offset copies. Compared with PCR, isothermal DNA reaction can effectively inhibit the increase of heterogeneity and the spread of variation error. In addition, isothermal DNA reaction can support continuous reading of duplicate DNA in the same oligonucleotide library, with consistent high-quality errors and loss of statistical amplicons. In addition, we have developed a simple and effective method to calibrate the heterogeneity of oligomeric cells by stoichiometry. To sum up, the new biochemical framework proposed in this paper can reduce the required DNA material and sequencing resources by several orders of magnitude, and achieve a variety of stable reading information with high sequence complexity in the oligonucleotide library, which may be the construction of its hardware infrastructure.