Research On Plasmid Based DNA Storage Coding And Data Security

Deoxyribonucleic Acid serves as the storage medium for genetic material in life,characterized by its high storage density,long-term stability,low cost for replication and amplification,and no need for energy maintenance,making it a popular choice for the next generation of storage media.Based on DNA,biological computers will build a new era of networking.This thesis conducts research on DNA storage encoding and data security,exploring new models for biological computer network data security.Plasmids,with their stable circular double-stranded structure,abundant enzyme cutting sites,and natural biological affinity,are reliable carriers for DNA storage.Through biochemical operations,customized synthetic oligonucleotide chains can be embedded into plasmids to achieve stable long-term storage.If transfected into bacteria or cells,the stored information can be replicated along with the bacteria/cells,achieving low-cost data storage and amplification.Limited by the current storage media,synthesis,and sequencing technology conditions,DNA storage needs to meet additional biochemical constraints.This is similar to semiconductor storage media,which need to avoid dust,electric fields,magnetic fields,and other limiting factors during preparation,storage,and operation.When the synthesized DNA chains do not meet biochemical constraints,the probability of errors occurring during storage will significantly increase.Therefore,an efficient encoding method is required to meet biochemical constraints.We designed a shift encoder using the concept of shift transformation and a random code encoder using random matrices and Gaussian elimination methods.Both encoders can efficiently complete data encoding and have a certain error correction capability.The algorithm ensures that the output DNA chains meet biochemical constraints.Biochemical experiments have verified that the encoded encoder has high encoding efficiency,stable storage performance,strong information anti-interference capability,and high decoding accuracy,achieving actual storage densities of 1.85bits/nucleotide(shift encoder)and 1.78 bits/nucleotide(random code encoder).We amplified the DNA information encoded by the encoder through PCR and inserted it into the PUC57 plasmid using enzyme cutting.After sequencing and electrophoresis analysis of the plasmid,it was transfected into Escherichia coli and cultured to amplify and reproduce for ten generations.The progeny bacteria were shaken and plasmid extraction was performed.Sequencing showed no mutations in the plasmid genes of the progeny bacteria,confirming the high stability and biological affinity of plasmid-based DNA storage.Based on DNA strand displacement technology and biological enzyme catalysis technology,we have studied the security of DNA storage.By designing dedicated DNA timing logic gate circuits,different DNA input single strands are mapped to different encoder buttons.Through timing logic operations,the output results of the encoder can be controlled,and through biological enzyme catalysis,the output results can be precisely controlled to achieve the effect of targeted PCR amplification of the target chain.The DNA encoder uses DNA timing logic gates to encrypt DNA storage information.Biochemical experiments have verified the performance of the DNA encoder and explored a new path for DNA data security and integrated storage and computation.In summary,this thesis has conducted research on plasmid-based DNA storage in terms of encoder design and information data security.It has explored the design of efficient DNA storage encoders and their application in information replication and encryption,achieving high-density DNA storage encoding,stable information replication,and reliable DNA storage information encryption.