At present,the polymerase chain reaction(PCR)amplification-based file retrieval method is the mostcommonly used and effective means of DNA file retrieval.The number of orthogonal primers limitsthe number of files that...At present,the polymerase chain reaction(PCR)amplification-based file retrieval method is the mostcommonly used and effective means of DNA file retrieval.The number of orthogonal primers limitsthe number of files that can be accurately accessed,which in turn affects the density in a single oligo poolof digital DNA storage.In this paper,a multi-mode DNA sequence design method based on PCR file retrie-val in a single oligonucleotide pool is proposed for high-capacity DNA data storage.Firstly,by analyzingthe maximum number of orthogonal primers at each predicted primer length,it was found that the rela-tionship between primer length and the maximum available primer number does not increase linearly,and the maximum number of orthogonal primers is on the order of 10^(4).Next,this paper analyzes themaximum address space capacity of DNA sequences with different types of primer binding sites for filemapping.In the case where the capacity of the primer library is R(where R is even),the number ofaddress spaces that can be mapped by the single-primer DNA sequence design scheme proposed in thispaper is four times that of the previous one,and the two-level primer DNA sequence design scheme can reach [R/2·(R/2-1)]^(2)times.Finally,a multi-mode DNA sequence generation method is designed based onthe number of files to be stored in the oligonucleotide pool,in order to meet the requirements of the ran-dom retrieval of target files in an oligonucleotide pool with large-scale file numbers.The performance ofthe primers generated by the orthogonal primer library generator proposed in this paper is verified,andthe average Gibbs free energy of the most stable heterodimer formed between the orthogonal primersproduced is−1 kcal·(mol·L^(−1))^(−1)(1 kcal=4.184 kJ).At the same time,by selectively PCR-amplifying theDNA sequences of the two-level primer binding sites for random access,the target sequence can be accu-rately read with a minimum of 10^(3) reads,when the primer binding site sequences at different positionsare mutually different.This paper provides a pipeline for orthogonal primer library generation and multi-mode mapping schemes between files and primers,which can help achieve precise random access to filesin large-scale DNA oligo pools.展开更多
基金supported by the fund from Tianjin Municipal Science and Technology Bureau(22JCYBJC01390).
文摘At present,the polymerase chain reaction(PCR)amplification-based file retrieval method is the mostcommonly used and effective means of DNA file retrieval.The number of orthogonal primers limitsthe number of files that can be accurately accessed,which in turn affects the density in a single oligo poolof digital DNA storage.In this paper,a multi-mode DNA sequence design method based on PCR file retrie-val in a single oligonucleotide pool is proposed for high-capacity DNA data storage.Firstly,by analyzingthe maximum number of orthogonal primers at each predicted primer length,it was found that the rela-tionship between primer length and the maximum available primer number does not increase linearly,and the maximum number of orthogonal primers is on the order of 10^(4).Next,this paper analyzes themaximum address space capacity of DNA sequences with different types of primer binding sites for filemapping.In the case where the capacity of the primer library is R(where R is even),the number ofaddress spaces that can be mapped by the single-primer DNA sequence design scheme proposed in thispaper is four times that of the previous one,and the two-level primer DNA sequence design scheme can reach [R/2·(R/2-1)]^(2)times.Finally,a multi-mode DNA sequence generation method is designed based onthe number of files to be stored in the oligonucleotide pool,in order to meet the requirements of the ran-dom retrieval of target files in an oligonucleotide pool with large-scale file numbers.The performance ofthe primers generated by the orthogonal primer library generator proposed in this paper is verified,andthe average Gibbs free energy of the most stable heterodimer formed between the orthogonal primersproduced is−1 kcal·(mol·L^(−1))^(−1)(1 kcal=4.184 kJ).At the same time,by selectively PCR-amplifying theDNA sequences of the two-level primer binding sites for random access,the target sequence can be accu-rately read with a minimum of 10^(3) reads,when the primer binding site sequences at different positionsare mutually different.This paper provides a pipeline for orthogonal primer library generation and multi-mode mapping schemes between files and primers,which can help achieve precise random access to filesin large-scale DNA oligo pools.
