Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval.

Publisher: MDPI Country of Publication: Switzerland NLM ID: 101092791 Publication Model: Electronic Cited Medium: Internet ISSN: 1422-0067 (Electronic) Linking ISSN: 14220067 NLM ISO Abbreviation: Int J Mol Sci Subsets: MEDLINE

Original Publication: Basel, Switzerland : MDPI, [2000-

Algorithms* ; Polymerase Chain Reaction*/methods; DNA/genetics ; Information Storage and Retrieval/methods ; DNA Primers/genetics ; Base Sequence

Polymerase Chain Reaction (PCR) amplification is widely used for retrieving information from DNA storage. During the PCR amplification process, nonspecific pairing between the 3' end of the primer and the DNA sequence can cause cross-talk in the amplification reaction, leading to the generation of interfering sequences and reduced amplification accuracy. To address this issue, we propose an efficient coding algorithm for PCR amplification information retrieval (ECA-PCRAIR). This algorithm employs variable-length scanning and pruning optimization to construct a codebook that maximizes storage density while satisfying traditional biological constraints. Subsequently, a codeword search tree is constructed based on the primer library to optimize the codebook, and a variable-length interleaver is used for constraint detection and correction, thereby minimizing the likelihood of nonspecific pairing. Experimental results demonstrate that ECA-PCRAIR can reduce the probability of nonspecific pairing between the 3' end of the primer and the DNA sequence to 2-25%, enhancing the robustness of the DNA sequences. Additionally, ECA-PCRAIR achieves a storage density of 2.14-3.67 bits per nucleotide (bits/nt), significantly improving storage capacity.

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22JCYBJCO1390 Tianjin Science and Technology Planning Project

Keywords: DNA coding; DNA storage; ECA-PCRAIR; biological constraint; nonspecific pairing constraint; storage density

9007-49-2 (DNA)
0 (DNA Primers)

Date Created: 20240627 Date Completed: 20240627 Latest Revision: 20240629

20240629

PMC11204281

10.3390/ijms25126449

38928155