Efficient DNA Coding Algorithm for Polymerase Chain Reaction Amplification Information Retrieval

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Jun 27

PMID 38928155

Authors

Qing Wang

Shufang Zhang

Yuhui Li

Affiliations

Soon will be listed here.

Abstract

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.

References

Crossley B, Bai J, Glaser A, Maes R, Porter E, Killian M . Guidelines for Sanger sequencing and molecular assay monitoring. J Vet Diagn Invest. 2020; 32(6):767-775. PMC: 7649556. DOI: 10.1177/1040638720905833. View

Matange K, Tuck J, Keung A . DNA stability: a central design consideration for DNA data storage systems. Nat Commun. 2021; 12(1):1358. PMC: 7921107. DOI: 10.1038/s41467-021-21587-5. View

Doricchi A, Platnich C, Gimpel A, Horn F, Earle M, Lanzavecchia G . Emerging Approaches to DNA Data Storage: Challenges and Prospects. ACS Nano. 2022; 16(11):17552-17571. PMC: 9706676. DOI: 10.1021/acsnano.2c06748. View

Izquierdo E, Proszek P, Pericoli G, Temelso S, Clarke M, Carvalho D . Droplet digital PCR-based detection of circulating tumor DNA from pediatric high grade and diffuse midline glioma patients. Neurooncol Adv. 2021; 3(1):vdab013. PMC: 8218704. DOI: 10.1093/noajnl/vdab013. View

Li M, Wu J, Dai J, Jiang Q, Qu Q, Huang X . A self-contained and self-explanatory DNA storage system. Sci Rep. 2021; 11(1):18063. PMC: 8433296. DOI: 10.1038/s41598-021-97570-3. View

Tomek K, Volkel K, Indermaur E, Tuck J, Keung A . Promiscuous molecules for smarter file operations in DNA-based data storage. Nat Commun. 2021; 12(1):3518. PMC: 8192770. DOI: 10.1038/s41467-021-23669-w. View

Press W, Hawkins J, Jones Jr S, Schaub J, Finkelstein I . HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints. Proc Natl Acad Sci U S A. 2020; 117(31):18489-18496. PMC: 7414044. DOI: 10.1073/pnas.2004821117. View

Zan X, Xie R, Yao X, Xu P, Liu W . A Robust and Efficient DNA Storage Architecture Based on Modulation Encoding and Decoding. J Chem Inf Model. 2023; 63(12):3967-3976. DOI: 10.1021/acs.jcim.3c00629. View

Tabatabaei Yazdi S, Yuan Y, Ma J, Zhao H, Milenkovic O . A Rewritable, Random-Access DNA-Based Storage System. Sci Rep. 2015; 5:14138. PMC: 4585656. DOI: 10.1038/srep14138. View

10.

Chen W, Han M, Zhou J, Ge Q, Wang P, Zhang X . An artificial chromosome for data storage. Natl Sci Rev. 2021; 8(5):nwab028. PMC: 8288405. DOI: 10.1093/nsr/nwab028. View

11.

Foo P, Nurul Najian A, Muhamad N, Ahamad M, Mohamed M, Yean Yean C . Loop-mediated isothermal amplification (LAMP) reaction as viable PCR substitute for diagnostic applications: a comparative analysis study of LAMP, conventional PCR, nested PCR (nPCR) and real-time PCR (qPCR) based on Entamoeba histolytica DNA.... BMC Biotechnol. 2020; 20(1):34. PMC: 7310076. DOI: 10.1186/s12896-020-00629-8. View

12.

Dong Y, Sun F, Ping Z, Ouyang Q, Qian L . DNA storage: research landscape and future prospects. Natl Sci Rev. 2021; 7(6):1092-1107. PMC: 8288837. DOI: 10.1093/nsr/nwaa007. View

13.

Kayama K, Kanno M, Chisaki N, Tanaka M, Yao R, Hanazono K . Prediction of PCR amplification from primer and template sequences using recurrent neural network. Sci Rep. 2021; 11(1):7493. PMC: 8021588. DOI: 10.1038/s41598-021-86357-1. View

14.

Zhang R, Wu H . On secondary structure avoidance of codes for DNA storage. Comput Struct Biotechnol J. 2023; 23:140-147. PMC: 10749251. DOI: 10.1016/j.csbj.2023.11.035. View

15.

Ping Z, Chen S, Zhou G, Huang X, Zhu S, Zhang H . Towards practical and robust DNA-based data archiving using the yin-yang codec system. Nat Comput Sci. 2024; 2(4):234-242. PMC: 10766522. DOI: 10.1038/s43588-022-00231-2. View

16.

Hu T, Chitnis N, Monos D, Dinh A . Next-generation sequencing technologies: An overview. Hum Immunol. 2021; 82(11):801-811. DOI: 10.1016/j.humimm.2021.02.012. View

17.

Bohmann K, Elbrecht V, Caroe C, Bista I, Leese F, Bunce M . Strategies for sample labelling and library preparation in DNA metabarcoding studies. Mol Ecol Resour. 2021; 22(4):1231-1246. PMC: 9293284. DOI: 10.1111/1755-0998.13512. View

18.

Erlich Y, Zielinski D . DNA Fountain enables a robust and efficient storage architecture. Science. 2017; 355(6328):950-954. DOI: 10.1126/science.aaj2038. View

19.

Ceze L, Nivala J, Strauss K . Molecular digital data storage using DNA. Nat Rev Genet. 2019; 20(8):456-466. DOI: 10.1038/s41576-019-0125-3. View

20.

Bonsu D, Higgins D, Simon C, Goodwin C, Henry J, Austin J . Quantitative PCR overestimation of DNA in samples contaminated with tin. J Forensic Sci. 2023; 68(4):1302-1309. DOI: 10.1111/1556-4029.15312. View