{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T15:46:42Z","timestamp":1753890402956,"version":"3.41.2"},"reference-count":50,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,10,12]],"date-time":"2023-10-12T00:00:00Z","timestamp":1697068800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>DNA, as the storage medium in organisms, can address the shortcomings of existing electromagnetic storage media, such as low information density, high maintenance power consumption, and short storage time. Current research on DNA storage mainly focuses on designing corresponding encoders to convert binary data into DNA base data that meets biological constraints. We have created a new Chinese character code table that enables exceptionally high information storage density for storing Chinese characters (compared to traditional UTF-8 encoding). To meet biological constraints, we have devised a DNA shift coding scheme with low algorithmic complexity, which can encode any strand of DNA even has excessively long homopolymer. The designed DNA sequence will be stored in a double-stranded plasmid of 744bp, ensuring high reliability during storage. Additionally, the plasmid\u2018s resistance to environmental interference ensuring long-term stable information storage. Moreover, it can be replicated at a lower cost.<\/jats:p>","DOI":"10.3389\/fbinf.2023.1276934","type":"journal-article","created":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T07:56:27Z","timestamp":1697356587000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Towards Chinese text and DNA shift encoding scheme based on biomass plasmid storage"],"prefix":"10.3389","volume":"3","author":[{"given":"Xu","family":"Yang","sequence":"first","affiliation":[]},{"given":"Langwen","family":"Lai","sequence":"additional","affiliation":[]},{"given":"Xiaoli","family":"Qiang","sequence":"additional","affiliation":[]},{"given":"Ming","family":"Deng","sequence":"additional","affiliation":[]},{"given":"Yuhao","family":"Xie","sequence":"additional","affiliation":[]},{"given":"Xiaolong","family":"Shi","sequence":"additional","affiliation":[]},{"given":"Zheng","family":"Kou","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2023,10,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"4724","DOI":"10.1098\/rspb.2012.1745","article-title":"The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils","volume":"279","author":"Allentoft","year":"2012","journal-title":"Proc. R. Soc. B Biol. Sci."},{"key":"B3","doi-asserted-by":"publisher","first-page":"433524","DOI":"10.1101\/433524","article-title":"Improved DNA based storage capacity and fidelity using composite DNA letters","author":"Anavy","year":"2018","journal-title":"bioRxiv"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1229","DOI":"10.1038\/s41587-019-0240-x","article-title":"Data storage in DNA with fewer synthesis cycles using composite DNA letters","volume":"37","author":"Anavy","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"e72","DOI":"10.1093\/nar\/gks001","article-title":"Summarizing and correcting the GC content bias in high-throughput sequencing","volume":"40","author":"Benjamini","year":"2012","journal-title":"Nucleic acids Res."},{"key":"B5","first-page":"1","article-title":"Galois field in cryptography","volume":"1","author":"Benvenuto","year":"2012","journal-title":"Univ. Wash."},{"key":"B6","doi-asserted-by":"publisher","first-page":"1531","DOI":"10.1093\/nar\/gkp1060","article-title":"Chain and conformation stability of solid-state DNA: implications for room temperature storage","volume":"38","author":"Bonnet","year":"2010","journal-title":"Nucleic acids Res."},{"key":"B7","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1145\/2872362.2872397","article-title":"A DNA-based archival storage system","volume-title":"Proceedings of the Twenty-First International Conference on Architectural Support for Programming Languages and Operating Systems","author":"Bornholt","year":"2016"},{"key":"B8","doi-asserted-by":"publisher","first-page":"1151","DOI":"10.1038\/nbt.1590","article-title":"Genome engineering","volume":"27","author":"Carr","year":"2009","journal-title":"Nat. Biotechnol."},{"key":"B9","doi-asserted-by":"publisher","first-page":"165","DOI":"10.1089\/dna.1985.4.165","article-title":"Supercoil sequencing: a fast and simple method for sequencing plasmid DNA","volume":"4","author":"Chen","year":"1985","journal-title":"Dna"},{"key":"B10","doi-asserted-by":"publisher","first-page":"6582","DOI":"10.1038\/s41598-019-43105-w","article-title":"High information capacity DNA-based data storage with augmented encoding characters using degenerate bases","volume":"9","author":"Choi","year":"2019","journal-title":"Sci. Rep."},{"key":"B11","first-page":"2149","article-title":"Chinese Characters Mapping Table of Japanese, Traditional Chinese and Simplified Chinese","author":"Chu","year":"2012","journal-title":"LREC. Citeseer"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1126\/science.1226355","article-title":"Next-generation digital information storage in DNA","volume":"337","author":"Church","year":"2012","journal-title":"Science"},{"key":"B13","doi-asserted-by":"publisher","first-page":"a003889","DOI":"10.1101\/cshperspect.a003889","article-title":"Chromosome territories","volume":"2","author":"Cremer","year":"2010","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"B48","first-page":"139","article-title":"Information security technology in DNA computing[J]","volume":"43","author":"Cui","year":"2007","journal-title":"Comput. Appl. Eng."},{"key":"B14","doi-asserted-by":"publisher","first-page":"70","DOI":"10.2307\/777811","article-title":"Microvenus","volume":"55","author":"Davis","year":"1996","journal-title":"Art J."},{"key":"B15","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1006\/jtbi.2000.2207","article-title":"Memory and DNA","volume":"208","author":"Dietrich","year":"2001","journal-title":"J. Theor. Biol."},{"key":"B16","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1126\/science.aaj2038","article-title":"DNA Fountain enables a robust and efficient storage architecture","volume":"355","author":"Erlich","year":"2017","journal-title":"science"},{"key":"B17","doi-asserted-by":"publisher","first-page":"22","DOI":"10.1038\/537022a","article-title":"How DNA could store all the world's data","volume":"537","author":"Extance","year":"2016","journal-title":"Nature"},{"key":"B18","first-page":"157","article-title":"Efficiency and reliability of semantic retrieval in DNA-based memories","author":"Garzon","year":"2004"},{"key":"B19","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.1109\/jproc.2012.2189787","article-title":"The history of storage systems","volume":"100","author":"Goda","year":"2012","journal-title":"Proc. IEEE"},{"key":"B20","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1038\/nature11875","article-title":"Towards practical, high-capacity, low-maintenance information storage in synthesized DNA","volume":"494","author":"Goldman","year":"2013","journal-title":"nature"},{"key":"B21","doi-asserted-by":"publisher","first-page":"26","DOI":"10.5120\/12722-9558","article-title":"Modified caesar cipher for better security enhancement","volume":"73","author":"Goyal","year":"2013","journal-title":"Int. J. Comput. Appl."},{"key":"B22","doi-asserted-by":"publisher","first-page":"2552","DOI":"10.1002\/anie.201411378","article-title":"Robust chemical preservation of digital information on DNA in silica with error\u2010correcting codes","volume":"54","author":"Grass","year":"2015","journal-title":"Angew. Chem. Int. Ed."},{"key":"B23","first-page":"113","article-title":"Review of big data storage based on DNA computing","author":"Hakami","year":"2015"},{"key":"B24","doi-asserted-by":"crossref","DOI":"10.17487\/rfc4648","volume-title":"The base16, base32, and base64 data encodings","author":"Josefsson","year":"2006"},{"key":"B25","doi-asserted-by":"publisher","first-page":"615","DOI":"10.3732\/ajb.91.4.615","article-title":"DNA sequences from Miocene fossils: an ndhF sequence of Magnolia latahensis (Magnoliaceae) and an rbcL sequence of Persea pseudocarolinensis (Lauraceae)","volume":"91","author":"Kim","year":"2004","journal-title":"Am. J. Bot."},{"key":"B50","doi-asserted-by":"publisher","first-page":"10","DOI":"10.12113\/202003002","article-title":"DNA encoding technology of storage [J]","volume":"18","author":"Kun","year":"2020","journal-title":"J. Bioinform."},{"key":"B26","first-page":"271","article-title":"LT codes","author":"Luby","year":"2002"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1062","DOI":"10.1049\/ip-com:20050237","article-title":"Fountain codes","volume":"152","author":"MacKay","year":"2005","journal-title":"IEE Proceedings-Communications"},{"key":"B28","doi-asserted-by":"publisher","first-page":"E2382","DOI":"10.1073\/pnas.1210506109","article-title":"Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change","volume":"109","author":"Miller","year":"2012","journal-title":"Proc. Natl. Acad. Sci."},{"key":"B29","article-title":"Hamming distance metric learning","volume":"25","author":"Norouzi","year":"2012","journal-title":"Adv. neural Inf. Process. Syst."},{"key":"B30","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1038\/nbt.4079","article-title":"Random access in large-scale DNA data storage","volume":"36","author":"Organick","year":"2018","journal-title":"Nat. Biotechnol."},{"key":"B31","doi-asserted-by":"publisher","first-page":"74","DOI":"10.1038\/nature12323","article-title":"Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse","volume":"499","author":"Orlando","year":"2013","journal-title":"Nature"},{"key":"B32","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1007\/s13205-018-1246-7","article-title":"DNA as a digital information storage device: hope or hype?","volume":"8","author":"Panda","year":"2018","journal-title":"3 Biotech."},{"key":"B33","doi-asserted-by":"crossref","DOI":"10.1126\/science.336.6081.534","volume-title":"Search for pore-fection","author":"Pennisi","year":"2012"},{"key":"B34","doi-asserted-by":"publisher","first-page":"234","DOI":"10.1038\/s43588-022-00231-2","article-title":"Towards practical and robust DNA-based data archiving using the yin\u2013yang codec system","volume":"2","author":"Ping","year":"2022","journal-title":"Nat. Comput. Sci."},{"key":"B35","first-page":"93","volume-title":"Dna to the rescue for data storage","author":"Ritter","year":"2015"},{"key":"B36","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/s41570-018-0051-5","article-title":"Encoding information into polymers","volume":"2","author":"Rutten","year":"2018","journal-title":"Nat. Rev. Chem."},{"key":"B37","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1093\/infdis\/158.6.1154","article-title":"Polymerase chain reaction","volume":"158","author":"Schochetman","year":"1988","journal-title":"J. Infect. Dis."},{"key":"B38","doi-asserted-by":"publisher","first-page":"1084","DOI":"10.1038\/nbt.2421","article-title":"The expanding scope of DNA sequencing","volume":"30","author":"Shendure","year":"2012","journal-title":"Nat. Biotechnol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"5361","DOI":"10.1038\/s41467-022-33046-w","article-title":"Robust data storage in DNA by de Bruijn graph-based de novo strand assembly","volume":"13","author":"Song","year":"2022","journal-title":"Nat. Commun."},{"key":"B40","doi-asserted-by":"publisher","first-page":"866","DOI":"10.1021\/acssynbio.7b00382","article-title":"Orthogonal information encoding in living cells with high error-tolerance, safety, and fidelity","volume":"7","author":"Song","year":"2018","journal-title":"ACS Synth. Biol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"5149","DOI":"10.1093\/nar\/20.19.5149","article-title":"Synthesis of oligodeoxyribonucleotides containing degenerate bases and their use as primers in the polymerase chain reaction","volume":"20","author":"Thoo","year":"1992","journal-title":"Nucleic acids Res."},{"key":"B42","doi-asserted-by":"crossref","first-page":"5504","DOI":"10.1021\/es025643o","article-title":"The 1.7 kilogram microchip: energy and material use in the production of semiconductor devices","volume":"36","author":"Williams","year":"2002","journal-title":"Environ. Sci. Technol."},{"key":"B43","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1145\/602421.602426","article-title":"Organic data memory using the DNA approach","volume":"46","author":"Wong","year":"2003","journal-title":"Commun. ACM"},{"key":"B49","doi-asserted-by":"publisher","first-page":"1326","DOI":"10.11999\/JEIT190863","article-title":"DNA storage and its research progress[J]","volume":"42","author":"Xu","year":"2020","journal-title":"J. Inf. Technol."},{"key":"B44","doi-asserted-by":"publisher","first-page":"230","DOI":"10.1109\/tmbmc.2016.2537305","article-title":"DNA-based storage: trends and methods","volume":"1","author":"Yazdi","year":"2015","journal-title":"IEEE Trans. Mol. Biol. Multi-Scale Commun."},{"key":"B45","doi-asserted-by":"crossref","DOI":"10.17487\/rfc3629","volume-title":"UTF-8, a transformation format of ISO 10646","author":"Yergeau","year":"2003"},{"key":"B46","doi-asserted-by":"publisher","first-page":"100871","DOI":"10.1016\/j.nantod.2020.100871","article-title":"Information stored in nanoscale: encoding data in a single dna strand with base 64","volume":"33","author":"Zhang","year":"2020","journal-title":"Nano Today"},{"key":"B47","doi-asserted-by":"publisher","first-page":"366","DOI":"10.1038\/nmat4594","article-title":"Nucleic acid memory","volume":"15","author":"Zhirnov","year":"2016","journal-title":"Nat. Mater."}],"container-title":["Frontiers in Bioinformatics"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1276934\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,10,15]],"date-time":"2023-10-15T07:56:39Z","timestamp":1697356599000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fbinf.2023.1276934\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,10,12]]},"references-count":50,"alternative-id":["10.3389\/fbinf.2023.1276934"],"URL":"https:\/\/doi.org\/10.3389\/fbinf.2023.1276934","relation":{},"ISSN":["2673-7647"],"issn-type":[{"type":"electronic","value":"2673-7647"}],"subject":[],"published":{"date-parts":[[2023,10,12]]},"article-number":"1276934"}}