Citation: | ZAN Xiangzhen, YAO Xiangyu, XU Peng, BAO Zhenshen, LI Xianbin, LI Xiaoyan, LIU Wenbin. A Survey on File Architecture in DNA Storage[J]. Journal of Electronics & Information Technology, 2023, 45(6): 1911-1920. doi: 10.11999/JEIT220561 |
[1] |
ZHIRNOV V, ZADEGAN R M, SANDHU G S, et al. Nucleic acid memory[J]. Nature Materials, 2016, 15(4): 366–370. doi: 10.1038/nmat4594
|
[2] |
沈鹏, 李颢, 孙清江, 等. DNA存储技术[J]. 生命科学仪器, 2020, 18(2): 3–13,39. doi: 10.11967/2020180401
SHEN Peng, LI Hao, SUN Qingjiang, et al. Advance of data storage using DNA[J]. Life Science Instruments, 2020, 18(2): 3–13,39. doi: 10.11967/2020180401
|
[3] |
PANDA D, MOLLA K A, BAIG M J, et al. DNA as a digital information storage device: Hope or hype?[J]. 3 Biotech, 2018, 8(5): 239. doi: 10.1007/s13205-018-1246-7
|
[4] |
许鹏, 方刚, 石晓龙, 等. DNA存储及其研究进展[J]. 电子与信息学报, 2020, 42(6): 1326–1331. doi: 10.11999/JEIT190863
XU Peng, FANG Gang, SHI Xiaolong, et al. DNA storage and its research progress[J]. Journal of Electronics &Information Technology, 2020, 42(6): 1326–1331. doi: 10.11999/JEIT190863
|
[5] |
CEZE L, NIVALA J, and STRAUSS K. Molecular digital data storage using DNA[J]. Nature Reviews Genetics, 2019, 20(8): 456–466. doi: 10.1038/s41576-019-0125-3
|
[6] |
CHURCH G M, GAO Yuan, and KOSURI S. Next-generation digital information storage in DNA[J]. Science, 2012, 337(6102): 1628. doi: 10.1126/science.1226355
|
[7] |
ORGANICK L, ANG S D, CHEN Y J, et al. Random access in large-scale DNA data storage[J]. Nature Biotechnology, 2018, 36(3): 242–248. doi: 10.1038/nbt.4079
|
[8] |
ZHANG Yinan, WANG Fei, CHAO Jie, et al. DNA origami cryptography for secure communication[J]. Nature Communications, 2019, 10(1): 5469. doi: 10.1038/s41467-019-13517-3
|
[9] |
SONG Xin, SHAH S, and REIF J. Multidimensional data organization and random access in large-scale DNA storage systems[J]. Theoretical Computer Science, 2021, 894: 190–202. doi: 10.1016/j.tcs.2021.09.021
|
[10] |
TOMEK K J, VOLKEL K, SIMPSON A, et al. Driving the scalability of DNA-based information storage systems[J]. ACS Synthetic Biology, 2019, 8(6): 1241–1248. doi: 10.1021/acssynbio.9b00100
|
[11] |
WINSTON C, ORGANICK L, WARD D, et al. Combinatorial PCR method for efficient, selective oligo retrieval from complex oligo pools[J]. ACS Synthetic Biology, 2022, 11(5): 1727–1734. doi: 10.1021/acssynbio.1c00482
|
[12] |
YAZDI S M H T, YUAN Yongbo, MA Jian, et al. A rewritable, random-access DNA-based storage system[J]. Scientific Reports, 2015, 5(1): 14138. doi: 10.1038/srep14138
|
[13] |
YAZDI S M H T, GABRYS R, and MILENKOVIC O. Portable and error-free DNA-based data storage[J]. Scientific Reports, 2017, 7(1): 5011. doi: 10.1038/s41598-017-05188-1
|
[14] |
陈为刚, 黄刚, 李炳志, 等. 音视频文件的DNA信息存储[J]. 中国科学:生命科学, 2020, 50(1): 81–85. doi: 10.1360/ssv-2019-0211
CHEN Weigang, HUANG Gang, LI Bingzhi, et al. DNA information storage for audio and video files[J]. Scientia Sinica Vitae, 2020, 50(1): 81–85. doi: 10.1360/ssv-2019-0211
|
[15] |
NEWMAN S, STEPHENSON A P, WILLSEY M, et al. High density DNA data storage library via dehydration with digital microfluidic retrieval[J]. Nature Communications, 2019, 10(1): 1706. doi: 10.1038/s41467-019-09517-y
|
[16] |
ANTKOWIAK P L, KOCH J, NGUYEN B H, et al. Integrating DNA encapsulates and digital microfluidics for automated data storage in DNA[J]. Small, 2022, 18(15): 2107381. doi: 10.1002/smll.202107381
|
[17] |
BANAL J L, SHEPHERD T R, BERLEANT J, et al. Random access DNA memory using Boolean search in an archival file storage system[J]. Nature Materials, 2021, 20(9): 1272–1280. doi: 10.1038/s41563-021-01021-3
|
[18] |
YAMAMOTO M, KASHIWAMURA S, OHUCHI A, et al. Large-scale DNA memory based on the nested PCR[J]. Natural Computing, 2008, 7(3): 335–346. doi: 10.1007/s11047-008-9076-x
|
[19] |
LIN K N, VOLKEL K, TUCK J M, et al. Dynamic and scalable DNA-based information storage[J]. Nature Communications, 2020, 11(1): 2981. doi: 10.1038/s41467-020-16797-2
|
[20] |
BEE C, CHEN Y J, QUEEN M, et al. Molecular-level similarity search brings computing to DNA data storage[J]. Nature Communications, 2021, 12(1): 4764. doi: 10.1038/s41467-021-24991-z
|
[21] |
TOMEK K J, VOLKEL K, INDERMAUR E W, et al. Promiscuous molecules for smarter file operations in DNA-based data storage[J]. Nature Communications, 2021, 12(1): 3518. doi: 10.1038/s41467-021-23669-w
|
[22] |
HAO Min, QIAO Hongyan, GAO Yanmin, et al. A mixed culture of bacterial cells enables an economic DNA storage on a large scale[J]. Communications Biology, 2020, 3: 416. doi: 10.1038/s42003-020-01141-7
|
[23] |
ZHANG Yi, KONG Linlin, WANG Fei, et al. Information stored in nanoscale: Encoding data in a single DNA strand with Base64[J]. Nano Today, 2020, 33: 100871. doi: 10.1016/j.nantod.2020.100871
|
[24] |
LEE U J, HWANG S, KIM K E, et al. DNA data storage in Perl[J]. Biotechnology and Bioprocess Engineering, 2020, 25(4): 607–615. doi: 10.1007/s12257-020-0022-9
|
[25] |
SHIPMAN S L, NIVALA J, MACKLIS J D, et al. CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria[J]. Nature, 2017, 547(7663): 345–349. doi: 10.1038/nature23017
|
[26] |
CHEN Y J, TAKAHASHI C N, ORGANICK L, et al. Quantifying molecular bias in DNA data storage[J]. Nature Communications, 2020, 11(1): 3264. doi: 10.1038/s41467-020-16958-3
|
[27] |
ERLICH Y and ZIELINSKI D. DNA Fountain enables a robust and efficient storage architecture[J]. Science, 2017, 355(6328): 950–954. doi: 10.1126/science.aaj2038
|
[28] |
GAO Yanmin, CHEN Xin, QIAO Hongyan, et al. Low-bias manipulation of DNA oligo pool for robust data storage[J]. ACS Synthetic Biology, 2020, 9(12): 3344–3352. doi: 10.1021/acssynbio.0c00419
|
[29] |
CHEN Weigang, HAN Mingzhe, ZHOU Jianting, et al. An artificial chromosome for data storage[J]. National Science Review, 2021, 8(5): 62–70. doi: 10.1093/nsr/nwab028
|
[30] |
郜艳敏, 唐梦童, 刘倩, 等. DNA信息存储中关键生化方法的研究[J]. 合成生物学, 2021, 2(3): 384–398. doi: 10.12211/2096-8280.2020-085
GAO Yanmin, TANG Mengtong, LIU Qian, et al. The pivotal biochemical methods in DNA data storage[J]. Synthetic Biology Journal, 2021, 2(3): 384–398. doi: 10.12211/2096-8280.2020-085
|
[31] |
MAKAROVA K S, GRISHIN N V, SHABALINA S A, et al. A putative RNA-interference-based immune system in prokaryotes: Computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action[J]. Biology Direct, 2006, 1: 7. doi: 10.1186/1745-6150-1-7
|
[32] |
BRYKSIN A V and MATSUMURA I. Overlap extension PCR cloning: A simple and reliable way to create recombinant plasmids[J]. Biotechniques, 2010, 48(6): 463–464. doi: 10.2144/000113418
|
[33] |
SETLOW J K and SETLOW R B. Nature of the photoreactivable ultra-violet lesion in deoxyribonucleic acid[J]. Nature, 1963, 197(4867): 560–562. doi: 10.1038/197560a0
|
[34] |
OLIVIER M, AGGARWAL A, ALLEN J, et al. A high-resolution radiation hybrid map of the human genome draft sequence[J]. Science, 2001, 291(5507): 1298–1302. doi: 10.1126/science.1057437
|
[35] |
HEYROVSKA R. New insight into DNA damage by cisplatin at the atomic scale[J/OL]. Nature Precedings, 2012.
|
[36] |
KIM J, BAE J H, BAYM M, et al. Metastable hybridization-based DNA information storage to allow rapid and permanent erasure[J]. Nature Communications, 2020, 11(1): 5008. doi: 10.1038/s41467-020-18842-6
|
[37] |
昝乡镇, 姚翔宇, 许鹏, 等. DNA存储中的纠错方法综述[J]. 广州大学学报(自然科学版), 2021, 20(2): 13–22. doi: 10.3969/j.issn.1671-4229.2021.02.002
ZAN Xiangzhen, YAO Xiangyu, XU Peng, et al. A survey on error correcting algorithms in DNA storage[J]. Journal of Guangzhou University (Natural Science Edition), 2021, 20(2): 13–22. doi: 10.3969/j.issn.1671-4229.2021.02.002
|
[38] |
HECKEL R, MIKUTIS G, and GRASS R N. A characterization of the DNA data storage channel[J]. Scientific Reports, 2018, 9: 9663. doi: 10.1038/s41598-019-45832-6
|
[39] |
BORNHOLT J, LOPEZ R, CARMEAN D M, et al. Toward a DNA-based archival storage system[J]. IEEE Micro, 2017, 37(3): 98–104. doi: 10.1109/MM.2017.70
|
[40] |
WANG Yixin, NOOR-A-RAHIM M, ZHANG Jingyun, et al. High capacity DNA data storage with variable-length Oligonucleotides using repeat accumulate code and hybrid mapping[J]. Journal of Biological Engineering, 2019, 13: 89. doi: 10.1186/s13036-019-0211-2
|
[41] |
MEISER L C, ANTKOWIAK P L, KOCH J, et al. Reading and writing digital data in DNA[J]. Nature Protocols, 2019, 15(1): 86–101. doi: 10.1038/s41596-019-0244-5
|
[42] |
GRASS R N, HECKEL R, PUDDU M, et al. Robust chemical preservation of digital information on DNA in silica with error‐correcting codes[J]. Angewandte Chemie International Edition, 2015, 54(8): 2552–2555. doi: 10.1002/anie.201411378
|
[43] |
GOLDMAN N, BERTONE P, CHEN Siyuan, et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA[J]. Nature, 2013, 494(7435): 77–80. doi: 10.1038/nature11875
|
[44] |
ANTKOWIAK P L, LIETARD J, DARESTANI M Z, et al. Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction[J]. Nature Communications, 2020, 11(1): 5345. doi: 10.1038/s41467-020-19148-3
|
[45] |
陈为刚, 葛奇, 王盼盼, 等. 细胞内大片段DNA数据存储的多RS码交织编码[J]. 合成生物学, 2021, 2(3): 428–443. doi: 10.12211/2096-8280.2020-023
CHEN Weigang, GE Qi, WANG Panpan, et al. Multiple interleaved RS codes for data storage using up to Mb-scale synthetic DNA in living cells[J]. Synthetic Biology Journal, 2021, 2(3): 428–443. doi: 10.12211/2096-8280.2020-023
|
[46] |
ZHANG Shufang and PENG Kang. DNA information storage technology based on raptor code[J]. Laser & Optoelectronics Progress, 2020, 57(15): 151701. doi: 10.3788/Lop57.151701
|
[47] |
CHEN Weigang, WANG Lixia, HAN Mingzhe, et al. Sequencing barcode construction and identification methods based on block error-correction codes[J]. Science China Life Sciences, 2020, 63(10): 1580–1592. doi: 10.1007/s11427-019-1651-3
|
[48] |
BLAWAT M, GAEDKE K, HÜTTER I, et al. Forward error correction for DNA data storage[J]. Procedia Computer Science, 2016, 80: 1011–1022. doi: 10.1016/j.procs.2016.05.398
|
[49] |
DENG Li, WANG Yixin, NOOR-A-RAHIM M, et al. Optimized code design for constrained DNA data storage with asymmetric errors[J]. IEEE Access, 2019, 7: 84107–84121. doi: 10.1109/Access.2019.2924827
|
[50] |
XUE Tianbo and LAU F C M. Notice of violation of IEEE publication principles: Construction of GC-balanced DNA with deletion/insertion/mutation error correction for DNA storage system[J]. IEEE Access, 2020, 8: 140972–140980. doi: 10.1109/Access.2020.3012688
|
[51] |
PRESS W H, HAWKINS J A, JONES S K JR, et al. HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints[J]. Proceedings of the National Academy of Sciences of the United States of America, 2020, 117(31): 18489–18496. doi: 10.1073/pnas.2004821117
|
[52] |
SONG Lifu, GENG Feng, GONG Ziyi, et al. Super-robust data storage in DNA by de Bruijn graph-based decoding[Z]. bioRxiv, 2020.
|
[53] |
LENZ A, MAAROUF I, WELTER L, et al. Concatenated codes for recovery from multiple reads of DNA sequences[C]. 2020 IEEE Information Theory Workshop (ITW), Riva del Garda, Italy, 2020.
|
[54] |
DAVEY M C and MACKAY D J C. Reliable communication over channels with insertions, deletions, and substitutions[J]. IEEE Transactions on Information Theory, 2001, 47(2): 687–698. doi: 10.1109/18.910582
|
[55] |
ZAN Xiangzhen, YAO Xiangyu, XU Peng, et al. A hierarchical error correction strategy for text DNA storage[J]. Interdisciplinary Sciences:Computational Life Sciences, 2022, 14(1): 141–150. doi: 10.1007/s12539-021-00476-x
|
[56] |
ZAN Xiangzhen, XIE Ranze, YAO Xiangyu, et al. A robust and efficient DNA storage architecture based on modulation encoding and decoding[Z]. bioRxiv, 2022.
|
[57] |
YANG Jing, MA Jingjing, LIU Shi, et al. A molecular cryptography model based on structures of DNA self-assembly[J]. Chinese Science Bulletin, 2014, 59(11): 1192–1198. doi: 10.1007/s11434-014-0170-4
|
[58] |
ZAKERI B, CARR P A, and LU T K. Multiplexed sequence encoding: A framework for DNA communication[J]. PLoS One, 2016, 11(4): e0152774. doi: 10.1371/journal.pone.0152774
|
[59] |
PENG Weiping, CUI Shuang, and SONG Cheng. One-time-pad cipher algorithm based on confusion mapping and DNA storage technology[J]. PLoS One, 2021, 16(1): e0245506. doi: 10.1371/journal.pone.0245506
|
[60] |
GRASS R N, HECKEL R, DESSIMOZ C, et al. Genomic encryption of digital data stored in synthetic DNA[J]. Angewandte Chemie International Edition, 2020, 59(22): 8476–8480. doi: 10.1002/anie.202001162
|