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Hou Z, Qiang W, Wang X, Chen X, Hu X, Han X, Shen W, Zhang B, Xing P, Shi W, Dai J, Huang X, Zhao G. "Cell Disk" DNA Storage System Capable of Random Reading and Rewriting. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305921. [PMID: 38332565 PMCID: PMC11022697 DOI: 10.1002/advs.202305921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/23/2023] [Indexed: 02/10/2024]
Abstract
DNA has emerged as an appealing material for information storage due to its great storage density and durability. Random reading and rewriting are essential tasks for practical large-scale data storage. However, they are currently difficult to implement simultaneously in a single DNA-based storage system, strongly limiting their practicability. Here, a "Cell Disk" storage system is presented, achieving high-density in vivo DNA data storage that enables both random reading and rewriting. In this system, each yeast cell is used as a chamber to store information, similar to a "disk block" but with the ability to self-replicate. Specifically, each genome of yeast cell has a customized CRISPR/Cas9-based "lock-and-key" module inserted, which allows selective retrieval, erasure, or rewriting of the targeted cell "block" from a pool of cells ("disk"). Additionally, a codec algorithm with lossless compression ability is developed to improve the information density of each cell "block". As a proof of concept, target-specific reading and rewriting of the compressed data from a mimic cell "disk" comprising up to 105 "blocks" are demonstrated and achieve high specificity and reliability. The "Cell Disk" system described here concurrently supports random reading and rewriting, and it should have great scalability for practical data storage use.
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Affiliation(s)
- Zhaohua Hou
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Wei Qiang
- Shenzhen Key Laboratory of Synthetic GenomicsGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong518055P. R. China
| | - Xiangxiang Wang
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Xiaoxu Chen
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Xin Hu
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Xuye Han
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Wenlu Shen
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Bing Zhang
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Peng Xing
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Wenping Shi
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
| | - Junbiao Dai
- Shenzhen Key Laboratory of Synthetic GenomicsGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong518055P. R. China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenP. R. China
| | - Xiaoluo Huang
- Shenzhen Key Laboratory of Synthetic GenomicsGuangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenGuangdong518055P. R. China
| | - Guanghou Zhao
- School of Ecology and EnvironmentNorthwestern Polytechnical University1 Dongxiang Road, Chang'an DistrictXi'anShaanxi710129P. R. China
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Chen J, Shi W, Ren Y, Zhao K, Liu Y, Jia B, Zhao L, Li M, Liu Y, Su J, Ma C, Wang F, Sun J, Tian Y, Li J, Zhang H, Liu K. Strong Protein Adhesives through Lanthanide-enhanced Structure Folding and Stack Density. Angew Chem Int Ed Engl 2023; 62:e202304483. [PMID: 37670725 DOI: 10.1002/anie.202304483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
Generating strong adhesion by engineered proteins has the potential for high technical applications. Current studies of adhesive proteins are primarily limited to marine organisms, e.g., mussel adhesive proteins. Here, we present a modular engineering strategy to generate a type of exotic protein adhesives with super strong adhesion behaviors. In the protein complexes, the lanmodulin (LanM) underwent α-helical conformational transition induced by lanthanides, thereby enhancing the stacking density and molecular interactions of adhesive protein. The resulting adhesives exhibited outstanding lap-shear strength of ≈31.7 MPa, surpassing many supramolecular and polymer adhesives. The extreme temperature (-196 to 200 °C) resistance capacity and underwater adhesion performance can significantly broaden their practical application scenarios. Ex vivo and in vivo experiments further demonstrated the persistent adhesion performance for surgical sealing and healing applications.
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Affiliation(s)
- Jing Chen
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Weiwei Shi
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yubin Ren
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Kelu Zhao
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yangyi Liu
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Jia
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Lai Zhao
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Ming Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Juanjuan Su
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Ma
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Jing Sun
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Yang Tian
- School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Hongjie Zhang
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Xiangfu Laboratory, Jiaxing, 314102, China
| | - Kai Liu
- Engineering Research Center of Advanced Rare Earth Materials, Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- Xiangfu Laboratory, Jiaxing, 314102, China
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Xu C, Ma B, Dong X, Lei L, Hao Q, Zhao C, Liu H. Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing. ACS APPLIED MATERIALS & INTERFACES 2023; 15:24097-24108. [PMID: 37184884 DOI: 10.1021/acsami.3c01860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Xing Dong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Qing Hao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
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Liu Y, Ren Y, Li J, Wang F, Wang F, Ma C, Chen D, Jiang X, Fan C, Zhang H, Liu K. In vivo processing of digital information molecularly with targeted specificity and robust reliability. SCIENCE ADVANCES 2022; 8:eabo7415. [PMID: 35930647 PMCID: PMC9355361 DOI: 10.1126/sciadv.abo7415] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 06/22/2022] [Indexed: 05/28/2023]
Abstract
DNA has attracted increasing interest as an appealing medium for information storage. However, target-specific rewriting of the digital data stored in intracellular DNA remains a grand challenge because the highly repetitive nature and uneven guanine-cytosine content render the encoded DNA sequences poorly compatible with endogenous ones. In this study, a dual-plasmid system based on gene editing tools was introduced into Escherichia coli to process information accurately. Digital data containing large repeat units in binary codes, such as text, codebook, or image, were involved in the realization of target-specific rewriting in vivo, yielding up to 94% rewriting reliability. An optical reporter was introduced as an advanced tool for presenting data processing at the molecular level. Rewritten information was stored stably and amplified over hundreds of generations. Our work demonstrates a digital-to-biological information processing approach for highly efficient data storage, amplification, and rewriting, thus robustly promoting the application of DNA-based information technology.
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Affiliation(s)
- Yangyi Liu
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Fei Wang
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Chao Ma
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Dong Chen
- College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Southern University of Science and Technology, No. 1088 Xueyuan Road, Nanshan District, Shenzhen, Guangdong, China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, and Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, China
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, China
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Wei Z, Liu Y, Li B, Li J, Lu S, Xing X, Liu K, Wang F, Zhang H. Rare-earth based materials: an effective toolbox for brain imaging, therapy, monitoring and neuromodulation. LIGHT, SCIENCE & APPLICATIONS 2022; 11:175. [PMID: 35688804 PMCID: PMC9187711 DOI: 10.1038/s41377-022-00864-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Brain diseases, including tumors and neurodegenerative disorders, are among the most serious health problems. Non-invasively high-resolution imaging methods are required to gain anatomical structures and information of the brain. In addition, efficient diagnosis technology is also needed to treat brain disease. Rare-earth based materials possess unique optical properties, superior magnetism, and high X-ray absorption abilities, enabling high-resolution imaging of the brain through magnetic resonance imaging, computed tomography imaging, and fluorescence imaging technologies. In addition, rare-earth based materials can be used to detect, treat, and regulate of brain diseases through fine modulation of their structures and functions. Importantly, rare-earth based materials coupled with biomolecules such as antibodies, peptides, and drugs can overcome the blood-brain barrier and be used for targeted treatment. Herein, this review highlights the rational design and application of rare-earth based materials in brain imaging, therapy, monitoring, and neuromodulation. Furthermore, the development prospect of rare-earth based materials is briefly introduced.
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Affiliation(s)
- Zheng Wei
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Bo Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Jingjing Li
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
| | - Shuang Lu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Xiwen Xing
- Department of Biotechnology, College of Life Science and Technology, Jinan University, Guangzhou, 510632, China.
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China.
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, 230026, China
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
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