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Cao B, Zheng Y, Shao Q, Liu Z, Xie L, Zhao Y, Wang B, Zhang Q, Wei X. Efficient data reconstruction: The bottleneck of large-scale application of DNA storage. Cell Rep 2024; 43:113699. [PMID: 38517891 DOI: 10.1016/j.celrep.2024.113699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 03/24/2024] Open
Abstract
Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.
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Affiliation(s)
- Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China; Centre for Frontier AI Research, Agency for Science, Technology, and Research (A(∗)STAR), 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
| | - Qi Shao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Zhenlu Liu
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Lei Xie
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Yunzhu Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China.
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
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2
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Gomes CP, Martins AGC, Nunes SE, Ramos B, Wisinewski HR, Reis JLMS, Lima AP, Aoyagi TY, Goncales I, Maia DS, Tunussi AS, Menossi MS, Pereira SM, Turrini PCG, Gervasio JHDB, Verona BM, Cerize NNP. Coding, Decoding and Retrieving a Message Using DNA: An Experience from a Brazilian Center Research on DNA Data Storage. MICROMACHINES 2024; 15:474. [PMID: 38675287 PMCID: PMC11051810 DOI: 10.3390/mi15040474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/21/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024]
Abstract
DNA data storage based on synthetic oligonucleotides is a major attraction due to the possibility of storage over long periods. Nowadays, the quantity of data generated has been growing exponentially, and the storage capacity needs to keep pace with the growth caused by new technologies and globalization. Since DNA can hold a large amount of information with a high density and remains stable for hundreds of years, this technology offers a solution for current long-term data centers by reducing energy consumption and physical storage space. Currently, research institutes, technology companies, and universities are making significant efforts to meet the growing need for data storage. DNA data storage is a promising field, especially with the advancement of sequencing techniques and equipment, which now make it possible to read genomes (i.e., to retrieve the information) and process this data easily. To overcome the challenges associated with developing new technologies for DNA data storage, a message encoding and decoding exercise was conducted at a Brazilian research center. The exercise performed consisted of synthesizing oligonucleotides by the phosphoramidite route. An encoded message, using a coding scheme that adheres to DNA sequence constraints, was synthesized. After synthesis, the oligonucleotide was sequenced and decoded, and the information was fully recovered.
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Affiliation(s)
- Caio P. Gomes
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - André G. C. Martins
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Sabrina E. Nunes
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Bruno Ramos
- Microfluidic & Photoelectrocatalytic Engineering Group, Department of Chemical Engineering, FEI University Center, São Bernardo do Campo 09850-901, SP, Brazil;
| | - Henrique R. Wisinewski
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - João L. M. S. Reis
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Ariel P. Lima
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Thiago Y. Aoyagi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Icaro Goncales
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Danilo S. Maia
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Ariane S. Tunussi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Marília S. Menossi
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Sergio M. Pereira
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Paula C. G. Turrini
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - João H. D. B. Gervasio
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Bruno M. Verona
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
| | - Natalia N. P. Cerize
- Bionanomanufacturing Center, Institute for Technological Research—IPT, Sao Paulo 05508-901, SP, Brazil; (A.G.C.M.); (S.E.N.); (H.R.W.); (J.L.M.S.R.); (A.P.L.); (T.Y.A.); (I.G.); (D.S.M.); (A.S.T.); (M.S.M.); (S.M.P.J.); (P.C.G.T.); (B.M.V.); (N.N.P.C.)
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3
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Zheng Y, Cao B, Zhang X, Cui S, Wang B, Zhang Q. DNA-QLC: an efficient and reliable image encoding scheme for DNA storage. BMC Genomics 2024; 25:266. [PMID: 38461245 PMCID: PMC10925009 DOI: 10.1186/s12864-024-10178-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/01/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND DNA storage has the advantages of large capacity, long-term stability, and low power consumption relative to other storage mediums, making it a promising new storage medium for multimedia information such as images. However, DNA storage has a low coding density and weak error correction ability. RESULTS To achieve more efficient DNA storage image reconstruction, we propose DNA-QLC (QRes-VAE and Levenshtein code (LC)), which uses the quantized ResNet VAE (QRes-VAE) model and LC for image compression and DNA sequence error correction, thus improving both the coding density and error correction ability. Experimental results show that the DNA-QLC encoding method can not only obtain DNA sequences that meet the combinatorial constraints, but also have a net information density that is 2.4 times higher than DNA Fountain. Furthermore, at a higher error rate (2%), DNA-QLC achieved image reconstruction with an SSIM value of 0.917. CONCLUSIONS The results indicate that the DNA-QLC encoding scheme guarantees the efficiency and reliability of the DNA storage system and improves the application potential of DNA storage for multimedia information such as images.
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Affiliation(s)
- Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, DalianLiaoning, 116024, China
| | - Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, DalianLiaoning, 116024, China
| | - Xiaokang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, DalianLiaoning, 116024, China
| | - Shuang Cui
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, DalianLiaoning, 116024, China
| | - Bin Wang
- The Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, DalianLiaoning, 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, DalianLiaoning, 116024, China.
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4
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Shah A, Pathak S, Li K, Garaj S, Bazant MZ, Gupta A, Doyle PS. A Universal Approximation for Conductance Blockade in Thin Nanopore Membranes. NANO LETTERS 2024. [PMID: 38437028 DOI: 10.1021/acs.nanolett.3c04997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
Nanopore-based sensing platforms have transformed single-molecule detection and analysis. The foundation of nanopore translocation experiments lies in conductance measurements, yet existing models, which are largely phenomenological, are inaccurate in critical experimental conditions such as thin and tightly fitting pores. Of the two components of the conductance blockade, channel and access resistance, the access resistance is poorly modeled. We present a comprehensive investigation of the access resistance and associated conductance blockade in thin nanopore membranes. By combining a first-principles approach, multiscale modeling, and experimental validation, we propose a unified theoretical modeling framework. The analytical model derived as a result surpasses current approaches across a broad parameter range. Beyond advancing our theoretical understanding, our framework's versatility enables analyte size inference and predictive insights into conductance blockade behavior. Our results will facilitate the design and optimization of nanopore devices for diverse applications, including nanopore base calling and data storage.
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Affiliation(s)
- Arjav Shah
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Shakul Pathak
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Kun Li
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
| | - Slaven Garaj
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
- Department of Physics, National University of Singapore, Singapore 119077
| | - Martin Z Bazant
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
| | - Patrick S Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Singapore-MIT Alliance for Research and Technology Centre, Singapore 138602
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5
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Liu Z, Rong G, Dong H, Zhang Y, Xu M, Baoxian Ye, Zhou Y. Ratiometric electrochemical biosensor based on lateral movement of multi-pedal DNA tetrahedron machine on biomimetic interface. Talanta 2024; 269:125454. [PMID: 38029606 DOI: 10.1016/j.talanta.2023.125454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 09/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
In this work, a lateral moving multi-pedal DNA tetrahedron machine (MTM) is designed and coupled with dual-signal output system to construct a biomimetic electrochemical ratiometric strategy for ultrasensitive target DNA analysis. The tetrahedral structure provided rigid support for the pedal, ensuring efficient replacement of the rail chain modified with ferrocene. By conjugating cholesterol molecules to one vertex of MTM, it is decorated on a lipid bilayer. This molecular architecture confers lateral movement of MTM on an electrode surface while prevents its detachment from the system. The methylene blue tagged hairpin probe provides constant power to support MTM swim on lipid bilayer. Compared with the conventional motion mode, the lateral moving mechanism has the fastest reaction rate and the highest signal-to-noise ratio. Additionally, the dual-signal reporting system further improves the accuracy of target detection on the basis of ensuring motion efficiency. The work improved movement efficiency and shortened time fragment. A linear relationship between the ratio value of two reporters and target DNA concentration was observed from 0.5 fM to 50 pM with a detection limit of 28 aM. The lateral motion mode of DNA machine coalescing with ratiometric system made this sensing platform ultrasensitive and accurate, which holds new avenue of early diagnosis.
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Affiliation(s)
- Zi Liu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China.
| | - Guoxiang Rong
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Hui Dong
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Yintang Zhang
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Maotian Xu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China
| | - Baoxian Ye
- College of Chemistry, Green Catalysis Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yanli Zhou
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu, 476000, PR China.
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6
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Sandler SE, Weckman NE, Yorke S, Das A, Chen K, Gutierrez R, Keyser UF. Sensing the DNA-mismatch tolerance of catalytically inactive Cas9 via barcoded DNA nanostructures in solid-state nanopores. Nat Biomed Eng 2024; 8:325-334. [PMID: 37550424 DOI: 10.1038/s41551-023-01078-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 06/30/2023] [Indexed: 08/09/2023]
Abstract
Single-molecule quantification of the strength and sequence specificity of interactions between proteins and nucleic acids would facilitate the probing of protein-DNA binding. Here we show that binding events between the catalytically inactive Cas9 ribonucleoprotein and any pre-defined short sequence of double-stranded DNA can be identified by sensing changes in ionic current as suitably designed barcoded linear DNA nanostructures with Cas9-binding double-stranded DNA overhangs translocate through solid-state nanopores. We designed barcoded DNA nanostructures to study the relationships between DNA sequence and the DNA-binding specificity, DNA-binding efficiency and DNA-mismatch tolerance of Cas9 at the single-nucleotide level. Nanopore-based sensing of DNA-barcoded nanostructures may help to improve the design of efficient and specific ribonucleoproteins for biomedical applications, and could be developed into sensitive protein-sensing assays.
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Affiliation(s)
- Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | - Nicole E Weckman
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Institute for Studies in Transdisciplinary Engineering Education & Practice, Department of Chemical Engineering & Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sarah Yorke
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
- Yusuf Hamied Department of Chemistry, Cambridge, UK
| | - Akashaditya Das
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, Cambridge, UK
| | | | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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7
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Yang S, Bögels BWA, Wang F, Xu C, Dou H, Mann S, Fan C, de Greef TFA. DNA as a universal chemical substrate for computing and data storage. Nat Rev Chem 2024; 8:179-194. [PMID: 38337008 DOI: 10.1038/s41570-024-00576-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
DNA computing and DNA data storage are emerging fields that are unlocking new possibilities in information technology and diagnostics. These approaches use DNA molecules as a computing substrate or a storage medium, offering nanoscale compactness and operation in unconventional media (including aqueous solutions, water-in-oil microemulsions and self-assembled membranized compartments) for applications beyond traditional silicon-based computing systems. To build a functional DNA computer that can process and store molecular information necessitates the continued development of strategies for computing and data storage, as well as bridging the gap between these fields. In this Review, we explore how DNA can be leveraged in the context of DNA computing with a focus on neural networks and compartmentalized DNA circuits. We also discuss emerging approaches to the storage of data in DNA and associated topics such as the writing, reading, retrieval and post-synthesis editing of DNA-encoded data. Finally, we provide insights into how DNA computing can be integrated with DNA data storage and explore the use of DNA for near-memory computing for future information technology and health analysis applications.
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Affiliation(s)
- Shuo Yang
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Bas W A Bögels
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Can Xu
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Hongjing Dou
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China
| | - Stephen Mann
- State Key Laboratory of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Zhangjiang Institute for Advanced Study (ZIAS), Shanghai Jiao Tong University, Shanghai, China.
- Centre for Protolife Research and Centre for Organized Matter Chemistry, School of Chemistry, University of Bristol, Bristol, UK.
- Max Planck-Bristol Centre for Minimal Biology, School of Chemistry, University of Bristol, Bristol, UK.
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Tom F A de Greef
- Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, The Netherlands.
- Computational Biology Group, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.
- Institute for Molecules and Materials, Radboud University, Nijmegen, The Netherlands.
- Center for Living Technologies, Eindhoven-Wageningen-Utrecht Alliance, Utrecht, The Netherlands.
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8
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [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: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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9
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Akash A, Bencurova E, Dandekar T. How to make DNA data storage more applicable. Trends Biotechnol 2024; 42:17-30. [PMID: 37591721 DOI: 10.1016/j.tibtech.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/19/2023]
Abstract
The storage of digital data is becoming a worldwide problem. DNA has been recognized as a biological solution due to its ability to store genetic information without alteration over long periods. The first demonstrations of high-capacity long-lasting DNA digital data storage have been shown. However, high storage costs and slow retrieval of the data must be overcome to make DNA data storage more applicable and marketable. Herein, we discuss the issues and recent advances in DNA data storage methods and highlight pathways to make this technology more applicable to real-world digital data storage. We envision that a combination of molecular biology, nanotechnology, novel polymers, electronics, and automation with systematic development will allow DNA data storage sufficient for everyday use.
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Affiliation(s)
- Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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10
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Mao R, Minevich B, McKeen D, Chen Q, Lu F, Gang O, Mittal J. Regulating phase behavior of nanoparticle assemblies through engineering of DNA-mediated isotropic interactions. Proc Natl Acad Sci U S A 2023; 120:e2302037120. [PMID: 38109548 PMCID: PMC10756293 DOI: 10.1073/pnas.2302037120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 11/14/2023] [Indexed: 12/20/2023] Open
Abstract
Self-assembly of isotropically interacting particles into desired crystal structures could allow for creating designed functional materials via simple synthetic means. However, the ability to use isotropic particles to assemble different crystal types remains challenging, especially for generating low-coordinated crystal structures. Here, we demonstrate that isotropic pairwise interparticle interactions can be rationally tuned through the design of DNA shells in a range that allows transition from common, high-coordinated FCC-CuAu and BCC-CsCl lattices, to more exotic symmetries for spherical particles such as the SC-NaCl lattice and to low-coordinated crystal structures (i.e., cubic diamond, open honeycomb). The combination of computational and experimental approaches reveals such a design strategy using DNA-functionalized nanoparticles and successfully demonstrates the realization of BCC-CsCl, SC-NaCl, and a weakly ordered cubic diamond phase. The study reveals the phase behavior of isotropic nanoparticles for DNA-shell tunable interaction, which, due to the ease of synthesis is promising for the practical realization of non-close-packed lattices.
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Affiliation(s)
- Runfang Mao
- Department of Chemical Engineering and Materials Science, University of Minnesota–Twin Cities, Minneapolis, MN55455
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, NY10027
| | - Daniel McKeen
- Department of Chemical Engineering, Columbia University, New York, NY10027
| | - Qizan Chen
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
| | - Fang Lu
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY11973
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, NY10027
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, NY11973
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY10027
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX77843
- Department of Chemistry, Texas A&M University, College Station, TX77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX77843
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11
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Zheng F, Alawami M, Zhu J, Platnich CM, Sha J, Keyser UF, Chen K. DNA Carrier-Assisted Molecular Ping-Pong in an Asymmetric Nanopore. NANO LETTERS 2023; 23:11145-11151. [PMID: 38033205 PMCID: PMC10722531 DOI: 10.1021/acs.nanolett.3c03605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 11/28/2023] [Accepted: 11/28/2023] [Indexed: 12/02/2023]
Abstract
Nanopore analysis relies on ensemble averaging of translocation signals obtained from numerous molecules, requiring a relatively high sample concentration and a long turnaround time from the sample to results. The recapture and subsequent re-reading of the same molecule is a promising alternative that enriches the signal information from a single molecule. Here, we describe how an asymmetric nanopore improves molecular ping-pong by promoting the recapture of the molecule in the trans reservoir. We also demonstrate that the molecular recapture could be improved by linking the target molecule to a long DNA carrier to reduce the diffusion, thereby achieving over 100 recapture events. Using this ping-pong methodology, we demonstrate its use in accurately resolving nanostructure motifs along a DNA scaffold through repeated detection. Our method offers novel insights into the control of DNA polymer dynamics within nanopore confinement and opens avenues for the development of a high-fidelity DNA detection platform.
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Affiliation(s)
- Fei Zheng
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Mohammed Alawami
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, Dalian 116024, China
| | - Casey M Platnich
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-Nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211100, China
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
| | - Kaikai Chen
- Cavendish Laboratory, University of Cambridge, CB3 0HE Cambridge, United Kingdom
- School of Nanoscience and Nanotechnology, University of Chinese Academy of Sciences, Beijing 101408, China
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12
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Yu M, Lim D, Kim J, Song Y. Processing DNA Storage through Programmable Assembly in a Droplet-Based Fluidics System. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303197. [PMID: 37755129 PMCID: PMC10646262 DOI: 10.1002/advs.202303197] [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: 05/18/2023] [Revised: 07/11/2023] [Indexed: 09/28/2023]
Abstract
DNA can be used to store digital data, and synthetic short-sequence DNA pools are developed to store high quantities of digital data. However, synthetic DNA data cannot be actively processed in DNA pools. An active DNA data editing process is developed using splint ligation in a droplet-controlled fluidics (DCF) system. DNA fragments of discrete sizes (100-500 bps) are synthesized for droplet assembly, and programmed sequence information exchange occurred. The encoded DNA sequences are processed in series and parallel to synthesize the determined DNA pools, enabling random access using polymerase chain reaction amplification. The sequencing results of the assembled DNA data pools can be orderly aligned for decoding and have high fidelity through address primer scanning. Furthermore, eight 90 bps DNA pools with pixel information (png: 0.27-0.28 kB), encoded by codons, are synthesized to create eight 270 bps DNA pools with an animation movie chip file (mp4: 12 kB) in the DCF system.
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Affiliation(s)
- Minsang Yu
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
| | - Doyeon Lim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Jungwoo Kim
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
| | - Youngjun Song
- Standard Bioelectronics. Co., 511 Michuhol Tower, Gaetbeol-ro 12, Incheon, 21999, South Korea
- Department of Nano-Bioengineering, Incheon National University, Academy-ro 119, Incheon, 22012, South Korea
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13
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Yang J, Wang J, Liu X, Chen Y, Liang Y, Wang Q, Jiang S, Zhang C. Translocation of Proteins through Solid-State Nanopores Using DNA Polyhedral Carriers. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2303715. [PMID: 37496044 DOI: 10.1002/smll.202303715] [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: 05/03/2023] [Revised: 07/11/2023] [Indexed: 07/28/2023]
Abstract
The detection of biomolecules at the single molecule level has important applications in the fields of biosensing and biomedical diagnosis. The solid-state nanopore (SS nanopore) is a sensitive tool for detecting single molecules because of its unique label-free and low sample consumption properties. SS nanopore translocation of small biomolecules is typically driven by an electronic field force and is thus influenced by the charge, shape, and size of the target molecules. Therefore, it remains challenging to control the translocation of biomolecules through SS nanopores, particularly for different proteins with complex conformations and unique charges. Toward this problem, a DNA polyhedral carrier coating strategy to assist protein translocation through SS nanopores is developed, which facilitates target protein detection. The current signal-to-noise ratios are improved significantly using this DNA carrier loading strategy. The proposed method should aid the detection of proteins, which are difficult to translocate through nanopores. This coating-assisted method offers a wide range of applications for SS nanopore detection and promotes the development of single-molecule detection.
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Affiliation(s)
- Jing Yang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Juan Wang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Xuan Liu
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yiming Chen
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
| | - Yuan Liang
- School of Control and Computer Engineering, North China Electric Power University, Beijing, 102206, China
| | - Qi Wang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Shuoxing Jiang
- Department of Biomedical Engineering, College of Engineering and Applied Sciences, Nanjing University, Nanjing, Jiangsu, 210023, China
| | - Cheng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, 100871, China
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14
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Solanki A, Griffin Z, Sutradhar PR, Pradhan K, Merritt C, Ganguly A, Riedel M. Neural network execution using nicked DNA and microfluidics. PLoS One 2023; 18:e0292228. [PMID: 37856428 PMCID: PMC10586678 DOI: 10.1371/journal.pone.0292228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/17/2023] [Indexed: 10/21/2023] Open
Abstract
DNA has been discussed as a potential medium for data storage. Potentially it could be denser, could consume less energy, and could be more durable than conventional storage media such as hard drives, solid-state storage, and optical media. However, performing computations on the data stored in DNA is a largely unexplored challenge. This paper proposes an integrated circuit (IC) based on microfluidics that can perform complex operations such as artificial neural network (ANN) computation on data stored in DNA. We envision such a system to be suitable for highly dense, throughput-demanding bio-compatible applications such as an intelligent Organ-on-Chip or other biomedical applications that may not be latency-critical. It computes entirely in the molecular domain without converting data to electrical form, making it a form of in-memory computing on DNA. The computation is achieved by topologically modifying DNA strands through the use of enzymes called nickases. A novel scheme is proposed for representing data stochastically through the concentration of the DNA molecules that are nicked at specific sites. The paper provides details of the biochemical design, as well as the design, layout, and operation of the microfluidics device. Benchmarks are reported on the performance of neural network computation.
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Affiliation(s)
- Arnav Solanki
- Department of Electrical and Computer Engineering, University of Minnesota Twin-Cities, Minneapolis, MN, United States of America
| | - Zak Griffin
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Purab Ranjan Sutradhar
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Karisha Pradhan
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Caiden Merritt
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Amlan Ganguly
- Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Marc Riedel
- Department of Electrical and Computer Engineering, University of Minnesota Twin-Cities, Minneapolis, MN, United States of America
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15
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Zhang X, Song J, Li Z, Zheng YW, Zhao WW, Chen HY, Xu JJ. θ-Nanopipette for Single-Cell Resistive-Pulse Profiling of DNA Repair Proteins Accompanied by Drug Evaluation. NANO LETTERS 2023; 23:8249-8255. [PMID: 37642327 DOI: 10.1021/acs.nanolett.3c02423] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Single-cell analysis of the DNA repair protein is important but remains unachieved. Exploration of nanopipettte technologies in single-cell electroanalysis has recently seen rapid growth, while the θ-nanopipette represents an emerging technological frontier with its potential largely veiled. Here a θ-nanopipette is first applied for single-cell resistive-pulse sensing (RPS) of the important DNA repair protein O6-alkylguanine DNA alkyltransferase (hAGT). The removal of alkyl mutations by hAGT could restore the damaged aptamer linking with a structural DNA carrier, allowing the selective binding of the aptamer to thrombin with precisely matched size to produce distinct RPS signals when passing through the orifice. Kinetic analysis of hAGT repair was studied. Meanwhile, the device shows the simultaneous on-demand infusion of inhibitors to inactivate the hAGT activity, indicative of its potential in drug screening for enhanced chemotherapy. This work provides a new paradigm for θ-nanopipette-based single-cell RPS of a DNA repair protein accompanied by drug evaluation.
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Affiliation(s)
- Xian Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Juan Song
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, P.R. China
| | - Zheng Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - You-Wei Zheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Wei-Wei Zhao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
| | - Jing-Juan Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P.R. China
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16
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Raza MH, Desai S, Aravamudhan S, Zadegan R. An outlook on the current challenges and opportunities in DNA data storage. Biotechnol Adv 2023; 66:108155. [PMID: 37068530 PMCID: PMC11060094 DOI: 10.1016/j.biotechadv.2023.108155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Silicon is the gold standard for information storage systems. The exponential generation of digital information will exhaust the global supply of refined silicon. Therefore, investing in alternative information storage materials such as DNA has gained momentum. DNA as a memory material possesses several advantages over silicon-based data storage, including higher storage capacity, data retention, and lower operational energy. Routine DNA data storage approaches encode data into chemically synthesized nucleotide sequences. The scalability of DNA data storage depends on factors such as the cost and the generation of hazardous waste during DNA synthesis, latency of writing and reading, and limited rewriting capacity. Here, we review the current status of DNA data storage encoding, writing, storing, retrieving and reading, and discuss the technology's challenges and opportunities.
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Affiliation(s)
- Muhammad Hassan Raza
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA
| | - Salil Desai
- Department of Industrial & Systems Engineering, North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA.
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17
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Roelen Z, Tabard-Cossa V. Synthesis of length-tunable DNA carriers for nanopore sensing. PLoS One 2023; 18:e0290559. [PMID: 37611030 PMCID: PMC10446168 DOI: 10.1371/journal.pone.0290559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Molecular carriers represent an increasingly common strategy in the field of nanopore sensing to use secondary molecules to selectively report on the presence of target analytes in solution, allowing for sensitive assays of otherwise hard-to-detect molecules such as small, weakly-charged proteins. However, existing carrier designs can often introduce drawbacks to nanopore experiments including higher levels of cost/complexity and carrier-pore interactions that lead to ambiguous signals and elevated clogging rates. In this work, we present a simple method of carrier production based on sticky-ended DNA molecules that emphasizes ease-of-synthesis and compatibility with nanopore sensing and analysis. In particular, our method incorporates the ability to flexibly control the length of the DNA carriers produced, enhancing the multiplexing potential of this carrier system through the separable nanopore signals they could generate for distinct targets. A proof-of-concept nanopore experiment is also presented, involving carriers produced by our method with multiple lengths and attached to DNA nanostructure targets, in order to validate the capabilities of the system. As the breadth of applications for nanopore sensors continues to expand, the availability of tools such as those presented here to help translate the outcomes of these applications into robust nanopore signals will be of major importance.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
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18
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Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
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Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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19
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Roelen Z, Briggs K, Tabard-Cossa V. Analysis of Nanopore Data: Classification Strategies for an Unbiased Curation of Single-Molecule Events from DNA Nanostructures. ACS Sens 2023; 8:2809-2823. [PMID: 37436112 PMCID: PMC10913896 DOI: 10.1021/acssensors.3c00751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Nanopores are versatile single-molecule sensors that are being used to sense increasingly complex mixtures of structured molecules with applications in molecular data storage and disease biomarker detection. However, increased molecular complexity presents additional challenges to the analysis of nanopore data, including more translocation events being rejected for not matching an expected signal structure and a greater risk of selection bias entering this event curation process. To highlight these challenges, here, we present the analysis of a model molecular system consisting of a nanostructured DNA molecule attached to a linear DNA carrier. We make use of recent advances in the event segmentation capabilities of Nanolyzer, a graphical analysis tool provided for nanopore event fitting, and describe approaches to the event substructure analysis. In the process, we identify and discuss important sources of selection bias that emerge in the analysis of this molecular system and consider the complicating effects of molecular conformation and variable experimental conditions (e.g., pore diameter). We then present additional refinements to existing analysis techniques, allowing for improved separation of multiplexed samples, fewer translocation events rejected as false negatives, and a wider range of experimental conditions for which accurate molecular information can be extracted. Increasing the coverage of analyzed events within nanopore data is not only important for characterizing complex molecular samples with high fidelity but is also becoming essential to the generation of accurate, unbiased training data as machine-learning approaches to data analysis and event identification continue to increase in prevalence.
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Affiliation(s)
- Zachary Roelen
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Kyle Briggs
- Department of Physics, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
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20
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Lim CK, Yeoh JW, Kunartama AA, Yew WS, Poh CL. A biological camera that captures and stores images directly into DNA. Nat Commun 2023; 14:3921. [PMID: 37400476 DOI: 10.1038/s41467-023-38876-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/19/2023] [Indexed: 07/05/2023] Open
Abstract
The increasing integration between biological and digital interfaces has led to heightened interest in utilizing biological materials to store digital data, with the most promising one involving the storage of data within defined sequences of DNA that are created by de novo DNA synthesis. However, there is a lack of methods that can obviate the need for de novo DNA synthesis, which tends to be costly and inefficient. Here, in this work, we detail a method of capturing 2-dimensional light patterns into DNA, by utilizing optogenetic circuits to record light exposure into DNA, encoding spatial locations with barcoding, and retrieving stored images via high-throughput next-generation sequencing. We demonstrate the encoding of multiple images into DNA, totaling 1152 bits, selective image retrieval, as well as robustness to drying, heat and UV. We also demonstrate successful multiplexing using multiple wavelengths of light, capturing 2 different images simultaneously using red and blue light. This work thus establishes a 'living digital camera', paving the way towards integrating biological systems with digital devices.
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Affiliation(s)
- Cheng Kai Lim
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
- Integrative Sciences and Engineering Programme (ISEP), NUS Graduate School, National University of Singapore, Singapore, Singapore
| | - Jing Wui Yeoh
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Aurelius Andrew Kunartama
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore
- Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore, 117597, Singapore
| | - Chueh Loo Poh
- Synthetic Biology for Clinical and Technological Innovation, National University of Singapore, 28 Medical Drive, Singapore, 117456, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
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21
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Zhu J, Tivony R, Bošković F, Pereira-Dias J, Sandler SE, Baker S, Keyser UF. Multiplexed Nanopore-Based Nucleic Acid Sensing and Bacterial Identification Using DNA Dumbbell Nanoswitches. J Am Chem Soc 2023. [PMID: 37220424 DOI: 10.1021/jacs.3c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Multiplexed nucleic acid sensing methods with high specificity are vital for clinical diagnostics and infectious disease control, especially in the postpandemic era. Nanopore sensing techniques have developed in the past two decades, offering versatile tools for biosensing while enabling highly sensitive analyte measurements at the single-molecule level. Here, we establish a nanopore sensor based on DNA dumbbell nanoswitches for multiplexed nucleic acid detection and bacterial identification. The DNA nanotechnology-based sensor switches from an "open" into a "closed" state when a target strand hybridizes to two sequence-specific sensing overhangs. The loop in the DNA pulls two groups of dumbbells together. The change in topology results in an easily recognized peak in the current trace. Simultaneous detection of four different sequences was achieved by assembling four DNA dumbbell nanoswitches on one carrier. The high specificity of the dumbbell nanoswitch was verified by distinguishing single base variants in DNA and RNA targets using four barcoded carriers in multiplexed measurements. By combining multiple dumbbell nanoswitches with barcoded DNA carriers, we identified different bacterial species even with high sequence similarity by detecting strain specific 16S ribosomal RNA (rRNA) fragments.
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Affiliation(s)
- Jinbo Zhu
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
- School of Biomedical Engineering, Faculty of Medicine, Dalian University of Technology, No. 2, Linggong Road, Dalian 116024, China
| | - Ran Tivony
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Filip Bošković
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Joana Pereira-Dias
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Sarah E Sandler
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Jeffery Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, U.K
| | - Ulrich F Keyser
- Cavendish Laboratory, University of Cambridge, JJ Thompson Avenue, Cambridge CB3 0HE, U.K
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22
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Luo Y, Cao Z, Liu Y, Zhang R, Yang S, Wang N, Shi Q, Li J, Dong S, Fan C, Zhao J. The emerging landscape of microfluidic applications in DNA data storage. LAB ON A CHIP 2023; 23:1981-2004. [PMID: 36946437 DOI: 10.1039/d2lc00972b] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
DNA has been considered a promising alternative to the current solid-state devices for digital information storage. The past decade has witnessed tremendous progress in the field of DNA data storage contributed by researchers from various disciplines. However, the current development status of DNA storage is still far from practical use, mainly due to its high material cost and time consumption for data reading/writing, as well as the lack of a comprehensive, automated, and integrated system. Microfluidics, being capable of handling and processing micro-scale fluid samples in a massively paralleled and highly integrated manner, has gradually been recognized as a promising candidate for addressing the aforementioned issues. In this review, we provide a discussion on recent efforts of applying microfluidics to advance the development of DNA data storage. Moreover, to showcase the tremendous potential that microfluidics can contribute to this field, we will further highlight the recent advancements of applying microfluidics to the key functional modules within the DNA data storage workflow. Finally, we share our perspectives on future directions for how to continue the infusion of microfluidics with DNA data storage and how to advance toward a truly integrated system and reach real-life applications.
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Affiliation(s)
- Yuan Luo
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen Cao
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Yifan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Shanghai Clinical Research and Trial Center, Shanghai, 201210, China
| | - Rong Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shijia Yang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ning Wang
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingyuan Shi
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jie Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Shurong Dong
- College of Information Science and Electronic Engineering, Zhejiang University, Hangzhou 310027, China.
- International Joint Innovation Center, Zhejiang University, Haining 314400, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China.
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, 100101, P.R. China
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23
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Bencurova E, Akash A, Dobson RC, Dandekar T. DNA storage-from natural biology to synthetic biology. Comput Struct Biotechnol J 2023; 21:1227-1235. [PMID: 36817961 PMCID: PMC9932295 DOI: 10.1016/j.csbj.2023.01.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/30/2023] [Accepted: 01/31/2023] [Indexed: 02/04/2023] Open
Abstract
Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).
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Affiliation(s)
- Elena Bencurova
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Aman Akash
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany
| | - Renwick C.J. Dobson
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, Australia
| | - Thomas Dandekar
- Department of Bioinformatics, University of Würzburg, Würzburg, Germany,Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany,Corresponding author at: Department of Bioinformatics, University of Würzburg, Würzburg, Germany.
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24
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Wang Y, Zhu Z, Yu C, Wu R, Zhu J, Li B. Lego-Like Catalytic Hairpin Assembly Enables Controllable DNA-Oligomer Formation and Spatiotemporal Amplification in Single Molecular Signaling. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206283. [PMID: 36436946 DOI: 10.1002/smll.202206283] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/14/2022] [Indexed: 06/16/2023]
Abstract
While the solid-state nanopore shows increasing potential during sensitive and label-free single molecular analysis, target concentration and signal amplification method is in urgent need. In this article, a solution via designing a model nucleic acid circuit reaction that can produce "Y" shape-structure three-way DNA oligomers with controllable size and polymerization degree is proposed. Such a so-called lego-like three-way catalytic hairpin assembly (LK-3W-CHA) can provide both concentration amplification (via CHA circuit) and programmable size control (via lego-like building mode) to enhance spatiotemporal resolution in single molecular sensing of solid-state nanopore. Oligomers containing 1-4 DNA three-way junctions (Y monomers, Y1-Y4) are designed in proof-of-concept experiments and applications. When the oligomers are applied to direct translocation measurements, Y2-Y4 can significantly increase the signal resolution and stability than that of Y1. Meanwhile, Y1 to Y4 can be used as the tags on the long DNA carrier to provide very legible secondary signals for specific identification, multiple assays, and information storage. Compared with other possible tags, Y1-Y4 provides higher signal density and amplitude, and quasi-linear "inner reference" for each other, which may provide more systematic, reliable, and controllable experimental results.
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Affiliation(s)
- Yesheng Wang
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Zhentong Zhu
- Key Laboratory of Bioelectrochemistry & Environmental Analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China
| | - Chunmiao Yu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Ruiping Wu
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
| | - Jinbo Zhu
- Cavendish Lab, University of Cambridge, Cambridge, CB3 0HE, UK
| | - Bingling Li
- State Key Lab of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, P. R. China
- University of Science & Technology of China, Hefei, Anhui, 230026, P. R. China
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25
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Confederat S, Sandei I, Mohanan G, Wälti C, Actis P. Nanopore fingerprinting of supramolecular DNA nanostructures. Biophys J 2022; 121:4882-4891. [PMID: 35986518 PMCID: PMC9808562 DOI: 10.1016/j.bpj.2022.08.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/05/2022] [Accepted: 08/16/2022] [Indexed: 01/07/2023] Open
Abstract
DNA nanotechnology has paved the way for new generations of programmable nanomaterials. Utilizing the DNA origami technique, various DNA constructs can be designed, ranging from single tiles to the self-assembly of large-scale, complex, multi-tile arrays. This technique relies on the binding of hundreds of short DNA staple strands to a long single-stranded DNA scaffold that drives the folding of well-defined nanostructures. Such DNA nanostructures have enabled new applications in biosensing, drug delivery, and other multifunctional materials. In this study, we take advantage of the enhanced sensitivity of a solid-state nanopore that employs a poly-ethylene glycol enriched electrolyte to deliver real-time, non-destructive, and label-free fingerprinting of higher-order assemblies of DNA origami nanostructures with single-entity resolution. This approach enables the quantification of the assembly yields for complex DNA origami nanostructures using the nanostructure-induced equivalent charge surplus as a discriminant. We compare the assembly yield of four supramolecular DNA nanostructures obtained with the nanopore with agarose gel electrophoresis and atomic force microscopy imaging. We demonstrate that the nanopore system can provide analytical quantification of the complex supramolecular nanostructures within minutes, without any need for labeling and with single-molecule resolution. We envision that the nanopore detection platform can be applied to a range of nanomaterial designs and enable the analysis and manipulation of large DNA assemblies in real time.
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Affiliation(s)
- Samuel Confederat
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Ilaria Sandei
- School of Chemistry, University of Leeds, Leeds, United Kingdom
| | - Gayathri Mohanan
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom
| | - Christoph Wälti
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, United Kingdom; Bragg Centre for Materials Research, Leeds, United Kingdom.
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26
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Soete M, Mertens C, Badi N, Du Prez FE. Reading Information Stored in Synthetic Macromolecules. J Am Chem Soc 2022; 144:22378-22390. [PMID: 36454647 DOI: 10.1021/jacs.2c10316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The storage of information in synthetic (macro)molecules provides an attractive alternative for current archival storage media, and the advancements made within this area have prompted the investigation of such molecules for numerous other applications (e.g., anti-counterfeiting tags, steganography). While different strategies have been described for storing information at the molecular level, this Perspective aims to provide a critical overview of the most prominent approaches that can be utilized for retrieving the encoded information. The major part will focus on the sequence determination of synthetic macromolecules, wherein information is stored by the precise arrangement of constituting monomers, with an emphasis on chemically aided strategies, (tandem) mass spectrometry, and nanopore sensing. In addition, recent progress in utilizing (mixtures of) small molecules for information storage will be discussed. Finally, the closing remarks aim to highlight which strategy we believe is the most suitable for a series of specific applications, and will also touch upon the future research avenues that can be pursued for reading (macro)molecular information.
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Affiliation(s)
- Matthieu Soete
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Chiel Mertens
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Nezha Badi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, B-9000 Ghent, Belgium
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27
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Doricchi A, Platnich CM, Gimpel A, Horn F, Earle M, Lanzavecchia G, Cortajarena AL, Liz-Marzán LM, Liu N, Heckel R, Grass RN, Krahne R, Keyser UF, Garoli D. Emerging Approaches to DNA Data Storage: Challenges and Prospects. ACS NANO 2022; 16:17552-17571. [PMID: 36256971 PMCID: PMC9706676 DOI: 10.1021/acsnano.2c06748] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103 GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.
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Affiliation(s)
- Andrea Doricchi
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
di Genova, via Dodecaneso
31, 16146 Genova, Italy
| | - Casey M. Platnich
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Andreas Gimpel
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Friederikee Horn
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Max Earle
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - German Lanzavecchia
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Aitziber L. Cortajarena
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11.
Planta 0, 28029 Madrid, Spain
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, 70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, 70569 Stuttgart, Germany
| | - Reinhard Heckel
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Robert N. Grass
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
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28
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Lin CY, Fotis R, Xia Z, Kavetsky K, Chou YC, Niedzwiecki DJ, Biondi M, Thei F, Drndić M. Ultrafast Polymer Dynamics through a Nanopore. NANO LETTERS 2022; 22:8719-8727. [PMID: 36315497 DOI: 10.1021/acs.nanolett.2c03546] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Ultrathin nanopore sensors allow single-molecule and polymer measurements at sub-microsecond time resolution enabled by high current signals (∼10-30 nA). We demonstrate for the first time the experimental probing of the ultrafast translocation and folded dynamics of double-stranded DNA (dsDNA) through a nanopore at 10 MHz bandwidth with acquisition of data points per 25 ns (150 MB/s). By introducing a rigorous algorithm, we are able to accurately identify each current level present within translocation events and elucidate the dynamic folded and unfolded behaviors. The remarkable sensitivity of this system reveals distortions of short-lived folded states at a lower bandwidth. This work revisits probing of dsDNA as a model polymer and develops broadly applicable methods. The combined improvements in sensor signals, instrumentation, and large data analysis methods uncover biomolecular dynamics at unprecedentedly small time scales.
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Affiliation(s)
- Chih-Yuan Lin
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Riley Fotis
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Zehui Xia
- Goeppert LLC, Philadelphia, Pennsylvania 19146, United States
| | - Kyril Kavetsky
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Material Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Yung-Chien Chou
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | | | | | | | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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29
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Ying YL, Hu ZL, Zhang S, Qing Y, Fragasso A, Maglia G, Meller A, Bayley H, Dekker C, Long YT. Nanopore-based technologies beyond DNA sequencing. NATURE NANOTECHNOLOGY 2022; 17:1136-1146. [PMID: 36163504 DOI: 10.1038/s41565-022-01193-2] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 06/02/2022] [Indexed: 06/16/2023]
Abstract
Inspired by the biological processes of molecular recognition and transportation across membranes, nanopore techniques have evolved in recent decades as ultrasensitive analytical tools for individual molecules. In particular, nanopore-based single-molecule DNA/RNA sequencing has advanced genomic and transcriptomic research due to the portability, lower costs and long reads of these methods. Nanopore applications, however, extend far beyond nucleic acid sequencing. In this Review, we present an overview of the broad applications of nanopores in molecular sensing and sequencing, chemical catalysis and biophysical characterization. We highlight the prospects of applying nanopores for single-protein analysis and sequencing, single-molecule covalent chemistry, clinical sensing applications for single-molecule liquid biopsy, and the use of synthetic biomimetic nanopores as experimental models for natural systems. We suggest that nanopore technologies will continue to be explored to address a number of scientific challenges as control over pore design improves.
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Affiliation(s)
- Yi-Lun Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Zheng-Li Hu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China
| | - Shengli Zhang
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Yujia Qing
- Department of Chemistry, University of Oxford, Oxford, UK
| | - Alessio Fragasso
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands
| | - Giovanni Maglia
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands.
| | - Amit Meller
- Faculty of Biomedical Engineering, Technion-IIT, Haifa, Israel.
| | - Hagan Bayley
- Department of Chemistry, University of Oxford, Oxford, UK.
| | - Cees Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, the Netherlands.
| | - Yi-Tao Long
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, People's Republic of China.
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30
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Tsutsui M, Yokota K, He Y, Kawai T. Ionic Signal Amplification of DNA in a Nanopore. SMALL METHODS 2022; 6:e2200761. [PMID: 36196624 DOI: 10.1002/smtd.202200761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/06/2022] [Indexed: 06/16/2023]
Abstract
Ionic signal amplification is a key challenge for single-molecule analyses by solid-state nanopore sensing. Here, a permittivity gradient approach for amplifying ionic blockade characteristics of DNA in a nanofluidic channel is reported. The transmembrane ionic current response is found to change substantially through modifying the liquid permittivity at one side of a pore with an organic solvent. Imposing positive liquid permittivity gradients with respect to the direction of DNA electrophoresis, this study observes the resistive ionic signals to become larger due to the varying contributions of molecular counterions. On the contrary, negative gradients render adverse effects causing conductive ionic current pulses upon polynucleotide translocations. Most importantly, both the positive and negative gradients are demonstrated to be capable of amplifying the ionic signals by an order of magnitude with a 1.3-fold difference in the transmembrane liquid dielectric constants. This phenomenon allows a novel way to enhance the single-molecule sensitivity of nanopore sensing that may be useful in analyzing secondary structures and genome sequence of DNA by ionic current measurements.
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Affiliation(s)
- Makusu Tsutsui
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
| | - Kazumichi Yokota
- National Institute of Advanced Industrial Science and Technology, Takamatsu, Kagawa, 761-0395, Japan
| | - Yuhui He
- Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Tomoji Kawai
- The Institute of Scientific and Industrial Research, Osaka University, Ibaraki, Osaka, 567-0047, Japan
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31
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Yin Q, Zheng Y, Wang B, Zhang Q. Design of Constraint Coding Sets for Archive DNA Storage. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:3384-3394. [PMID: 34762590 DOI: 10.1109/tcbb.2021.3127271] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
With the advent of the era of massive data, the increase of storage demand has far exceeded current storage capacity. DNA molecules provide a reliable solution for big data storage by virtue of their large capacity, high density, and long-term stability. To reduce errors in storing procedures, constructing a sufficient set of constraint encoding is critical for achieving DNA storage. A new version of the Marine Predator algorithm (called QRSS-MPA) is proposed in this paper to increase the lower bound of the coding set while satisfying the specific combination of constraints. In order to demonstrate the effectiveness of the improvement, the classical CEC-05 test function is used to test and compare the mean, variance, scalability, and significance. In terms of storage, the lower bound of construction is compared with previous works, and the result is found to be significantly improved. In order to prevent the emergence of a secondary structure that leads to sequencing failure, we give a more stringent lower bound for the constraint coding set, which is of great significance for reducing the error rate of DNA storage amidst its rapid development.
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Narayanan RP, Procyk J, Nandi P, Prasad A, Xu Y, Poppleton E, Williams D, Zhang F, Yan H, Chiu PL, Stephanopoulos N, Šulc P. Coarse-Grained Simulations for the Characterization and Optimization of Hybrid Protein-DNA Nanostructures. ACS NANO 2022; 16:14086-14096. [PMID: 35980981 PMCID: PMC9590280 DOI: 10.1021/acsnano.2c04013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
We present here the combination of experimental and computational modeling tools for the design and characterization of protein-DNA hybrid nanostructures. Our work incorporates several features in the design of these nanostructures: (1) modeling of the protein-DNA linker identity and length; (2) optimizing the design of protein-DNA cages to account for mechanical stresses; (3) probing the incorporation efficiency of protein-DNA conjugates into DNA nanostructures. The modeling tools were experimentally validated using structural characterization methods like cryo-TEM and AFM. Our method can be used for fitting low-resolution electron density maps when structural insights cannot be deciphered from experiments, as well as enable in-silico validation of nanostructured systems before their experimental realization. These tools will facilitate the design of complex hybrid protein-DNA nanostructures that seamlessly integrate the two different biomolecules.
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Affiliation(s)
- Raghu Pradeep Narayanan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Jonah Procyk
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Purbasha Nandi
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Abhay Prasad
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Yang Xu
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Erik Poppleton
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Dewight Williams
- Eyring Materials Center, Office of Knowledge Enterprise Development, Arizona State University, Tempe, Arizona 85287, United States
| | - Fei Zhang
- Department of Chemistry, Rutgers University, Newark, New Jersey 07102, United States
| | - Hao Yan
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Po-Lin Chiu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Petr Šulc
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
- Center for molecular design and biomimetics, The Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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33
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Luo Y, Wang S, Feng Z, Li J, Mao C, Wang R, Jiang X. Integrated Microfluidic DNA Storage Platform with Automated Sample Handling and Physical Data Partitioning. Anal Chem 2022; 94:13153-13162. [DOI: 10.1021/acs.analchem.2c02667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yuan Luo
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai200050, China
| | - Shuchen Wang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Zhuowei Feng
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Jie Li
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Cuiping Mao
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
| | - Xingyu Jiang
- Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Rd., Xili, Nanshan District, Shenzhen518055, Guangdong, P. R. China
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, No 1088, Xueyuan Rd., Xili, Nanshan
District, Shenzhen518055, Guangdong, P. R. China
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34
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Bencurova E, Shityakov S, Schaack D, Kaltdorf M, Sarukhanyan E, Hilgarth A, Rath C, Montenegro S, Roth G, Lopez D, Dandekar T. Nanocellulose Composites as Smart Devices With Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration. Front Bioeng Biotechnol 2022; 10:869111. [PMID: 36105598 PMCID: PMC9465592 DOI: 10.3389/fbioe.2022.869111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid development of green and sustainable materials opens up new possibilities in the field of applied research. Such materials include nanocellulose composites that can integrate many components into composites and provide a good chassis for smart devices. In our study, we evaluate four approaches for turning a nanocellulose composite into an information storage or processing device: 1) nanocellulose can be a suitable carrier material and protect information stored in DNA. 2) Nucleotide-processing enzymes (polymerase and exonuclease) can be controlled by light after fusing them with light-gating domains; nucleotide substrate specificity can be changed by mutation or pH change (read-in and read-out of the information). 3) Semiconductors and electronic capabilities can be achieved: we show that nanocellulose is rendered electronic by iodine treatment replacing silicon including microstructures. Nanocellulose semiconductor properties are measured, and the resulting potential including single-electron transistors (SET) and their properties are modeled. Electric current can also be transported by DNA through G-quadruplex DNA molecules; these as well as classical silicon semiconductors can easily be integrated into the nanocellulose composite. 4) To elaborate upon miniaturization and integration for a smart nanocellulose chip device, we demonstrate pH-sensitive dyes in nanocellulose, nanopore creation, and kinase micropatterning on bacterial membranes as well as digital PCR micro-wells. Future application potential includes nano-3D printing and fast molecular processors (e.g., SETs) integrated with DNA storage and conventional electronics. This would also lead to environment-friendly nanocellulose chips for information processing as well as smart nanocellulose composites for biomedical applications and nano-factories.
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Affiliation(s)
- Elena Bencurova
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russia
| | - Dominik Schaack
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Martin Kaltdorf
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Edita Sarukhanyan
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Alexander Hilgarth
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Christin Rath
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
| | - Sergio Montenegro
- Aerospace Information Technology, University of Würzburg, Würzburg, Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Freiburg, Germany
- BioCopy GmbH, Emmendingen, Germany
| | - Daniel Lopez
- Centro Nacional de Biotecnologia CNB, Universidad Autonoma de Madrid, Madrid, Spain
| | - Thomas Dandekar
- Functional Genomics and Systems Biology Group, Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg, Germany
- *Correspondence: Thomas Dandekar,
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35
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Wang P, Mu Z, Sun L, Si S, Wang B. Hidden Addressing Encoding for DNA Storage. Front Bioeng Biotechnol 2022; 10:916615. [PMID: 35928958 PMCID: PMC9344065 DOI: 10.3389/fbioe.2022.916615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
DNA is a natural storage medium with the advantages of high storage density and long service life compared with traditional media. DNA storage can meet the current storage requirements for massive data. Owing to the limitations of the DNA storage technology, the data need to be converted into short DNA sequences for storage. However, in the process, a large amount of physical redundancy will be generated to index short DNA sequences. To reduce redundancy, this study proposes a DNA storage encoding scheme with hidden addressing. Using the improved fountain encoding scheme, the index replaces part of the data to realize hidden addresses, and then, a 10.1 MB file is encoded with the hidden addressing. First, the Dottup dot plot generator and the Jaccard similarity coefficient analyze the overall self-similarity of the encoding sequence index, and then the sequence fragments of GC content are used to verify the performance of this scheme. The final results show that the encoding scheme indexes with overall lower self-similarity, and the local thermodynamic properties of the sequence are better. The hidden addressing encoding scheme proposed can not only improve the utilization of bases but also ensure the correct rate of DNA storage during the sequencing and decoding processes.
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36
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Zhang Y, Ren Y, Liu Y, Wang F, Zhang H, Liu K. Preservation and Encryption in DNA Digital Data Storage. Chempluschem 2022; 87:e202200183. [PMID: 35856827 DOI: 10.1002/cplu.202200183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Indexed: 11/08/2022]
Abstract
The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yangyi Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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37
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Zhu J, Bošković F, Keyser UF. Split G-Quadruplexes Enhance Nanopore Signals for Simultaneous Identification of Multiple Nucleic Acids. NANO LETTERS 2022; 22:4993-4998. [PMID: 35730196 PMCID: PMC9228402 DOI: 10.1021/acs.nanolett.2c01764] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/28/2022] [Indexed: 05/22/2023]
Abstract
Assembly of DNA structures based on hybridization like split G-quadruplex (GQ) have great potential for the base-pair specific identification of nucleic acid targets. Herein, we combine multiple split G-quadruplex (GQ) assemblies on designed DNA nanostructures (carrier) with a solid-state nanopore sensing platform. The split GQ probes recognize various nucleic acid sequences in a parallel assay that is based on glass nanopore analysis of molecular structures. Specifically, we split a GQ into two asymmetric parts extended with sequences complementary to the target. The longer G-segment is in solution, and the shorter one is on a DNA carrier. If the target is present, the two separate GQ parts will be brought together to facilitate the split GQ formation and enhance the nanopore signal. We demonstrated detection of multiple target sequences from different viruses with low crosstalk. Given the programmability of this DNA based nanopore sensing platform, it is promising in biosensing.
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38
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Pan C, Tabatabaei SK, Tabatabaei Yazdi SMH, Hernandez AG, Schroeder CM, Milenkovic O. Rewritable two-dimensional DNA-based data storage with machine learning reconstruction. Nat Commun 2022; 13:2984. [PMID: 35624096 PMCID: PMC9142566 DOI: 10.1038/s41467-022-30140-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/19/2022] [Indexed: 01/01/2023] Open
Abstract
DNA-based data storage platforms traditionally encode information only in the nucleotide sequence of the molecule. Here we report on a two-dimensional molecular data storage system that records information in both the sequence and the backbone structure of DNA and performs nontrivial joint data encoding, decoding and processing. Our 2DDNA method efficiently stores images in synthetic DNA and embeds pertinent metadata as nicks in the DNA backbone. To avoid costly worst-case redundancy for correcting sequencing/rewriting errors and to mitigate issues associated with mismatched decoding parameters, we develop machine learning techniques for automatic discoloration detection and image inpainting. The 2DDNA platform is experimentally tested by reconstructing a library of images with undetectable or small visual degradation after readout processing, and by erasing and rewriting copyright metadata encoded in nicks. Our results demonstrate that DNA can serve both as a write-once and rewritable memory for heterogenous data and that data can be erased in a permanent, privacy-preserving manner. Moreover, the storage system can be made robust to degrading channel qualities while avoiding global error-correction redundancy. Current DNA-based data storage platforms encode information only in the nucleotide sequence. Here, the authors report a 2DDNA platform that can store data in both sequence context and backbone structure, and has improved image inpainting and enhancement via automatic discoloration detection and deep learning.
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Affiliation(s)
- Chao Pan
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - S Kasra Tabatabaei
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Alvaro G Hernandez
- Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Charles M Schroeder
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA. .,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
| | - Olgica Milenkovic
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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39
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Yan S, Wang L, Wang Y, Cao Z, Zhang S, Du X, Fan P, Zhang P, Chen HY, Huang S. Non-binary Encoded Nucleic Acid Barcodes Directly Readable by a Nanopore. Angew Chem Int Ed Engl 2022; 61:e202116482. [PMID: 35261129 DOI: 10.1002/anie.202116482] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Indexed: 01/13/2023]
Abstract
A large collection of unique molecular barcodes is useful in the simultaneous sensing or screening of molecular analytes. Though the sequence of DNA has been widely applied to encode for molecular barcodes, decoding of these barcodes is normally assisted by sequencing. We here demonstrate a barcode system based solely on self-assembly of synthetic nucleic acids and direct nanopore decoding. Each molecular barcode is composed of "n" distinct information nodes in a non-binary manner and can be sequentially scanned and decoded by a Mycobacterium smegmatis porin A (MspA) nanopore. Nanopore events containing step-shaped features were consistently reported. 14 unique information nodes were developed which in principle could encode for 14n unique molecular barcodes in a barcode containing "n" information nodes. These barcode probes were adapted to detect different antibody proteins or cancer-related microRNAs, suggesting their immediate application in a wide variety of sensing applications.
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Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Hong-Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 210023, Nanjing, China.,Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, 210023, Nanjing, China
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40
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Alawami MF, Bošković F, Zhu J, Chen K, Sandler SE, Keyser UF. Lifetime of glass nanopores in a PDMS chip for single-molecule sensing. iScience 2022; 25:104191. [PMID: 35479403 PMCID: PMC9036133 DOI: 10.1016/j.isci.2022.104191] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 02/16/2022] [Accepted: 03/30/2022] [Indexed: 11/09/2022] Open
Abstract
Nanopore sensing is an emerging technology that has many biosensing applications ranging from DNA sequencing using biological pores to biomolecular analysis using solid-state pores. Solid-state nanopores that are more stable are an attractive choice for biosensing applications. Still, biomolecule interactions with the nanopore surface reduce nanopore stability and increase usage costs. In this study, we investigated the biosensing capability for 102 quartz glass nanopores with a diameter of 11–18 nm that were fabricated using laser-assisted capillary pulling. Nanopores were assembled into multiple microfluidic chips that were repeatedly used for up to 19 weeks. We find that using vacuum storage combined with minimal washing steps improved the number of use cycles for nanopores. The single-molecule biosensing capability over repeated use cycles was demonstrated by quantitative analysis of a DNA carrier designed for detection of short single-stranded DNA oligonucleotides. Maintaining low noise and linear current-voltage relation is crucial for biosensing Multiple nanopores embedded in a chip can make more than 90 different measurements Nanopores can be reused weekly over 19 weeks Nanopore failure can be attributed to contaminant accumulation and dissolution
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41
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Hagan JT, Gonzalez A, Shi Y, Han GGD, Dwyer JR. Photoswitchable Binary Nanopore Conductance and Selective Electronic Detection of Single Biomolecules under Wavelength and Voltage Polarity Control. ACS NANO 2022; 16:5537-5544. [PMID: 35286058 DOI: 10.1021/acsnano.1c10039] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We fabricated photoregulated thin-film nanopores by covalently linking azobenzene photoswitches to silicon nitride pores with ∼10 nm diameters. The photoresponsive coatings could be repeatedly optically switched with deterministic ∼6 nm changes to the effective nanopore diameter and of ∼3× to the nanopore ionic conductance. The sensitivity to anionic DNA and a neutral complex carbohydrate biopolymer (maltodextrin) could be photoswitched "on" and "off" with an analyte selectivity set by applied voltage polarity. Photocontrol of nanopore state and mass transport characteristics is important for their use as ionic circuit elements (e.g., resistors and binary bits) and as chemically tuned filters. It expands single-molecule sensing capabilities in personalized medicine, genomics, glycomics, and, augmented by voltage polarity selectivity, especially in multiplexed biopolymer information storage schemes. We demonstrate repeatedly photocontrolled stable nanopore size, polarity, conductance, and sensing selectivity, by illumination wavelength and voltage polarity, with broad utility including single-molecule sensing of biologically and technologically important polymers.
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Affiliation(s)
- James T Hagan
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Alejandra Gonzalez
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Yuran Shi
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Grace G D Han
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, Massachusetts 02453, United States
| | - Jason R Dwyer
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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42
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Lin K, Chen C, Wang C, Lian P, Wang Y, Xue S, Sha J, Chen Y. Fabrication of solid-state nanopores. NANOTECHNOLOGY 2022; 33:272003. [PMID: 35349996 DOI: 10.1088/1361-6528/ac622b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are valuable single-molecule sensing tools that have been widely applied to the detection of DNA, RNA, proteins, viruses, glycans, etc. The prominent sensing platform is helping to improve our health-related quality of life and accelerate the rapid realization of precision medicine. Solid-state nanopores have made rapid progress in the past decades due to their flexible size, structure and compatibility with semiconductor fabrication processes. With the development of semiconductor fabrication techniques, materials science and surface chemistry, nanopore preparation and modification technologies have made great breakthroughs. To date, various solid-state nanopore materials, processing technologies, and modification methods are available to us. In the review, we outline the recent advances in nanopores fabrication and analyze the virtues and limitations of various membrane materials and nanopores drilling techniques.
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Affiliation(s)
- Kabin Lin
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Chen Chen
- Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Congsi Wang
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Peiyuan Lian
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Yan Wang
- School of Information and Control Engineering, Xi'an University of Architecture and Technology, Xi'an 710055, People's Republic of China
| | - Song Xue
- Key Laboratory of Electronic Equipment Structure Design, Ministry of Education, School of Mechano-Electronic Engineering, Xidian University, Xi'an 710071, People's Republic of China
| | - Jingjie Sha
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Yunfei Chen
- Jiangsu Key Laboratory for Design and Manufacture of Micro-nano Biomedical Instruments, School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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43
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Sharma V, Farajpour N, Lastra LS, Freedman KJ. DNA Coil Dynamics and Hydrodynamic Gating of Pressure-Biased Nanopores. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2106803. [PMID: 35266283 DOI: 10.1002/smll.202106803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Nanopores are ideally suited for the analysis of long DNA fragments including chromosomal DNA and synthetic DNA with applications in genome sequencing and DNA data storage, respectively. Hydrodynamic fluid flow has been shown to slow down DNA transit time within the pore, however other influences of hydrodynamic forces have yet to be explored. In this report, a broad analysis of pressure-biased nanopores and the impact of hydrodynamics on DNA transit time, capture rate, current blockade depth, and DNA folding are conducted. Using a 10 nm pore, it is shown that hydrodynamic flow inhibits the early stages of linearization of DNA and produces predominately folded events which are initiated by folded DNA (2-strands) entering the pore. Furthermore, utilizing larger pores (30 nm) leads to unique DNA gating behavior in which DNA events can be switched on and off with the application of pressure. A computational model, based on combining electrophoretic drift velocities with fluid velocities, accurately predicts the pore size required to observe DNA gating. Hydrodynamic fluid flow generated by a pressure bias, or potentially more generally by other mechanisms like electroosmotic flow, is shown to have significant effects on DNA sensing and can be useful for DNA sensing technologies.
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Affiliation(s)
- Vinay Sharma
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
- Department of Biosciences and Bioengineering, Indian Institute of Technology Jammu, NH-44, Jagti, Jammu, J & K, 181221, India
| | - Nasim Farajpour
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
| | - Lauren S Lastra
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
| | - Kevin J Freedman
- University of California Riverside, Department of Bioengineering, 900 University Ave, Riverside, CA, 92521, USA
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44
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Ren Y, Zhang Y, Liu Y, Wu Q, Su J, Wang F, Chen D, Fan C, Liu K, Zhang H. DNA-Based Concatenated Encoding System for High-Reliability and High-Density Data Storage. SMALL METHODS 2022; 6:e2101335. [PMID: 35146964 DOI: 10.1002/smtd.202101335] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/05/2022] [Indexed: 05/25/2023]
Abstract
Information storage based on DNA molecules provides a promising solution with advantages of low-energy consumption, high storage efficiency, and long lifespan. However, there are only four natural nucleotides and DNA storage is thus limited by 2 bits per nucleotide. Here, artificial nucleotides into DNA data storage to achieve higher coding efficiency than 2 bits per nucleotide is introduced. To accommodate the characteristics of DNA synthesis and sequencing, two high-reliability encoding systems suitable for four, six, and eight nucleotides, i.e., the RaptorQ-Arithmetic-LZW-RS (RALR) and RaptorQ-Arithmetic-Base64-RS (RABR) systems, are developed. The two concatenated encoding systems realize the advantages of correcting DNA sequence losses, correcting errors within DNA sequences, reducing homopolymers, and controlling specific nucleotide contents. The average coding efficiencies with error correction and without arithmetic compression by the RALR system using four, six, and eight nucleotides reach 1.27, 1.61, and 1.85 bits per nucleotide, respectively. While the average coding efficiencies by the RABR system are up to 1.50, 2.00, and 2.35 bits per nucleotide, respectively. The coding efficiency, versatility, and tunability of the developed artificial DNA systems might provide significant guidance for high-reliability and high-density data storage.
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Affiliation(s)
- Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Qinglin Wu
- Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, Zhejiang, 310027, China
| | - Juanjuan Su
- College of Materials Science and Opto-Electronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Dong Chen
- Institute of Process Equipment, College of Energy Engineering and State Key Laboratory of Fluid Power and Mechatronic Systems, Zhejiang University, Hangzhou, Zhejiang, 310027, 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, 200240, China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
| | - Hongjie Zhang
- Department of Chemistry, Tsinghua University, Beijing, 100084, China
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45
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Yan S, Wang L, Wang Y, Cao Z, Zhang S, Du X, Fan P, Zhang P, Chen H, Huang S. Non‐binary Encoded Nucleic Acid Barcodes Directly Readable by a Nanopore. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Shuanghong Yan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Liying Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Yuqin Wang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Zhenyuan Cao
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Shanyu Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Xiaoyu Du
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Pingping Fan
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
| | - Panke Zhang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
| | - Hong‐Yuan Chen
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
| | - Shuo Huang
- State Key Laboratory of Analytical Chemistry for Life Sciences School of Chemistry and Chemical Engineering Nanjing University 210023 Nanjing China
- Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University 210023 Nanjing China
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46
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Fried JP, Wu Y, Tilley RD, Gooding JJ. Optical Nanopore Sensors for Quantitative Analysis. NANO LETTERS 2022; 22:869-880. [PMID: 35089719 DOI: 10.1021/acs.nanolett.1c03976] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Nanopore sensors have received significant interest for the detection of clinically important biomarkers with single-molecule resolution. These sensors typically operate by detecting changes in the ionic current through a nanopore due to the translocation of an analyte. Recently, there has been interest in developing optical readout strategies for nanopore sensors for quantitative analysis. This is because they can utilize wide-field microscopy to independently monitor many nanopores within a high-density array. This significantly increases the amount of statistics that can be obtained, thus enabling the analysis of analytes present at ultralow concentrations. Here, we review the use of optical nanopore sensing strategies for quantitative analysis. We discuss optical nanopore sensing assays that have been developed to detect clinically relevant biomarkers, the potential for multiplexing such measurements, and techniques to fabricate high density arrays of nanopores with a view toward the use of these devices for clinical applications.
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Affiliation(s)
- Jasper P Fried
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Yanfang Wu
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Richard D Tilley
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - J Justin Gooding
- School of Chemistry, Australian Centre for NanoMedicine, ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, The University of New South Wales, Sydney, New South Wales 2052, Australia
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47
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Choudhary A, Maffeo C, Aksimentiev A. Multi-resolution simulation of DNA transport through large synthetic nanostructures. Phys Chem Chem Phys 2022; 24:2706-2716. [PMID: 35050282 PMCID: PMC8855663 DOI: 10.1039/d1cp04589j] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Modeling and simulation has become an invaluable partner in development of nanopore sensing systems. The key advantage of the nanopore sensing method - the ability to rapidly detect individual biomolecules as a transient reduction of the ionic current flowing through the nanopore - is also its key deficiency, as the current signal itself rarely provides direct information about the chemical structure of the biomolecule. Complementing experimental calibration of the nanopore sensor readout, coarse-grained and all-atom molecular dynamics simulations have been used extensively to characterize the nanopore translocation process and to connect the microscopic events taking place inside the nanopore to the experimentally measured ionic current blockades. Traditional coarse-grained simulations, however, lack the precision needed to predict ionic current blockades with atomic resolution whereas traditional all-atom simulations are limited by the length and time scales amenable to the method. Here, we describe a multi-resolution framework for modeling electric field-driven passage of DNA molecules and nanostructures through to-scale models of synthetic nanopore systems. We illustrate the method by simulating translocation of double-stranded DNA through a solid-state nanopore and a micron-scale slit, capture and translocation of single-stranded DNA in a double nanopore system, and modeling ionic current readout from a DNA origami nanostructure passage through a nanocapillary. We expect our multi-resolution simulation framework to aid development of the nanopore field by providing accurate, to-scale modeling capability to research laboratories that do not have access to leadership supercomputer facilities.
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Affiliation(s)
- Adnan Choudhary
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
| | - Christopher Maffeo
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Aleksei Aksimentiev
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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48
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Zhang M, Chen C, Zhang Y, Geng J. Biological nanopores for sensing applications. Proteins 2022; 90:1786-1799. [PMID: 35092317 DOI: 10.1002/prot.26308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/27/2021] [Accepted: 01/27/2022] [Indexed: 02/05/2023]
Abstract
Biological nanopores are proteins with transmembrane pore that can be embedded in lipid bilayer. With the development of single-channel current measurement technologies, biological nanopores have been reconstituted into planar lipid bilayer and used for single-molecule sensing of various analytes and events such as single-molecule DNA sensing and sequencing. To improve the sensitivity for specific analytes, various engineered nanopore proteins and strategies are deployed. Here, we introduce the origin and principle of nanopore sensing technology as well as the structure and associated properties of frequently used protein nanopores. Furthermore, sensing strategies for different applications are reviewed, with focus on the alteration of buffer condition, protein engineering, and deployment of accessory proteins and adapter-assisted sensing. Finally, outlooks for de novo design of nanopore and nanopore beyond sensing are discussed.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Chen Chen
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Yanjing Zhang
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, China
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49
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A Double-Layer Image Encryption Scheme Based on Chaotic Maps and DNA Strand Displacement. J CHEM-NY 2022. [DOI: 10.1155/2022/3906392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The image encryption schemes combining chaotic maps, DNA coding, and DNA sequence operation can effectively protect the image. In this paper, a double-layer image encryption scheme is proposed by combining chaotic maps with DNA strand displacement (DSD). Chaotic maps are used to generate pseudorandom sequences and perform routine scrambling and diffusion operations on the plaintext image. We propose three DSD-based encryption rules according to the diversity of DNA strand displacement, and these three encryption rules are used to encrypt the image at the DNA sequence level. The plaintext image can be transformed into the cipher image, which is difficult to be recognized without the correct keys through the double-layer encryption at the level of chaotic maps and DNA. Simulation results and security analysis show that the proposed encryption scheme can effectively protect image information and resist conventional information attacks.
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50
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Affiliation(s)
- Jason S. Kahn
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
| | - Oleg Gang
- Department of Chemical Engineering Columbia University New York NY 10027 USA
- Department of Applied Physics and Applied Mathematics Columbia University New York NY 10027 USA
- Center for Functional Nanomaterials Brookhaven National Laboratory Upton NY 11973 USA
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