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Jo S, Shin H, Joe SY, Baek D, Park C, Chun H. Recent progress in DNA data storage based on high-throughput DNA synthesis. Biomed Eng Lett 2024; 14:993-1009. [PMID: 39220021 PMCID: PMC11362454 DOI: 10.1007/s13534-024-00386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 09/04/2024] Open
Abstract
DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects.
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Affiliation(s)
- Seokwoo Jo
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Haewon Shin
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Sung-yune Joe
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - David Baek
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Chaewon Park
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Honggu Chun
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
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2
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Ma Y, Zhang Z, Jia B, Yuan Y. Automated high-throughput DNA synthesis and assembly. Heliyon 2024; 10:e26967. [PMID: 38500977 PMCID: PMC10945133 DOI: 10.1016/j.heliyon.2024.e26967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of lengthy oligonucleotides and the seamless assembly of numerous DNA fragments. With the advent of automated pipetting workstations and integrated experimental equipment, a substantial portion of repetitive tasks in the field of synthetic biology can now be efficiently accomplished through integrated liquid handling workstations. This not only reduces the need for manual labor but also enhances overall efficiency. This review explores the ongoing advancements in the oligonucleotide synthesis platform, automated DNA assembly techniques, and biofoundries. The development of accurate and high-throughput DNA synthesis and assembly technologies presents both challenges and opportunities.
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Affiliation(s)
- Yuxin Ma
- Frontier 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
| | - Zhaoyang Zhang
- Frontier 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
| | - Bin Jia
- Frontier 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
| | - Yingjin Yuan
- Frontier 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
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3
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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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4
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Torres-Huerta AL, Antonio-Pérez A, García-Huante Y, Alcázar-Ramírez NJ, Rueda-Silva JC. Biomolecule-Based Optical Metamaterials: Design and Applications. BIOSENSORS 2022; 12:962. [PMID: 36354471 PMCID: PMC9688573 DOI: 10.3390/bios12110962] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 06/16/2023]
Abstract
Metamaterials are broadly defined as artificial, electromagnetically homogeneous structures that exhibit unusual physical properties that are not present in nature. They possess extraordinary capabilities to bend electromagnetic waves. Their size, shape and composition can be engineered to modify their characteristics, such as iridescence, color shift, absorbance at different wavelengths, etc., and harness them as biosensors. Metamaterial construction from biological sources such as carbohydrates, proteins and nucleic acids represents a low-cost alternative, rendering high quantities and yields. In addition, the malleability of these biomaterials makes it possible to fabricate an endless number of structured materials such as composited nanoparticles, biofilms, nanofibers, quantum dots, and many others, with very specific, invaluable and tremendously useful optical characteristics. The intrinsic characteristics observed in biomaterials make them suitable for biomedical applications. This review addresses the optical characteristics of metamaterials obtained from the major macromolecules found in nature: carbohydrates, proteins and DNA, highlighting their biosensor field use, and pointing out their physical properties and production paths.
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Affiliation(s)
- Ana Laura Torres-Huerta
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Aurora Antonio-Pérez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Yolanda García-Huante
- Departamento de Ciencias Básicas, Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional (UPIITA-IPN), Mexico City 07340, Mexico
| | - Nayelhi Julieta Alcázar-Ramírez
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
| | - Juan Carlos Rueda-Silva
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Estado de México, Av. Lago de Guadalupe KM 3.5, Margarita Maza de Juárez, Cd. López Mateos, Atizapán de Zaragoza 52926, Mexico
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
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5
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Zhang Z, Ma P, Ahmed R, Wang J, Akin D, Soto F, Liu BF, Li P, Demirci U. Advanced Point-of-Care Testing Technologies for Human Acute Respiratory Virus Detection. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2103646. [PMID: 34623709 DOI: 10.1002/adma.202103646] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/25/2021] [Indexed: 04/14/2023]
Abstract
The ever-growing global threats to human life caused by the human acute respiratory virus (RV) infections have cost billions of lives, created a significant economic burden, and shaped society for centuries. The timely response to emerging RVs could save human lives and reduce the medical care burden. The development of RV detection technologies is essential for potentially preventing RV pandemic and epidemics. However, commonly used detection technologies lack sensitivity, specificity, and speed, thus often failing to provide the rapid turnaround times. To address this problem, new technologies are devised to address the performance inadequacies of the traditional methods. These emerging technologies offer improvements in convenience, speed, flexibility, and portability of point-of-care test (POCT). Herein, recent developments in POCT are comprehensively reviewed for eight typical acute respiratory viruses. This review discusses the challenges and opportunities of various recognition and detection strategies and discusses these according to their detection principles, including nucleic acid amplification, optical POCT, electrochemistry, lateral flow assays, microfluidics, enzyme-linked immunosorbent assays, and microarrays. The importance of limits of detection, throughput, portability, and specificity when testing clinical samples in resource-limited settings is emphasized. Finally, the evaluation of commercial POCT kits for both essential RV diagnosis and clinical-oriented practices is included.
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Affiliation(s)
- Zhaowei Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Peng Ma
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Rajib Ahmed
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Jie Wang
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Demir Akin
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Fernando Soto
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, P. R. China
| | - Peiwu Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, National Reference Laboratory for Agricultural Testing (Biotoxin), Key Laboratory of Biology and Genetic Improvement of Oil Crops, Key Laboratory of Detection for Mycotoxins, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, P. R. China
| | - Utkan Demirci
- Bio-Acoustic MEMS in Medicine (BAMM) Laboratory, Canary Center at Stanford for Cancer Early Detection, Department of Radiology, Stanford School of Medicine, Palo Alto, CA, 94304, USA
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6
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Multiplexed sensing of biomolecules with optically detected magnetic resonance of nitrogen-vacancy centers in diamond. Proc Natl Acad Sci U S A 2021; 118:2112664118. [PMID: 34903662 DOI: 10.1073/pnas.2112664118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/06/2021] [Indexed: 01/21/2023] Open
Abstract
In the past decade, a great effort has been devoted to develop new biosensor platforms for the detection of a wide range of analytes. Among the various approaches, magneto-DNA assay platforms have received extended interest for high sensitive and specific detection of targets with a simultaneous manipulation capacity. Here, using nitrogen-vacancy quantum centers in diamond as transducers for magnetic nanotags (MNTs), a hydrogel-based, multiplexed magneto-DNA assay is presented. Near-background-free sensing with diamond-based imaging combined with noninvasive control of chemically robust nanotags renders it a promising platform for applications in medical diagnostics, life science, and pharmaceutical drug research. To demonstrate its potential for practical applications, we employed the sensor platform in the sandwich DNA hybridization process and achieved a limit of detection in the attomolar range with single-base mismatch differentiation.
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7
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Kuiper BP, Prins RC, Billerbeck S. Oligo Pools as an Affordable Source of Synthetic DNA for Cost-Effective Library Construction in Protein- and Metabolic Pathway Engineering. Chembiochem 2021; 23:e202100507. [PMID: 34817110 PMCID: PMC9300125 DOI: 10.1002/cbic.202100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/23/2021] [Indexed: 11/11/2022]
Abstract
The construction of custom libraries is critical for rational protein engineering and directed evolution. Array‐synthesized oligo pools of thousands of user‐defined sequences (up to ∼350 bases in length) have emerged as a low‐cost commercially available source of DNA. These pools cost ≤10 % (depending on error rate and length) of other commercial sources of custom DNA, and this significant cost difference can determine whether an enzyme engineering project can be realized on a given research budget. However, while being cheap, oligo pools do suffer from a low concentration of individual oligos and relatively high error rates. Several powerful techniques that specifically make use of oligo pools have been developed and proven valuable or even essential for next‐generation protein and pathway engineering strategies, such as sequence‐function mapping, enzyme minimization, or de‐novo design. Here we consolidate the knowledge on these techniques and their applications to facilitate the use of oligo pools within the protein engineering community.
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Affiliation(s)
- Bastiaan P Kuiper
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Rianne C Prins
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Sonja Billerbeck
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
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8
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Bennet D, Vo‐Dinh T, Zenhausern F. Current and emerging opportunities in biological medium‐based computing and digital data storage. NANO SELECT 2021. [DOI: 10.1002/nano.202100275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Devasier Bennet
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
| | - Tuan Vo‐Dinh
- Department of Biomedical Engineering Department of Chemistry Fitzpatrick Institute for Photonics Duke University Durham North Carolina USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
- Department of Basic Medical Sciences College of Medicine Phoenix The University of Arizona Phoenix Arizona USA
- Department of Biomedical Engineering; and BIO5 Institute College of Engineering The University of Arizona Tucson Arizona USA
- School of Pharmaceutical Sciences University of Geneva Geneva Switzerland
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9
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Vashist SK. Trends in Multiplex Immunoassays for In Vitro Diagnostics and Point-of-Care Testing. Diagnostics (Basel) 2021; 11:diagnostics11091630. [PMID: 34573972 PMCID: PMC8471512 DOI: 10.3390/diagnostics11091630] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 09/02/2021] [Indexed: 11/17/2022] Open
Affiliation(s)
- Sandeep Kumar Vashist
- Sensing Self Pte. Ltd., 160 Robinson Road, #20-03, Singapore Business Federation Ctr., Singapore 068914, Singapore
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10
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Drees A, Fischer M. High-Throughput Selection and Characterisation of Aptamers on Optical Next-Generation Sequencers. Int J Mol Sci 2021; 22:9202. [PMID: 34502110 PMCID: PMC8431662 DOI: 10.3390/ijms22179202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Aptamers feature a number of advantages, compared to antibodies. However, their application has been limited so far, mainly because of the complex selection process. 'High-throughput sequencing fluorescent ligand interaction profiling' (HiTS-FLIP) significantly increases the selection efficiency and is consequently a very powerful and versatile technology for the selection of high-performance aptamers. It is the first experiment to allow the direct and quantitative measurement of the affinity and specificity of millions of aptamers simultaneously by harnessing the potential of optical next-generation sequencing platforms to perform fluorescence-based binding assays on the clusters displayed on the flow cells and determining their sequence and position in regular high-throughput sequencing. Many variants of the experiment have been developed that allow automation and in situ conversion of DNA clusters into base-modified DNA, RNA, peptides, and even proteins. In addition, the information from mutational assays, performed with HiTS-FLIP, provides deep insights into the relationship between the sequence, structure, and function of aptamers. This enables a detailed understanding of the sequence-specific rules that determine affinity, and thus, supports the evolution of aptamers. Current variants of the HiTS-FLIP experiment and its application in the field of aptamer selection, characterisation, and optimisation are presented in this review.
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Affiliation(s)
- Alissa Drees
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
| | - Markus Fischer
- Hamburg School of Food Science, Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany;
- Center for Hybrid Nanostructures (CHyN), Department of Physics, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
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11
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Song LF, Deng ZH, Gong ZY, Li LL, Li BZ. Large-Scale de novo Oligonucleotide Synthesis for Whole-Genome Synthesis and Data Storage: Challenges and Opportunities. Front Bioeng Biotechnol 2021; 9:689797. [PMID: 34239862 PMCID: PMC8258115 DOI: 10.3389/fbioe.2021.689797] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Over the past decades, remarkable progress on phosphoramidite chemistry-based large-scale de novo oligonucleotide synthesis has been achieved, enabling numerous novel and exciting applications. Among them, de novo genome synthesis and DNA data storage are striking. However, to make these two applications more practical, the synthesis length, speed, cost, and throughput require vast improvements, which is a challenge to be met by the phosphoramidite chemistry. Harnessing the power of enzymes, the recently emerged enzymatic methods provide a competitive route to overcome this challenge. In this review, we first summarize the status of large-scale oligonucleotide synthesis technologies including the basic methodology and large-scale synthesis approaches, with special focus on the emerging enzymatic methods. Afterward, we discuss the opportunities and challenges of large-scale oligonucleotide synthesis on de novo genome synthesis and DNA data storage respectively.
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Affiliation(s)
- Li-Fu Song
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zheng-Hua Deng
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zi-Yi Gong
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Lu-Lu Li
- LC-BIO Technologies Co., Ltd., Hangzhou, China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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12
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Yarman A, Scheller FW. How Reliable Is the Electrochemical Readout of MIP Sensors? SENSORS (BASEL, SWITZERLAND) 2020; 20:E2677. [PMID: 32397160 PMCID: PMC7248831 DOI: 10.3390/s20092677] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/01/2020] [Accepted: 05/06/2020] [Indexed: 01/15/2023]
Abstract
Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration.
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Affiliation(s)
- Aysu Yarman
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Frieder W. Scheller
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
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13
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Trotter M, Borst N, Thewes R, von Stetten F. Review: Electrochemical DNA sensing – Principles, commercial systems, and applications. Biosens Bioelectron 2020; 154:112069. [DOI: 10.1016/j.bios.2020.112069] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 02/06/2023]
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14
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15
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Peyvan K, Karouia F, Cooper JJ, Chamberlain J, Suciu D, Slota M, Pohorille A. Gene Expression Measurement Module (GEMM) for space application: Design and validation. LIFE SCIENCES IN SPACE RESEARCH 2019; 22:55-67. [PMID: 31421849 DOI: 10.1016/j.lssr.2019.07.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/05/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
In order to facilitate studies on the impact of the space environment on biological systems, we have developed a prototype of GEMM (Gene Expression Measurement Module) - an automated, miniaturized, integrated fluidic system for in-situ measurements of gene expression in microbial samples. The GEMM instrument is capable of (1) lysing bacterial cell walls, (2) extracting and purifying RNA released from cells, (3) hybridizing the RNA to probes attached to a microarray and (4) providing electrochemical readout, all in a microfluidics cartridge. To function on small, uncrewed spacecraft, the conventional, laboratory protocols for both sample preparation and hybridization required significant modifications. Biological validation of the instrument was carried out on Synechococcus elongatus, a photosynthetic cyanobacterium known for its metabolic diversity and resilience to adverse conditions. It was demonstrated that GEMM yielded reliable, reproducible gene expression profiles. GEMM is the only high throughput instrument that can be deployed in near future on space platforms other than the ISS to advance biological research in space. It can also prove useful for numerous terrestrial applications in the field.
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Affiliation(s)
| | - Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Space Biosciences Research Branch, Moffett Field, CA 94035, USA; NASA Ames Research Center, Exobiology Branch, MS 239-4, Moffett Field, CA 94035, USA.
| | | | | | | | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS 239-4, Moffett Field, CA 94035, USA.
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16
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Qiu C, Kaplan CD. Functional assays for transcription mechanisms in high-throughput. Methods 2019; 159-160:115-123. [PMID: 30797033 PMCID: PMC6589137 DOI: 10.1016/j.ymeth.2019.02.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/18/2019] [Indexed: 01/12/2023] Open
Abstract
Dramatic increases in the scale of programmed synthesis of nucleic acid libraries coupled with deep sequencing have powered advances in understanding nucleic acid and protein biology. Biological systems centering on nucleic acids or encoded proteins greatly benefit from such high-throughput studies, given that large DNA variant pools can be synthesized and DNA, or RNA products of transcription, can be easily analyzed by deep sequencing. Here we review the scope of various high-throughput functional assays for studies of nucleic acids and proteins in general, followed by discussion of how these types of study have yielded insights into the RNA Polymerase II (Pol II) active site as an example. We discuss methodological considerations in the design and execution of these experiments that should be valuable to studies in any system.
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Affiliation(s)
- Chenxi Qiu
- Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Research Institute, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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17
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Lim CC, Choong YS, Lim TS. Cognizance of Molecular Methods for the Generation of Mutagenic Phage Display Antibody Libraries for Affinity Maturation. Int J Mol Sci 2019; 20:E1861. [PMID: 30991723 PMCID: PMC6515083 DOI: 10.3390/ijms20081861] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/10/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Antibodies leverage on their unique architecture to bind with an array of antigens. The strength of interaction has a direct relation to the affinity of the antibodies towards the antigen. In vivo affinity maturation is performed through multiple rounds of somatic hypermutation and selection in the germinal centre. This unique process involves intricate sequence rearrangements at the gene level via molecular mechanisms. The emergence of in vitro display technologies, mainly phage display and recombinant DNA technology, has helped revolutionize the way antibody improvements are being carried out in the laboratory. The adaptation of molecular approaches in vitro to replicate the in vivo processes has allowed for improvements in the way recombinant antibodies are designed and tuned. Combinatorial libraries, consisting of a myriad of possible antibodies, are capable of replicating the diversity of the natural human antibody repertoire. The isolation of target-specific antibodies with specific affinity characteristics can also be accomplished through modification of stringent protocols. Despite the ability to screen and select for high-affinity binders, some 'fine tuning' may be required to enhance antibody binding in terms of its affinity. This review will provide a brief account of phage display technology used for antibody generation followed by a summary of different combinatorial library characteristics. The review will focus on available strategies, which include molecular approaches, next generation sequencing, and in silico approaches used for antibody affinity maturation in both therapeutic and diagnostic applications.
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Affiliation(s)
- Chia Chiu Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Penang 11800, Malaysia.
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, Penang 11800, Malaysia.
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18
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An Aptamer-Based Biosensor for Direct, Label-Free Detection of Melamine in Raw Milk. SENSORS 2018; 18:s18103227. [PMID: 30257498 PMCID: PMC6210019 DOI: 10.3390/s18103227] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 01/19/2023]
Abstract
Melamine, a nitrogen-rich compound, has been used as a food and milk additive to falsely increase the protein content. However, melamine is toxic, and high melamine levels in food or in milk can cause kidney and urinary problems, or even death. Hence, the detection of melamine in food and milk is desirable, for which numerous detection methods have been developed. Several methods have successfully detected melamine in raw milk; however, they require a sample preparation before the analyses. This study aimed to develop an aptamer-DNAzyme conjugated biosensor for label-free detection of melamine, in raw milk, without any sample preparation. An aptamer-DNAzyme conjugated biosensor was developed via screening using microarray analysis to identify the candidate aptamers followed by an optimization, to reduce the background noise and improve the aptamer properties, thereby, enhancing the signal-to-noise (S/N) ratio of the screened biosensor. The developed biosensor was evaluated via colorimetric detection and tested with raw milk without any sample preparation, using N-methylmesoporphyrin IX for fluorescence detection. The biosensor displayed significantly higher signal intensity at 2 mM melamine (S/N ratio, 20.2), which was sufficient to detect melamine at high concentrations, in raw milk.
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19
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Bianchessi M, Burgarella S, Cereda M. Point-of-Care Systems for Rapid DNA Quantification in Oncology. TUMORI JOURNAL 2018; 94:216-25. [DOI: 10.1177/030089160809400214] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The development of new powerful applications and the improvement in fabrication techniques are promising an explosive growth in lab-on-chip use in the upcoming future. As the demand reaches significant levels, the semiconductor industry may enter in the field, bringing its capability to produce complex devices in large volumes, high quality and low cost. The lab-on-chip concept, when applied to medicine, leads to the point-of-care concept, where simple, compact and cheap instruments allow diagnostic assays to be performed quickly by untrained personnel directly at the patient's side. In this paper, some practical and economical considerations are made to support the advantages of point-of-care testing. A series of promising technologies developed by STMicroelectronics on lab-on-chips is also presented, mature enough to enter in the common medical practice. The possible use of these techniques for cancer research, diagnosis and treatment are illustrated together with the benefits offered by their implementation in point-of-care testing.
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Affiliation(s)
| | | | - Marco Cereda
- Università degli Studi di Milano-Bicocca, Milan, Italy
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20
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DNA multi-bit non-volatile memory and bit-shifting operations using addressable electrode arrays and electric field-induced hybridization. Nat Commun 2018; 9:281. [PMID: 29348493 PMCID: PMC5773625 DOI: 10.1038/s41467-017-02705-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/20/2017] [Indexed: 11/09/2022] Open
Abstract
DNA has been employed to either store digital information or to perform parallel molecular computing. Relatively unexplored is the ability to combine DNA-based memory and logical operations in a single platform. Here, we show a DNA tri-level cell non-volatile memory system capable of parallel random-access writing of memory and bit shifting operations. A microchip with an array of individually addressable electrodes was employed to enable random access of the memory cells using electric fields. Three segments on a DNA template molecule were used to encode three data bits. Rapid writing of data bits was enabled by electric field-induced hybridization of fluorescently labeled complementary probes and the data bits were read by fluorescence imaging. We demonstrated the rapid parallel writing and reading of 8 (23) combinations of 3-bit memory data and bit shifting operations by electric field-induced strand displacement. Our system may find potential applications in DNA-based memory and computations. DNA based technology holds promise for non-volatile memory and computational tasks, yet the relatively slow hybridization kinetics remain a bottleneck. Here, Song et al. have developed an electric field-induced hybridization platform that can speed up multi-bit memory and logic operations.
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21
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Kanno Y, Ino K, Abe H, Sakamoto C, Onodera T, Inoue KY, Suda A, Kunikata R, Matsudaira M, Shiku H, Matsue T. Electrochemicolor Imaging Using an LSI-Based Device for Multiplexed Cell Assays. Anal Chem 2017; 89:12778-12786. [PMID: 29090905 DOI: 10.1021/acs.analchem.7b03042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Multiplexed bioimaging systems have triggered the development of effective assays, contributing new biological information. Although electrochemical imaging is beneficial for quantitative analysis in real time, monitoring multiple cell functions is difficult. We have developed a novel electrochemical imaging system, herein, using a large-scale integration (LSI)-based amperometric device for detecting multiple biomolecules simultaneously. This system is designated as an electrochemicolor imaging system in which the current signals from two different types of biomolecules are depicted as a multicolor electrochemical image. The mode-selectable function of the 400-electrode device enables the imaging system and two different potentials can be independently applied to the selected electrodes. The imaging system is successfully applied for detecting multiple cell functions of the embryonic stem (ES) cell and the rat pheochromocytoma (PC12) cell aggregates. To the best of our knowledge, this is the first time that a real-time electrochemical mapping technique for multiple electroactive species, simultaneously, has been reported. The imaging system is a promising bioanalytical method for exploring complex biological phenomena.
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Affiliation(s)
- Yusuke Kanno
- Graduate School of Environmental Studies, Tohoku University , 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kosuke Ino
- Graduate School of Engineering, Tohoku University , 6-6-11-406 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Hiroya Abe
- Graduate School of Environmental Studies, Tohoku University , 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Chika Sakamoto
- Graduate School of Environmental Studies, Tohoku University , 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Takehiro Onodera
- Graduate School of Engineering, Tohoku University , 6-6-11-406 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kumi Y Inoue
- Graduate School of Environmental Studies, Tohoku University , 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Atsushi Suda
- Japan Aviation Electronics Industry, Ltd. , 1-1 Musashino 3-chome, Akishima-shi, Tokyo 196-8555, Japan
| | - Ryota Kunikata
- Japan Aviation Electronics Industry, Ltd. , 1-1 Musashino 3-chome, Akishima-shi, Tokyo 196-8555, Japan
| | - Masahki Matsudaira
- Micro System Integration Center, Tohoku University , 519-1176 Aramaki-aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Hitoshi Shiku
- Graduate School of Engineering, Tohoku University , 6-6-11-406 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Tomokazu Matsue
- Graduate School of Environmental Studies, Tohoku University , 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
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22
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Hiramoto K, Yasumi M, Ushio H, Shunori A, Ino K, Shiku H, Matsue T. Development of Oxygen Consumption Analysis with an on-Chip Electrochemical Device and Simulation. Anal Chem 2017; 89:10303-10310. [DOI: 10.1021/acs.analchem.7b02074] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Kaoru Hiramoto
- Corporate
Engineering Division, Automotive and Industrial Systems Company, Panasonic Corporation, 1006 Kadoma, Kadomashi, 571-0050, Japan
| | - Masahiro Yasumi
- Corporate
Engineering Division, Automotive and Industrial Systems Company, Panasonic Corporation, 1006 Kadoma, Kadomashi, 571-0050, Japan
| | - Hiroshi Ushio
- Corporate
Engineering Division, Automotive and Industrial Systems Company, Panasonic Corporation, 1006 Kadoma, Kadomashi, 571-0050, Japan
| | - Atsushi Shunori
- Corporate
Engineering Division, Automotive and Industrial Systems Company, Panasonic Corporation, 1006 Kadoma, Kadomashi, 571-0050, Japan
| | - Kosuke Ino
- Graduate
School of Engineering, Tohoku University, 6-6-11-406 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Hitoshi Shiku
- Graduate
School of Engineering, Tohoku University, 6-6-11-406 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Tomokazu Matsue
- Graduate School of Environmental Studies, Tohoku University, 6-6-11-605
Aramaki-aza Aoba, Aoba-ku, Sendai, 980-8579, Japan
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23
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Bruch R, Chatelle C, Kling A, Rebmann B, Wirth S, Schumann S, Weber W, Dincer C, Urban G. Clinical on-site monitoring of ß-lactam antibiotics for a personalized antibiotherapy. Sci Rep 2017; 7:3127. [PMID: 28600499 PMCID: PMC5466632 DOI: 10.1038/s41598-017-03338-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 04/26/2017] [Indexed: 01/07/2023] Open
Abstract
An appropriate antibiotherapy is crucial for the safety and recovery of patients. Depending on the clinical conditions of patients, the required dose to effectively eradicate an infection may vary. An inadequate dosing not only reduces the efficacy of the antibiotic, but also promotes the emergence of antimicrobial resistances. Therefore, a personalized therapy is of great interest for improved patients' outcome and will reduce in long-term the prevalence of multidrug-resistances. In this context, on-site monitoring of the antibiotic blood concentration is fundamental to facilitate an individual adjustment of the antibiotherapy. Herein, we present a bioinspired approach for the bedside monitoring of free accessible ß-lactam antibiotics, including penicillins (piperacillin) and cephalosporins (cefuroxime and cefazolin) in untreated plasma samples. The introduced system combines a disposable microfluidic chip with a naturally occurring penicillin-binding protein, resulting in a high-performance platform, capable of gauging very low antibiotic concentrations (less than 6 ng ml-1) from only 1 µl of serum. The system's applicability to a personalized antibiotherapy was successfully demonstrated by monitoring the pharmacokinetics of patients, treated with ß-lactam antibiotics, undergoing surgery.
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Affiliation(s)
- R Bruch
- Department of Microsystems Engineering, University of Freiburg, 79110, Freiburg, Germany
| | - C Chatelle
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - A Kling
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - B Rebmann
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - S Wirth
- Department of Anaesthesiology and Critical Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - S Schumann
- Department of Anaesthesiology and Critical Care, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, 79106, Freiburg, Germany
| | - W Weber
- Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany.,BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104, Freiburg, Germany
| | - C Dincer
- Department of Microsystems Engineering, University of Freiburg, 79110, Freiburg, Germany. .,Freiburg Materials Research Center, University of Freiburg, 79104, Freiburg, Germany.
| | - G Urban
- Department of Microsystems Engineering, University of Freiburg, 79110, Freiburg, Germany.,Freiburg Materials Research Center, University of Freiburg, 79104, Freiburg, Germany
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24
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Dincer C, Bruch R, Kling A, Dittrich PS, Urban GA. Multiplexed Point-of-Care Testing - xPOCT. Trends Biotechnol 2017; 35:728-742. [PMID: 28456344 PMCID: PMC5538621 DOI: 10.1016/j.tibtech.2017.03.013] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/13/2022]
Abstract
Multiplexed point-of-care testing (xPOCT), which is simultaneous on-site detection of different analytes from a single specimen, has recently gained increasing importance for clinical diagnostics, with emerging applications in resource-limited settings (such as in the developing world, in doctors’ offices, or directly at home). Nevertheless, only single-analyte approaches are typically considered as the major paradigm in many reviews of point-of-care testing. Here, we comprehensively review the present diagnostic systems and techniques for xPOCT applications. Different multiplexing technologies (e.g., bead- or array-based systems) are considered along with their detection methods (e.g., electrochemical or optical). We also address the unmet needs and challenges of xPOCT. Finally, we critically summarize the in-field applicability and the future perspectives of the presented approaches. Simultaneous on-site measurement of different substances from a single sample, called multiplexed point-of-care testing, has recently become more and more important for in vitro diagnostics. The major aim for the development of xPOCT systems is the smart combination of a high-performing device with a low system complexity. Thus, the on-site tests are realized in a short time by non-experts and ensure comparable results with clinical and central laboratory findings. A multiplexing capability of up to 10 analytes has been sufficient for many recent xPOCT applications. The future of xPOCT devices will be driven by novel biotechnologies (e.g., aptamers) or targets (e.g., circulating RNAs or tumor cells, exosomes, and miRNAs), as well as applications like personalized medicine, homecare monitoring, and wearables.
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Affiliation(s)
- Can Dincer
- University of Freiburg, Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; University of Freiburg, Freiburg Materials Research Center (FMF), Stefan-Meier-Straße 21, 79104 Freiburg, Germany.
| | - Richard Bruch
- University of Freiburg, Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, Georges-Koehler-Allee 103, 79110 Freiburg, Germany
| | - André Kling
- ETH Zurich, Department of Biosystems Science and Engineering, Bioanalytics Group, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Petra S Dittrich
- ETH Zurich, Department of Biosystems Science and Engineering, Bioanalytics Group, Mattenstrasse 26, 4058 Basel, Switzerland
| | - Gerald A Urban
- University of Freiburg, Department of Microsystems Engineering (IMTEK), Laboratory for Sensors, Georges-Koehler-Allee 103, 79110 Freiburg, Germany; University of Freiburg, Freiburg Materials Research Center (FMF), Stefan-Meier-Straße 21, 79104 Freiburg, Germany
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25
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Karouia F, Peyvan K, Pohorille A. Toward biotechnology in space: High-throughput instruments for in situ biological research beyond Earth. Biotechnol Adv 2017; 35:905-932. [PMID: 28433608 DOI: 10.1016/j.biotechadv.2017.04.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 03/27/2017] [Accepted: 04/12/2017] [Indexed: 12/18/2022]
Abstract
Space biotechnology is a nascent field aimed at applying tools of modern biology to advance our goals in space exploration. These advances rely on our ability to exploit in situ high throughput techniques for amplification and sequencing DNA, and measuring levels of RNA transcripts, proteins and metabolites in a cell. These techniques, collectively known as "omics" techniques have already revolutionized terrestrial biology. A number of on-going efforts are aimed at developing instruments to carry out "omics" research in space, in particular on board the International Space Station and small satellites. For space applications these instruments require substantial and creative reengineering that includes automation, miniaturization and ensuring that the device is resistant to conditions in space and works independently of the direction of the gravity vector. Different paths taken to meet these requirements for different "omics" instruments are the subjects of this review. The advantages and disadvantages of these instruments and technological solutions and their level of readiness for deployment in space are discussed. Considering that effects of space environments on terrestrial organisms appear to be global, it is argued that high throughput instruments are essential to advance (1) biomedical and physiological studies to control and reduce space-related stressors on living systems, (2) application of biology to life support and in situ resource utilization, (3) planetary protection, and (4) basic research about the limits on life in space. It is also argued that carrying out measurements in situ provides considerable advantages over the traditional space biology paradigm that relies on post-flight data analysis.
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Affiliation(s)
- Fathi Karouia
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA; NASA Ames Research Center, Flight Systems Implementation Branch, Moffett Field, CA 94035, USA.
| | | | - Andrew Pohorille
- University of California San Francisco, Department of Pharmaceutical Chemistry, San Francisco, CA 94158, USA; NASA Ames Research Center, Exobiology Branch, MS239-4, Moffett Field, CA 94035, USA.
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26
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Acero Sánchez JL, Joda H, Henry OYF, Solnestam BW, Kvastad L, Akan PS, Lundeberg J, Laddach N, Ramakrishnan D, Riley I, Schwind C, Latta D, O'Sullivan CK. Electrochemical Genetic Profiling of Single Cancer Cells. Anal Chem 2017; 89:3378-3385. [PMID: 28211676 DOI: 10.1021/acs.analchem.6b03973] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent understandings in the development and spread of cancer have led to the realization of novel single cell analysis platforms focused on circulating tumor cells (CTCs). A simple, rapid, and inexpensive analytical platform capable of providing genetic information on these rare cells is highly desirable to support clinicians and researchers alike to either support the selection or adjustment of therapy or provide fundamental insights into cell function and cancer progression mechanisms. We report on the genetic profiling of single cancer cells, exploiting a combination of multiplex ligation-dependent probe amplification (MLPA) and electrochemical detection. Cells were isolated using laser capture and lysed, and the mRNA was extracted and transcribed into DNA. Seven markers were amplified by MLPA, which allows for the simultaneous amplification of multiple targets with a single primer pair, using MLPA probes containing unique barcode sequences. Capture probes complementary to each of these barcode sequences were immobilized on a printed circuit board (PCB) manufactured electrode array and exposed to single-stranded MLPA products and subsequently to a single stranded DNA reporter probe bearing a HRP molecule, followed by substrate addition and fast electrochemical pulse amperometric detection. We present a simple, rapid, flexible, and inexpensive approach for the simultaneous quantification of multiple breast cancer related mRNA markers, with single tumor cell sensitivity.
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Affiliation(s)
- Josep Ll Acero Sánchez
- Universitat Rovira i Virgili , Departament de Enginyeria Química, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Hamdi Joda
- Universitat Rovira i Virgili , Departament de Enginyeria Química, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Olivier Y F Henry
- Universitat Rovira i Virgili , Departament de Enginyeria Química, Av. Països Catalans 26, 43007 Tarragona, Spain
| | - Beata W Solnestam
- KTH Royal Institute of Technology , Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65 Solna, Sweden
| | - Linda Kvastad
- KTH Royal Institute of Technology , Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65 Solna, Sweden
| | - Pelin S Akan
- KTH Royal Institute of Technology , Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65 Solna, Sweden
| | - Joakim Lundeberg
- KTH Royal Institute of Technology , Science for Life Laboratory (SciLifeLab Stockholm), School of Biotechnology, Division of Gene Technology, SE-171 65 Solna, Sweden
| | - Nadja Laddach
- MRC-Holland , Willem Schoutenstraat 1, 1057 DL Amsterdam, The Netherlands
| | - Dheeraj Ramakrishnan
- Labman Automation Ltd. , Seamer Hill, Seamer, Stokesley, North Yorkshire TS9 5NQ, United Kingdom
| | - Ian Riley
- Labman Automation Ltd. , Seamer Hill, Seamer, Stokesley, North Yorkshire TS9 5NQ, United Kingdom
| | - Carmen Schwind
- Fraunhofer (ICT-IMM) , Carl-Zeiss-Str. 18-20, 55129 Mainz, Germany
| | - Daniel Latta
- Fraunhofer (ICT-IMM) , Carl-Zeiss-Str. 18-20, 55129 Mainz, Germany
| | - Ciara K O'Sullivan
- Universitat Rovira i Virgili , Departament de Enginyeria Química, Av. Països Catalans 26, 43007 Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats , Passeig Lluís Companys 23, 08010 Barcelona, Spain
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27
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Kuhn P, Wagner K, Heil K, Liss M, Netuschil N. Next generation gene synthesis: From microarrays to genomes. Eng Life Sci 2016; 17:6-13. [PMID: 32624724 DOI: 10.1002/elsc.201600121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/29/2016] [Accepted: 07/25/2016] [Indexed: 11/11/2022] Open
Abstract
Similar to the incredible advances in DNA sequencing, the de novo synthesis of DNA is subject to innovations and fast progress in terms of synthesis speed and cost. We will discuss novel techniques that are expected to enable high-throughput synthesis of oligonucleotides on microarrays and the subsequent assembly into longer fragments, up to whole genomes. Especially, the inherent disadvantages of microarray-derived oligonucleotide pools for gene synthesis will be discussed in detail, and also the different approaches to still render these oligonucleotides useful for gene assembly. These so-called next-generation techniques will lead to a significant cost reduction of gene synthesis and to the possibility of much larger projects, such as whole genome synthesis.
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Affiliation(s)
- Phillip Kuhn
- Thermo Fisher Scientific/Geneart GmbH Regensburg Germany
| | - Katrin Wagner
- Thermo Fisher Scientific/Geneart GmbH Regensburg Germany
| | - Korbinian Heil
- Thermo Fisher Scientific/Geneart GmbH Regensburg Germany
| | - Michael Liss
- Thermo Fisher Scientific/Geneart GmbH Regensburg Germany
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28
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Sánchez JA, Henry O, Joda H, Solnestam B, Kvastad L, Johansson E, Akan P, Lundeberg J, Lladach N, Ramakrishnan D, Riley I, O'Sullivan C. Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach. Biosens Bioelectron 2016; 82:224-32. [DOI: 10.1016/j.bios.2016.04.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
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29
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Kling A, Chatelle C, Armbrecht L, Qelibari E, Kieninger J, Dincer C, Weber W, Urban G. Multianalyte Antibiotic Detection on an Electrochemical Microfluidic Platform. Anal Chem 2016; 88:10036-10043. [DOI: 10.1021/acs.analchem.6b02294] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- André Kling
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
| | - Claire Chatelle
- University of Freiburg, Faculty of Biology and Centre
for Biological Signalling Studies, Schänzlestraße 18, DE-79104 Freiburg, Germany
| | - Lucas Armbrecht
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
| | - Edvina Qelibari
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
| | - Jochen Kieninger
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
| | - Can Dincer
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
- University of Freiburg, Freiburg Materials Research
Center, Stefan-Meier-Straße
21, DE-79104 Freiburg, Germany
| | - Wilfried Weber
- University of Freiburg, Faculty of Biology and Centre
for Biological Signalling Studies, Schänzlestraße 18, DE-79104 Freiburg, Germany
| | - Gerald Urban
- University of Freiburg, Department of Microsystems
Engineering, Georges-Koehler-Allee
103, DE-79110 Freiburg, Germany
- University of Freiburg, Freiburg Materials Research
Center, Stefan-Meier-Straße
21, DE-79104 Freiburg, Germany
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30
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Oh JM, Chow KF. Naked-Eye Coulometric Sensor Using a Longitudinally Oriented Ag Band Electrode in a Microfluidic Channel. Anal Chem 2016; 88:4849-56. [DOI: 10.1021/acs.analchem.6b00552] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jung-Min Oh
- Department
of Chemistry, University of Massachusetts Lowell, One University
Ave., Lowell, Massachusetts 01854, United States
| | - Kwok-Fan Chow
- Department
of Chemistry, University of Massachusetts Lowell, One University
Ave., Lowell, Massachusetts 01854, United States
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31
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Klein JC, Lajoie MJ, Schwartz JJ, Strauch EM, Nelson J, Baker D, Shendure J. Multiplex pairwise assembly of array-derived DNA oligonucleotides. Nucleic Acids Res 2015; 44:e43. [PMID: 26553805 PMCID: PMC4797260 DOI: 10.1093/nar/gkv1177] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 10/22/2015] [Indexed: 01/16/2023] Open
Abstract
While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.
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Affiliation(s)
- Jason C Klein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Marc J Lajoie
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jerrod J Schwartz
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Eva-Maria Strauch
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jorgen Nelson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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32
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Yazdi SMHT, Kiah HM, Garcia-Ruiz E, Ma J, Zhao H, Milenkovic O. DNA-Based Storage: Trends and Methods. ACTA ACUST UNITED AC 2015. [DOI: 10.1109/tmbmc.2016.2537305] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Abe H, Ino K, Li CZ, Kanno Y, Inoue KY, Suda A, Kunikata R, Matsudaira M, Takahashi Y, Shiku H, Matsue T. Electrochemical Imaging of Dopamine Release from Three-Dimensional-Cultured PC12 Cells Using Large-Scale Integration-Based Amperometric Sensors. Anal Chem 2015; 87:6364-70. [DOI: 10.1021/acs.analchem.5b01307] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Hiroya Abe
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kosuke Ino
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Chen-Zhong Li
- Nanobioengineering/Nanobioelectronics Laboratory, Department
of Biomedical Engineering, Florida International University, 10555 West
Flagler Street, Miami, Florida 33174, United States
- WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1
Katahira, Aoba, Sendai 980-8577, Japan
| | - Yusuke Kanno
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Kumi Y. Inoue
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Atsushi Suda
- Japan Aviation Electronics Industry, Ltd. 1-1, Musashino 3-chome, Akishima-shi, Tokyo 196-8555, Japan
| | - Ryota Kunikata
- Japan Aviation Electronics Industry, Ltd. 1-1, Musashino 3-chome, Akishima-shi, Tokyo 196-8555, Japan
| | - Masahki Matsudaira
- Micro
System Integration Center, Tohoku University, 519-1176 Aramaki-aza Aoba, Aoba-ku, Sendai 980-0845, Japan
| | - Yasufumi Takahashi
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
- WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1
Katahira, Aoba, Sendai 980-8577, Japan
- PRESTO, JST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Hitoshi Shiku
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
| | - Tomokazu Matsue
- Graduate School
of Environmental Studies, Tohoku University, 6-6-11-604 Aramaki-aza Aoba, Aoba-ku, Sendai 980-8579, Japan
- WPI-Advanced Institute for Materials Research, Tohoku University, 2-1-1
Katahira, Aoba, Sendai 980-8577, Japan
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34
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Aptamer Microarrays—Current Status and Future Prospects. MICROARRAYS 2015; 4:115-32. [PMID: 27600216 PMCID: PMC4996391 DOI: 10.3390/microarrays4020115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/09/2015] [Accepted: 03/18/2015] [Indexed: 12/16/2022]
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Abstract
Molecular diagnostics comprises a main analytical division in clinical laboratory diagnostics. The analysis of RNA or DNA helps to diagnose infectious diseases and identify genetic determined disorders or even cancer. Starting from mono-parametric tests within the last years, technologies have evolved that allow for the detection of many parameters in parallel, e.g., by using multiplex nucleic acid amplification techniques, microarrays, or next-generation sequencing technologies. The introduction of closed-tube systems as well as lab-on-a-chip devices further resulted in a higher automation degree with a reduced contamination risk. These applications complement or even stepwise replace classical methods in clinical microbiology like virus cultures, resistance determination, microscopic and metabolic analyses, as well as biochemical or immunohistochemical assays. In addition, novel diagnostic markers appear, like noncoding RNAs and miRNAs providing additional room for novel biomarkers. This article provides an overview of microarrays as diagnostics devices and research tools. Introduced in 1995 for transcription analysis, microarrays are used today to detect several different biomolecules like DNA, RNA, miRNA, and proteins among others. Mainly used in research, some microarrays also found their way to clinical diagnostics. Further, closed lab-on-a-chip devices that use DNA microarrays as detection tools are discussed, and additionally, an outlook toward applications of next-generation sequencing tools in diagnostics will be given.
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Affiliation(s)
- Volker A. Erdmann
- Free University of Berlin Institute of Chemistry/Biochemistry, Thielallee 63, Berlin Germany
| | - Stefan Jurga
- Nanobiomedical Center, Adam Mickiewicz University, Umultowska 85 Poznań, Poland
| | - Jan Barciszewski
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14 Poznań, Poland
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36
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Inoue KY, Matsudaira M, Nakano M, Ino K, Sakamoto C, Kanno Y, Kubo R, Kunikata R, Kira A, Suda A, Tsurumi R, Shioya T, Yoshida S, Muroyama M, Ishikawa T, Shiku H, Satoh S, Esashi M, Matsue T. Advanced LSI-based amperometric sensor array with light-shielding structure for effective removal of photocurrent and mode selectable function for individual operation of 400 electrodes. LAB ON A CHIP 2015; 15:848-856. [PMID: 25483361 DOI: 10.1039/c4lc01099j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We have developed a large-scale integrated (LSI) complementary metal-oxide semiconductor (CMOS)-based amperometric sensor array system called "Bio-LSI" as a platform for electrochemical bio-imaging and multi-point biosensing with 400 measurement points. In this study, we newly developed a Bio-LSI chip with a light-shield structure and a mode-selectable function with the aim of extending the application range of Bio-LSI. The light shield created by the top metal layer of the LSI chip significantly reduces the noise generated by the photocurrent, whose value is less than 1% of the previous Bio-LSI without the light shield. The mode-selectable function enables the individual operation of 400 electrodes in off, electrometer, V1, and V2 mode. The off-mode cuts the electrode from the electric circuit. The electrometer-mode reads out the electrode potential. The V1-mode and the V2-mode set the selected sensor electrode at two different independent voltages and read out the current. We demonstrated the usefulness of the mode-selectable function. First, we displayed a dot picture based on the redox reactions of 2.0 mM ferrocenemethanol at 400 electrodes by applying two different independent voltages using the V1 and V2 modes. Second, we carried out a simultaneous detection of O2 and H2O2 using the V1 and V2 modes. Third, we used the off and V1 modes for the modification of the osmium-polyvinylpyridine gel polymer containing horseradish peroxidase (Os-HRP) at the selected electrodes, which act as sensors for H2O2. These results confirm that the advanced version of Bio-LSI is a promising tool that can be applied to a wide range of analytical fields.
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Affiliation(s)
- Kumi Y Inoue
- Graduate School of Environmental Studies, Tohoku University, 6-6-11 Aramaki-Aza-Aoba, Aoba-ku, Sendai 980-8579, Japan.
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37
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INO K. Microchemistry- and MEMS-based Integrated Electrochemical Devices for Bioassay Applications. ELECTROCHEMISTRY 2015. [DOI: 10.5796/electrochemistry.83.688] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Kosuke INO
- Graduate School of Environmental Studies, Tohoku University
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38
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Electrophoretic and field-effect graphene for all-electrical DNA array technology. Nat Commun 2014; 5:4866. [PMID: 25189574 DOI: 10.1038/ncomms5866] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 07/31/2014] [Indexed: 11/08/2022] Open
Abstract
Field-effect transistor biomolecular sensors based on low-dimensional nanomaterials boast sensitivity, label-free operation and chip-scale construction. Chemical vapour deposition graphene is especially well suited for multiplexed electronic DNA array applications, since its large two-dimensional morphology readily lends itself to top-down fabrication of transistor arrays. Nonetheless, graphene field-effect transistor DNA sensors have been studied mainly at single-device level. Here we create, from chemical vapour deposition graphene, field-effect transistor arrays with two features representing steps towards multiplexed DNA arrays. First, a robust array yield--seven out of eight transistors--is achieved with a 100-fM sensitivity, on par with optical DNA microarrays and at least 10 times higher than prior chemical vapour deposition graphene transistor DNA sensors. Second, each graphene acts as an electrophoretic electrode for site-specific probe DNA immobilization, and performs subsequent site-specific detection of target DNA as a field-effect transistor. The use of graphene as both electrode and transistor suggests a path towards all-electrical multiplexed graphene DNA arrays.
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39
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Lee SW, Saraf RF. Multianalyte electrochemical biosensor on a monolith electrode by optically scanning the electrical double layer. Biosens Bioelectron 2014; 57:41-7. [DOI: 10.1016/j.bios.2014.01.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 01/12/2014] [Accepted: 01/23/2014] [Indexed: 10/25/2022]
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40
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Kosuri S, Church GM. Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 2014; 11:499-507. [PMID: 24781323 PMCID: PMC7098426 DOI: 10.1038/nmeth.2918] [Citation(s) in RCA: 477] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 03/10/2014] [Indexed: 12/23/2022]
Abstract
For over 60 years, the synthetic production of new DNA sequences has helped researchers understand and engineer biology. Here we summarize methods and caveats for the de novo synthesis of DNA, with particular emphasis on recent technologies that allow for large-scale and low-cost production. In addition, we discuss emerging applications enabled by large-scale de novo DNA constructs, as well as the challenges and opportunities that lie ahead.
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Affiliation(s)
- Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - George M Church
- 1] Wyss Institute for Biologically Inspired Engineering, Boston, Massachusetts, USA. [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
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41
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Clausmeyer J, Schuhmann W, Plumeré N. Electrochemical patterning as a tool for fabricating biomolecule microarrays. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.03.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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42
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Reusable conductimetric array of interdigitated microelectrodes for the readout of low-density microarrays. Anal Chim Acta 2014; 832:44-50. [DOI: 10.1016/j.aca.2014.04.064] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 04/29/2014] [Accepted: 04/30/2014] [Indexed: 11/20/2022]
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43
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Smith MW, Ghindilis AL, Seoudi IA, Smith K, Billharz R, Simon HM. A new restriction endonuclease-based method for highly-specific detection of DNA targets from methicillin-resistant Staphylococcus aureus. PLoS One 2014; 9:e97826. [PMID: 24831802 PMCID: PMC4022673 DOI: 10.1371/journal.pone.0097826] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 04/24/2014] [Indexed: 11/18/2022] Open
Abstract
PCR multiplexing has proven to be challenging, and thus has provided limited means for pathogen genotyping. We developed a new approach for analysis of PCR amplicons based on restriction endonuclease digestion. The first stage of the restriction enzyme assay is hybridization of a target DNA to immobilized complementary oligonucleotide probes that carry a molecular marker, horseradish peroxidase (HRP). At the second stage, a target-specific restriction enzyme is added, cleaving the target-probe duplex at the corresponding restriction site and releasing the HRP marker into solution, where it is quantified colorimetrically. The assay was tested for detection of the methicillin-resistant Staphylococcus aureus (MRSA) pathogen, using the mecA gene as a target. Calibration curves indicated that the limit of detection for both target oligonucleotide and PCR amplicon was approximately 1 nM. Sequences of target oligonucleotides were altered to demonstrate that (i) any mutation of the restriction site reduced the signal to zero; (ii) double and triple point mutations of sequences flanking the restriction site reduced restriction to 50–80% of the positive control; and (iii) a minimum of a 16-bp target-probe dsDNA hybrid was required for significant cleavage. Further experiments showed that the assay could detect the mecA amplicon from an unpurified PCR mixture with detection limits similar to those with standard fluorescence-based qPCR. Furthermore, addition of a large excess of heterologous genomic DNA did not affect amplicon detection. Specificity of the assay is very high because it involves two biorecognition steps. The proposed assay is low-cost and can be completed in less than 1 hour. Thus, we have demonstrated an efficient new approach for pathogen detection and amplicon genotyping in conjunction with various end-point and qPCR applications. The restriction enzyme assay may also be used for parallel analysis of multiple different amplicons from the same unpurified mixture in broad-range PCR applications.
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Affiliation(s)
- Maria W. Smith
- Center for Coastal Margin Observation & Prediction, and Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America
- Cascade Biosystems, Inc., Colfax, Wisconsin, United States of America
- * E-mail:
| | | | | | - Kenneth Smith
- Cascade Biosystems, Inc., Colfax, Wisconsin, United States of America
| | - Rosalind Billharz
- Pacific Lutheran University, Department of Biology, Tacoma, Washington, United States of America
| | - Holly M. Simon
- Center for Coastal Margin Observation & Prediction, and Institute of Environmental Health, Oregon Health & Science University, Portland, Oregon, United States of America
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44
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Díaz-González M, Muñoz-Berbel X, Jiménez-Jorquera C, Baldi A, Fernández-Sánchez C. Diagnostics Using Multiplexed Electrochemical Readout Devices. ELECTROANAL 2014. [DOI: 10.1002/elan.201400015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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45
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Ino K, Kanno Y, Nishijo T, Komaki H, Yamada Y, Yoshida S, Takahashi Y, Shiku H, Matsue T. Densified Electrochemical Sensors Based on Local Redox Cycling between Vertically Separated Electrodes in Substrate Generation/Chip Collection and Extended Feedback Modes. Anal Chem 2014; 86:4016-23. [DOI: 10.1021/ac500435d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Kosuke Ino
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Yusuke Kanno
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Taku Nishijo
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Hirokazu Komaki
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Yuta Yamada
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Shinya Yoshida
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Yasufumi Takahashi
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Hitoshi Shiku
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
| | - Tomokazu Matsue
- Graduate School of Environmental Studies and §WPI Advanced Institute
for Materials Research, Tohoku University, Sendai, Japan 980-8579
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46
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Abstract
In the coming years, genetic test results will be increasingly used as indicators that influence medical decision making. Novel instrumentation that is able to detect relevant mutations in a point-of-care setting is being developed to facilitate this increase, frequently as a spin-off from recent research in the area of biothreat monitoring. This market review will describe the current generation of instrumentation that is most suitable for use in a point-of-care setting; it will also try to identify some of the technologies that will make-up the next generation of instrumentation currently being prepared for the market.
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Affiliation(s)
- Mark G Dobson
- National Centre for Medical Genetics, University College Dublin, Our Lady's Children's Hospital, Crumlin, Dublin 12, Ireland.
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47
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Şen M, Ino K, Inoue KY, Arai T, Nishijo T, Suda A, Kunikata R, Shiku H, Matsue T. LSI-based amperometric sensor for real-time monitoring of embryoid bodies. Biosens Bioelectron 2013; 48:12-8. [DOI: 10.1016/j.bios.2013.03.069] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 03/26/2013] [Accepted: 03/27/2013] [Indexed: 10/27/2022]
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48
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Grubaugh ND, McMenamy SS, Turell MJ, Lee JS. Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray. PLoS Negl Trop Dis 2013; 7:e2349. [PMID: 23967358 PMCID: PMC3744434 DOI: 10.1371/journal.pntd.0002349] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Accepted: 06/19/2013] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Arthropod-borne viruses are important emerging pathogens world-wide. Viruses transmitted by mosquitoes, such as dengue, yellow fever, and Japanese encephalitis viruses, infect hundreds of millions of people and animals each year. Global surveillance of these viruses in mosquito vectors using molecular based assays is critical for prevention and control of the associated diseases. Here, we report an oligonucleotide DNA microarray design, termed ArboChip5.1, for multi-gene detection and identification of mosquito-borne RNA viruses from the genera Flavivirus (family Flaviviridae), Alphavirus (Togaviridae), Orthobunyavirus (Bunyaviridae), and Phlebovirus (Bunyaviridae). METHODOLOGY/PRINCIPAL FINDINGS The assay utilizes targeted PCR amplification of three genes from each virus genus for electrochemical detection on a portable, field-tested microarray platform. Fifty-two viruses propagated in cell-culture were used to evaluate the specificity of the PCR primer sets and the ArboChip5.1 microarray capture probes. The microarray detected all of the tested viruses and differentiated between many closely related viruses such as members of the dengue, Japanese encephalitis, and Semliki Forest virus clades. Laboratory infected mosquitoes were used to simulate field samples and to determine the limits of detection. Additionally, we identified dengue virus type 3, Japanese encephalitis virus, Tembusu virus, Culex flavivirus, and a Quang Binh-like virus from mosquitoes collected in Thailand in 2011 and 2012. CONCLUSIONS/SIGNIFICANCE We demonstrated that the described assay can be utilized in a comprehensive field surveillance program by the broad-range amplification and specific identification of arboviruses from infected mosquitoes. Furthermore, the microarray platform can be deployed in the field and viral RNA extraction to data analysis can occur in as little as 12 h. The information derived from the ArboChip5.1 microarray can help to establish public health priorities, detect disease outbreaks, and evaluate control programs.
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Affiliation(s)
- Nathan D Grubaugh
- Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Frederick, Maryland, United States of America.
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49
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Kaneko N, Horii K, Kato S, Akitomi J, Waga I. High-throughput quantitative screening of peroxidase-mimicking DNAzymes on a microarray by using electrochemical detection. Anal Chem 2013; 85:5430-5. [PMID: 23621546 DOI: 10.1021/ac4002518] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Some guanine-rich DNA sequences, which are called DNAzymes, can adopt G-quadruplex structures and exhibit peroxidase activity by binding with hemin. Although known DNAzymes show less activity than horseradish peroxidase, they have the potential to be widely used for the detection of target molecules in enzyme-linked immunosorbent assays if sequences that exhibit higher activity can be identified. However, techniques for achieving this have not yet been described. Therefore, we compared the DNAzyme activities of more than 1000 novelistically designed sequences with that of the original DNAzyme by using an electrochemical detection system on a 12K DNA microarray platform. To the best of our knowledge, this is the first description of an array-based assessment of peroxidase activity of G-quadruplex-hemin complexes. By using this novel assay system, more than 200 different mutants were found that had significantly higher activities than the original DNAzyme sequence. This microarray-based DNAzyme evaluation system is useful for identifying highly active new DNAzymes that might have potential as tools for developing DNA-based biosensors with aptamers.
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Affiliation(s)
- Naoto Kaneko
- VALWAY Technology Center, NEC Soft, Ltd., 1-18-7 Shinkiba, Koto-ku, Tokyo 136-8627, Japan
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50
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An overview of transducers as platform for the rapid detection of foodborne pathogens. Appl Microbiol Biotechnol 2013; 97:1829-40. [PMID: 23329385 DOI: 10.1007/s00253-013-4692-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Revised: 12/29/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
The driving advent of portable, integrated biosensing ways for pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques. The miniaturization and automation of integrated detection systems present a significant advantage for rapid, portable detection of foodborne microbes. In this review, we have highlighted current developments and directions in foodborne pathogen detection systems. Recent progress in the biosensor protocols toward the detection of specific microbes has been elaborated in detail. It also includes strategies and challenges for the implementation of a portable platform toward rapid foodborne sensing systems.
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