1
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Dou C, Yang Y, Zhu F, Li B, Duan Y. Explorer: efficient DNA coding by De Bruijn graph toward arbitrary local and global biochemical constraints. Brief Bioinform 2024; 25:bbae363. [PMID: 39073829 DOI: 10.1093/bib/bbae363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/25/2024] [Accepted: 07/13/2024] [Indexed: 07/30/2024] Open
Abstract
With the exponential growth of digital data, there is a pressing need for innovative storage media and techniques. DNA molecules, due to their stability, storage capacity, and density, offer a promising solution for information storage. However, DNA storage also faces numerous challenges, such as complex biochemical constraints and encoding efficiency. This paper presents Explorer, a high-efficiency DNA coding algorithm based on the De Bruijn graph, which leverages its capability to characterize local sequences. Explorer enables coding under various biochemical constraints, such as homopolymers, GC content, and undesired motifs. This paper also introduces Codeformer, a fast decoding algorithm based on the transformer architecture, to further enhance decoding efficiency. Numerical experiments indicate that, compared with other advanced algorithms, Explorer not only achieves stable encoding and decoding under various biochemical constraints but also increases the encoding efficiency and bit rate by ¿10%. Additionally, Codeformer demonstrates the ability to efficiently decode large quantities of DNA sequences. Under different parameter settings, its decoding efficiency exceeds that of traditional algorithms by more than two-fold. When Codeformer is combined with Reed-Solomon code, its decoding accuracy exceeds 99%, making it a good choice for high-speed decoding applications. These advancements are expected to contribute to the development of DNA-based data storage systems and the broader exploration of DNA as a novel information storage medium.
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Affiliation(s)
- Chang Dou
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Yijie Yang
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Fei Zhu
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - BingZhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
- School of Chemical Engineering and Technology, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
| | - Yuping Duan
- Center for Applied Mathematics, Tianjin University, No. 92, Weijin Road, Nankai District, Tianjin 300072, China
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2
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy S. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. Nucleic Acids Res 2024; 52:e47. [PMID: 38709890 PMCID: PMC11162764 DOI: 10.1093/nar/gkae332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/23/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024] Open
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45 000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
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3
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Bonilla DA, Orozco CA, Forero DA, Odriozola A. Techniques, procedures, and applications in host genetic analysis. ADVANCES IN GENETICS 2024; 111:1-79. [PMID: 38908897 DOI: 10.1016/bs.adgen.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.
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Affiliation(s)
- Diego A Bonilla
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain; Research Division, Dynamical Business & Science Society-DBSS International SAS, Bogotá, Colombia.
| | - Carlos A Orozco
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología de Colombia, Bogotá, Colombia
| | - Diego A Forero
- School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá, Colombia
| | - Adrián Odriozola
- Hologenomiks Research Group, Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country (UPV/EHU), Leioa, Spain
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4
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Zhang X, Qi B, Niu Y. A dual-rule encoding DNA storage system using chaotic mapping to control GC content. Bioinformatics 2024; 40:btae113. [PMID: 38419588 PMCID: PMC10937898 DOI: 10.1093/bioinformatics/btae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024] Open
Abstract
MOTIVATION DNA as a novel storage medium is considered an effective solution to the world's growing demand for information due to its high density and long-lasting reliability. However, early coding schemes ignored the biologically constrained nature of DNA sequences in pursuit of high density, leading to DNA synthesis and sequencing difficulties. This article proposes a novel DNA storage coding scheme. The system encodes half of the binary data using each of the two GC-content complementary encoding rules to obtain a DNA sequence. RESULTS After simulating the encoding of representative document and image file formats, a DNA sequence strictly conforming to biological constraints was obtained, reaching a coding potential of 1.66 bit/nt. In the decoding process, a mechanism to prevent error propagation was introduced. The simulation results demonstrate that by adding Reed-Solomon code, 90% of the data can still be recovered after introducing a 2% error, proving that the proposed DNA storage scheme has high robustness and reliability. Availability and implementation: The source code for the codec scheme of this paper is available at https://github.com/Mooreniah/DNA-dual-rule-rotary-encoding-storage-system-DRRC.
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Affiliation(s)
- Xuncai Zhang
- College of Electrical Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan, China
| | - Baonan Qi
- College of Electrical Information Engineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan, China
| | - Ying Niu
- College of Building Environment Engineering, Zhengzhou University of Light Industry, Zhengzhou 450000, Henan, China
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5
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Li W, Miller D, Liu X, Tosi L, Chkaiban L, Mei H, Hung PH, Parekkadan B, Sherlock G, Levy SF. Arrayed in vivo barcoding for multiplexed sequence verification of plasmid DNA and demultiplexing of pooled libraries. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562064. [PMID: 37873145 PMCID: PMC10592806 DOI: 10.1101/2023.10.13.562064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Sequence verification of plasmid DNA is critical for many cloning and molecular biology workflows. To leverage high-throughput sequencing, several methods have been developed that add a unique DNA barcode to individual samples prior to pooling and sequencing. However, these methods require an individual plasmid extraction and/or in vitro barcoding reaction for each sample processed, limiting throughput and adding cost. Here, we develop an arrayed in vivo plasmid barcoding platform that enables pooled plasmid extraction and library preparation for Oxford Nanopore sequencing. This method has a high accuracy and recovery rate, and greatly increases throughput and reduces cost relative to other plasmid barcoding methods or Sanger sequencing. We use in vivo barcoding to sequence verify >45,000 plasmids and show that the method can be used to transform error-containing dispersed plasmid pools into sequence-perfect arrays or well-balanced pools. In vivo barcoding does not require any specialized equipment beyond a low-overhead Oxford Nanopore sequencer, enabling most labs to flexibly process hundreds to thousands of plasmids in parallel.
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Affiliation(s)
- Weiyi Li
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Darach Miller
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Xianan Liu
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Lorenzo Tosi
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Lamia Chkaiban
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Han Mei
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
| | - Po-Hsiang Hung
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Biju Parekkadan
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, USA
| | - Gavin Sherlock
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA
- Present Address: BacStitch DNA, Los Altos, CA, USA
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6
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Park SJ, Kim S, Jeong J, No A, No JS, Park H. Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads. Bioinformatics 2023; 39:btad548. [PMID: 37669160 PMCID: PMC10500082 DOI: 10.1093/bioinformatics/btad548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 08/30/2023] [Accepted: 09/04/2023] [Indexed: 09/07/2023] Open
Abstract
MOTIVATION DNA-based data storage is one of the most attractive research areas for future archival storage. However, it faces the problems of high writing and reading costs for practical use. There have been many efforts to resolve this problem, but existing schemes are not fully suitable for DNA-based data storage, and more cost reduction is needed. RESULTS We propose whole encoding and decoding procedures for DNA storage. The encoding procedure consists of a carefully designed single low-density parity-check code as an inter-oligo code, which corrects errors and dropouts efficiently. We apply new clustering and alignment methods that operate on variable-length reads to aid the decoding performance. We use edit distance and quality scores during the sequence analysis-aided decoding procedure, which can discard abnormal reads and utilize high-quality soft information. We store 548.83 KB of an image file in DNA oligos and achieve a writing cost reduction of 7.46% and a significant reading cost reduction of 26.57% and 19.41% compared with the two previous works. AVAILABILITY AND IMPLEMENTATION Data and codes for all the algorithms proposed in this study are available at: https://github.com/sjpark0905/DNA-LDPC-codes.
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Affiliation(s)
- Seong-Joon Park
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | - Sunghwan Kim
- Department of Electrical, Electronic and Computer Engineering, University of Ulsan, Ulsan 44610, South Korea
| | - Jaeho Jeong
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | - Albert No
- Department of Electronic and Electrical Engineering, Hongik University, Seoul 04066, South Korea
| | - Jong-Seon No
- Department of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | - Hosung Park
- Department of Computer Engineering, Chonnam National University, Gwangju 61186, South Korea
- Department of ICT Convergence System Engineering, Chonnam National University, Gwangju 61186, South Korea
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7
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Ramezani M, Bauman J, Singh A, Weisbart E, Yong J, Lozada M, Way GP, Kavari SL, Diaz C, Haghighi M, Batista TM, Pérez-Schindler J, Claussnitzer M, Singh S, Cimini BA, Blainey PC, Carpenter AE, Jan CH, Neal JT. A genome-wide atlas of human cell morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.06.552164. [PMID: 37609130 PMCID: PMC10441312 DOI: 10.1101/2023.08.06.552164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
A key challenge of the modern genomics era is developing data-driven representations of gene function. Here, we present the first unbiased morphology-based genome-wide perturbation atlas in human cells, containing three genome-scale genotype-phenotype maps comprising >20,000 single-gene CRISPR-Cas9-based knockout experiments in >30 million cells. Our optical pooled cell profiling approach (PERISCOPE) combines a de-stainable high-dimensional phenotyping panel (based on Cell Painting1,2) with optical sequencing of molecular barcodes and a scalable open-source analysis pipeline to facilitate massively parallel screening of pooled perturbation libraries. This approach provides high-dimensional phenotypic profiles of individual cells, while simultaneously enabling interrogation of subcellular processes. Our atlas reconstructs known pathways and protein-protein interaction networks, identifies culture media-specific responses to gene knockout, and clusters thousands of human genes by phenotypic similarity. Using this atlas, we identify the poorly-characterized disease-associated transmembrane protein TMEM251/LYSET as a Golgi-resident protein essential for mannose-6-phosphate-dependent trafficking of lysosomal enzymes, showing the power of these representations. In sum, our atlas and screening technology represent a rich and accessible resource for connecting genes to cellular functions at scale.
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Affiliation(s)
- Meraj Ramezani
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Julia Bauman
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Stanford University, Stanford, CA, USA
| | - Avtar Singh
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Genentech Department of Cellular and Tissue Genomics, South San Francisco, CA, USA
| | - Erin Weisbart
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - John Yong
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - Maria Lozada
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Gregory P Way
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Sanam L Kavari
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: University of Pennsylvania, Philadelphia, PA, USA
| | - Celeste Diaz
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Current address: Stanford University, Stanford, CA, USA
| | | | - Thiago M Batista
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
| | - Joaquín Pérez-Schindler
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
| | - Melina Claussnitzer
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | - Beth A Cimini
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- MIT Department of Biological Engineering, Cambridge, MA, USA
- Koch Institute for Integrative Research at MIT, Cambridge, MA, USA
| | | | - Calvin H Jan
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | - James T Neal
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Type 2 Diabetes Systems Genomics Initiative of the Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease at Broad Institute, Cambridge, MA, USA
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8
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Yang X, Shi X, Lai L, Chen C, Xu H, Deng M. Towards long double-stranded chains and robust DNA-based data storage using the random code system. Front Genet 2023; 14:1179867. [PMID: 37384333 PMCID: PMC10294226 DOI: 10.3389/fgene.2023.1179867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/31/2023] [Indexed: 06/30/2023] Open
Abstract
DNA has become a popular choice for next-generation storage media due to its high storage density and stability. As the storage medium of life's information, DNA has significant storage capacity and low-cost, low-power replication and transcription capabilities. However, utilizing long double-stranded DNA for storage can introduce unstable factors that make it difficult to meet the constraints of biological systems. To address this challenge, we have designed a highly robust coding scheme called the "random code system," inspired by the idea of fountain codes. The random code system includes the establishment of a random matrix, Gaussian preprocessing, and random equilibrium. Compared to Luby transform codes (LT codes), random code (RC) has better robustness and recovery ability of lost information. In biological experiments, we successfully stored 29,390 bits of data in 25,700 bp chains, achieving a storage density of 1.78 bits per nucleotide. These results demonstrate the potential for using long double-stranded DNA and the random code system for robust DNA-based data storage.
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Affiliation(s)
- Xu Yang
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Xiaolong Shi
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Langwen Lai
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Congzhou Chen
- College of Information Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Huaisheng Xu
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
| | - Ming Deng
- Institute of Computing Science and Technology, Guangzhou University, Guangzhou, China
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9
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Mortuza GM, Guerrero J, Llewellyn S, Tobiason MD, Dickinson GD, Hughes WL, Zadegan R, Andersen T. In-vitro validated methods for encoding digital data in deoxyribonucleic acid (DNA). BMC Bioinformatics 2023; 24:160. [PMID: 37085766 PMCID: PMC10120115 DOI: 10.1186/s12859-023-05264-6] [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: 11/16/2021] [Accepted: 03/30/2023] [Indexed: 04/23/2023] Open
Abstract
Deoxyribonucleic acid (DNA) is emerging as an alternative archival memory technology. Recent advancements in DNA synthesis and sequencing have both increased the capacity and decreased the cost of storing information in de novo synthesized DNA pools. In this survey, we review methods for translating digital data to and/or from DNA molecules. An emphasis is placed on methods which have been validated by storing and retrieving real-world data via in-vitro experiments.
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Affiliation(s)
- Golam Md Mortuza
- Department of Computer Science, Boise State University, Boise, Idaho, USA
| | - Jorge Guerrero
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC, USA
| | | | | | | | - William L Hughes
- School of Engineering, Kelowna, University of British Columbia, Kelowna, British Columbia, Canada
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience and Nanoengineering, North Carolina A&T State University, Greensboro, NC, USA.
| | - Tim Andersen
- Department of Computer Science, Boise State University, Boise, Idaho, USA.
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10
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Choi H, Kwon S, Ryu T, Choi Y. MOPSS: Toward high-fidelity oligonucleotides for clinical applications. Clin Transl Med 2022; 12:e809. [PMID: 35853099 PMCID: PMC9296019 DOI: 10.1002/ctm2.809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 03/26/2022] [Indexed: 11/24/2022] Open
Affiliation(s)
- Hansol Choi
- Department of Electrical and Computer EngineeringSeoul National UniversitySeoulRepublic of Korea
- Bio‐MAX InstituteSeoul National UniversitySeoulRepublic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer EngineeringSeoul National UniversitySeoulRepublic of Korea
- Bio‐MAX InstituteSeoul National UniversitySeoulRepublic of Korea
- Interdisciplinary Program in BioengineeringSeoul National UniversitySeoulRepublic of Korea
| | | | - Yeongjae Choi
- School of Materials Science and EngineeringGwangju Institute of Science and TechnologyGwangjuRepublic of Korea
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11
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Bi K, Lu Z, Ge Q, Gu W. Extended XOR algorithm with biotechnology constraints for Data Security in DNA Storage. Curr Bioinform 2022. [DOI: 10.2174/1574893617666220314114732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
DNA storage is becoming a global research hotspot in recent years and today, most researches are focused on storage density and big data. The security of DNA storage needs to be observed. Some DNA-based security methods were introduced for traditional information security problems. However, few encryption algorithm considered the limitation of biotechnology and applied it for DNA storage. The difference between DNA cryptography and the traditional one is that the former is based on the limitation of biotechnology, which is unrelated to numeracy.
Objective:
An extended XOR algorithm (EXA) was introduced for encryption with constriants of biotechnology, which can solve the problems of synthesis and sequencing partly, such as GC content and homopolymer in DNA storage..
Methods:
The target file was converted by a quaternary DNA storage model to maximize the storage efficiency. The key file could be ‘anything’ converted into DNA sequence by a binary DNA storage model to make the best utilization for the length of the key file.
Results:
The input files were encrypted into DNA storage and decrypted to error-free output files.
Conclusion:
This meant error-free encryption DNA storage is feasible and EXA paves the way for encryption in large-scale DNA storage.
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Affiliation(s)
- Kun Bi
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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12
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Choi H, Choi Y, Choi J, Lee AC, Yeom H, Hyun J, Ryu T, Kwon S. Purification of multiplex oligonucleotide libraries by synthesis and selection. Nat Biotechnol 2022; 40:47-53. [PMID: 34326548 DOI: 10.1038/s41587-021-00988-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/16/2021] [Indexed: 02/07/2023]
Abstract
Complex oligonucleotide (oligo) libraries are essential materials for diverse applications in synthetic biology, pharmaceutical production, nanotechnology and DNA-based data storage. However, the error rates in synthesizing complex oligo libraries can be substantial, leading to increment in cost and labor for the applications. As most synthesis errors arise from faulty insertions and deletions, we developed a length-based method with single-base resolution for purification of complex libraries containing oligos of identical or different lengths. Our method-purification of multiplex oligonucleotide libraries by synthesis and selection-can be performed either step-by-step manually or using a next-generation sequencer. When applied to a digital data-encoded library containing oligos of identical length, the method increased the purity of full-length oligos from 83% to 97%. We also show that libraries encoding the complementarity-determining region H3 with three different lengths (with an empirically achieved diversity >106) can be simultaneously purified in one pot, increasing the in-frame oligo fraction from 49.6% to 83.5%.
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Affiliation(s)
- Hansol Choi
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Yeongjae Choi
- Nano Systems Institute, Seoul National University, Seoul, Republic of Korea.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Jaewon Choi
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea.,Integrated Major in Innovative Medical Science, Seoul National University, Seoul, Republic of Korea
| | - Amos Chungwon Lee
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Huiran Yeom
- Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea
| | - Jinwoo Hyun
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea
| | - Taehoon Ryu
- ATG Lifetech Inc., Seoul, Republic of Korea.
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, Seoul, Republic of Korea. .,Nano Systems Institute, Seoul National University, Seoul, Republic of Korea. .,Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, Republic of Korea. .,Bio-MAX Institute, Seoul National University, Seoul, Republic of Korea.
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13
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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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14
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Viswanatha R, Mameli E, Rodiger J, Merckaert P, Feitosa-Suntheimer F, Colpitts TM, Mohr SE, Hu Y, Perrimon N. Bioinformatic and cell-based tools for pooled CRISPR knockout screening in mosquitos. Nat Commun 2021; 12:6825. [PMID: 34819517 PMCID: PMC8613219 DOI: 10.1038/s41467-021-27129-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 11/02/2021] [Indexed: 12/20/2022] Open
Abstract
Mosquito-borne diseases present a worldwide public health burden. Current efforts to understand and counteract them have been aided by the use of cultured mosquito cells. Moreover, application in mammalian cells of forward genetic approaches such as CRISPR screens have identified essential genes and genes required for host-pathogen interactions, and in general, aided in functional annotation of genes. An equivalent approach for genetic screening of mosquito cell lines has been lacking. To develop such an approach, we design a new bioinformatic portal for sgRNA library design in several mosquito genomes, engineer mosquito cell lines to express Cas9 and accept sgRNA at scale, and identify optimal promoters for sgRNA expression in several mosquito species. We then optimize a recombination-mediated cassette exchange system to deliver CRISPR sgRNA and perform pooled CRISPR screens in an Anopheles cell line. Altogether, we provide a platform for high-throughput genome-scale screening in cell lines from disease vector species.
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Affiliation(s)
- Raghuvir Viswanatha
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Enzo Mameli
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA, 02118, USA
| | - Jonathan Rodiger
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Pierre Merckaert
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Fabiana Feitosa-Suntheimer
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA, 02118, USA
| | - Tonya M Colpitts
- Department of Microbiology, National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, 620 Albany Street, Boston, MA, 02118, USA
| | - Stephanie E Mohr
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Yanhui Hu
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, 02115, USA.
- HHMI, Harvard Medical School, Boston, MA, 02115, USA.
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15
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Sinyakov AN, Ryabinin VA, Kostina EV. Application of Array-Based Oligonucleotides for Synthesis of Genetic Designs. Mol Biol 2021. [DOI: 10.1134/s0026893321030109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Xu C, Zhao C, Ma B, Liu H. Uncertainties in synthetic DNA-based data storage. Nucleic Acids Res 2021; 49:5451-5469. [PMID: 33836076 PMCID: PMC8191772 DOI: 10.1093/nar/gkab230] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/16/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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17
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Knyphausen P, Lindenburg L, Hollfelder F. Error-Free Synthetic DNA by Molecular Dictation. Trends Biotechnol 2021; 39:861-865. [PMID: 33653603 DOI: 10.1016/j.tibtech.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 01/23/2023]
Abstract
Synthetic DNA is the linchpin of the rapidly accelerating biotechnological era and is perhaps the most promising candidate for long-term digital data storage. Despite huge advances, manufacturing error-free DNA at low cost and high throughput remains challenging. Borrowing from well-established sequencing-by-synthesis technologies, we describe a new solution for DNA error correction.
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Affiliation(s)
- Philipp Knyphausen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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18
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Zurek PJ, Knyphausen P, Neufeld K, Pushpanath A, Hollfelder F. UMI-linked consensus sequencing enables phylogenetic analysis of directed evolution. Nat Commun 2020; 11:6023. [PMID: 33243970 PMCID: PMC7691348 DOI: 10.1038/s41467-020-19687-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/12/2020] [Indexed: 11/09/2022] Open
Abstract
The success of protein evolution campaigns is strongly dependent on the sequence context in which mutations are introduced, stemming from pervasive non-additive interactions between a protein's amino acids ('intra-gene epistasis'). Our limited understanding of such epistasis hinders the correct prediction of the functional contributions and adaptive potential of mutations. Here we present a straightforward unique molecular identifier (UMI)-linked consensus sequencing workflow (UMIC-seq) that simplifies mapping of evolutionary trajectories based on full-length sequences. Attaching UMIs to gene variants allows accurate consensus generation for closely related genes with nanopore sequencing. We exemplify the utility of this approach by reconstructing the artificial phylogeny emerging in three rounds of directed evolution of an amine dehydrogenase biocatalyst via ultrahigh throughput droplet screening. Uniquely, we are able to identify lineages and their founding variant, as well as non-additive interactions between mutations within a full gene showing sign epistasis. Access to deep and accurate long reads will facilitate prediction of key beneficial mutations and adaptive potential based on in silico analysis of large sequence datasets.
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Affiliation(s)
- Paul Jannis Zurek
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Johnson Matthey Plc, Cambridge, CB4 0WE, UK
| | - Philipp Knyphausen
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
| | - Katharina Neufeld
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Johnson Matthey Plc, Cambridge, CB4 0WE, UK
| | | | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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19
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Wang Y, Noor-A-Rahim M, Zhang J, Gunawan E, Guan YL, Poh CL. Oligo Design with Single Primer Binding Site for High Capacity DNA-Based Data Storage. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:2176-2182. [PMID: 31514147 DOI: 10.1109/tcbb.2019.2940177] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA has become an attractive medium for long-term data archiving due to its extremely high storage density and longevity. Short single-stranded DNAs, called oligonucleotides (oligos), have been designed and synthesized to store digital data. Previous works designed the oligos with a pair of primer binding sites (PBSs) (each with a length of around 200) attached at the two ends of each basic readable data block. The addition of PBSs decreases the data density significantly because in the current DNA synthesis, the maximum length of a synthesized oligo in good quality is around 200. Furthermore, the maximum homopolymer run allowed by the existing experiments has been reported to be three nucleotides. In this work, to increase the data density, we have devised and tested an oligo design for DNA-based storage with the basic readable data block appended by a single PBS at one end only, while allowing the maximum homopolymer run to be increased to 4. We also present an oligo assembly algorithm that can reconstruct oligos with a single PBS from the error-prone raw readouts obtained from the sequencing process. We have conducted a wet lab experiment to validate the proposed design, where we tested with 398KB of data stored into 10,750 oligos. The experimental results show that it is possible to recover over 99 percent of the oligo sequences without error, which proves that one PBS is sufficient for implementing a DNA-based data storage system with maximum homopolymer run relaxed to 4. The use of single PBS leads to a significant data density gain from 14.3 to 140.2 percent over the existing short-strand DNA data storage schemes by reserving more nucleotides for storing information bits.
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20
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Sidore AM, Plesa C, Samson JA, Lubock NB, Kosuri S. DropSynth 2.0: high-fidelity multiplexed gene synthesis in emulsions. Nucleic Acids Res 2020; 48:e95. [PMID: 32692349 PMCID: PMC7498354 DOI: 10.1093/nar/gkaa600] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/13/2020] [Accepted: 07/11/2020] [Indexed: 01/12/2023] Open
Abstract
Multiplexed assays allow functional testing of large synthetic libraries of genetic elements, but are limited by the designability, length, fidelity and scale of the input DNA. Here, we improve DropSynth, a low-cost, multiplexed method that builds gene libraries by compartmentalizing and assembling microarray-derived oligonucleotides in vortexed emulsions. By optimizing enzyme choice, adding enzymatic error correction and increasing scale, we show that DropSynth can build thousands of gene-length fragments at >20% fidelity.
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Affiliation(s)
- Angus M Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Calin Plesa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joyce A Samson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Nathan B Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA.,UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
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21
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Horns F, Quake SR. Cloning antibodies from single cells in pooled sequence libraries by selective PCR. PLoS One 2020; 15:e0236477. [PMID: 32756607 PMCID: PMC7406036 DOI: 10.1371/journal.pone.0236477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/06/2020] [Indexed: 11/19/2022] Open
Abstract
Antibodies function by binding to antigens. Antibodies must be cloned and expressed to determine their binding characteristics, but current methods for high-throughput antibody sequencing yield antibody DNA pooled from many cells and do not readily permit cloning of antibodies from single B cells. We present a strategy for retrieving and cloning antibody DNA from single cells within a pooled library of cells. Our strategy, called selective PCR for antibody retrieval (SPAR), takes advantage of the unique sequence barcodes attached to individual cDNA molecules during sample preparation to enable specific amplification by PCR of antibody heavy- and light-chain cDNA originating from a single cell. We show through computational analysis that most human antibodies sequenced using typical high-throughput methods can be retrieved using SPAR, and experimentally demonstrate retrieval of full-length antibody variable region cDNA from three cells within pools of ~5,000 cells. SPAR enables rapid low-cost cloning and expression of native human antibodies from pooled single-cell sequence libraries for functional characterization.
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Affiliation(s)
- Felix Horns
- Biophysics Graduate Program, Stanford University, Stanford, California, United States of America
| | - Stephen R. Quake
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Applied Physics, Stanford University, Stanford, California, United States of America
- Chan Zuckerberg Biohub, Stanford, California, United States of America
- * E-mail:
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22
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HAMADANI AMBREEN, GANAI NAZIRA, FAROOQ SHAHF, BHAT BASHARATA. Big data management: from hard drives to DNA drives. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2020. [DOI: 10.56093/ijans.v90i2.98761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Information Communication and Technology is transforming all aspects of modern life and in this digital era, there is a tremendous increase in the amount of data that is being generated every day. The current, conventional storage devices are unable to keep pace with this rapidly growing data. Thus, there is a need to look for alternative storage devices. DNA being exceptional in storage of biological information offers a promising storage capacity. With its unique abilities of dense storage and reliability, it may prove better than all conventional storage devices in near future. The nucleotide bases are present in DNA in a particular sequence representing the coded information. These are the equivalent of binary letters (0 &1). To store data in DNA, binary data is first converted to ternary or quaternary which is then translated into the nucleotide code comprising 4 nucleotide bases (A, C, G, T). A DNA strand is then synthesized as per the code developed. This may either be stored in pools or sequenced back. The nucleotide code is converted back into ternary and subsequently the binary code which is read just like digital data. DNA drives may have a wide variety of applications in information storage and DNA steganography.
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23
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Dong Y, Sun F, Ping Z, Ouyang Q, Qian L. DNA storage: research landscape and future prospects. Natl Sci Rev 2020; 7:1092-1107. [PMID: 34692128 PMCID: PMC8288837 DOI: 10.1093/nsr/nwaa007] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/06/2020] [Accepted: 01/18/2020] [Indexed: 02/06/2023] Open
Abstract
Abstract
The global demand for data storage is currently outpacing the world's storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.
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Affiliation(s)
- Yiming Dong
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fajia Sun
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhi Ping
- Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Qi Ouyang
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- The State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China
| | - Long Qian
- Center for Quantitative Biology and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
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24
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25
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Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC. Optical Pooled Screens in Human Cells. Cell 2019; 179:787-799.e17. [PMID: 31626775 PMCID: PMC6886477 DOI: 10.1016/j.cell.2019.09.016] [Citation(s) in RCA: 139] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 07/08/2019] [Accepted: 09/13/2019] [Indexed: 01/06/2023]
Abstract
Genetic screens are critical for the systematic identification of genes underlying cellular phenotypes. Pooling gene perturbations greatly improves scalability but is not compatible with imaging of complex and dynamic cellular phenotypes. Here, we introduce a pooled approach for optical genetic screens in mammalian cells. We use targeted in situ sequencing to demultiplex a library of genetic perturbations following image-based phenotyping. We screened a set of 952 genes across millions of cells for involvement in nuclear factor κB (NF-κB) signaling by imaging the translocation of RelA (p65) to the nucleus. Screening at a single time point across 3 cell lines recovered 15 known pathway components, while repeating the screen with live-cell imaging revealed a role for Mediator complex subunits in regulating the duration of p65 nuclear retention. These results establish a highly multiplexed approach to image-based screens of spatially and temporally defined phenotypes with pooled libraries.
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Affiliation(s)
- David Feldman
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Physics, MIT, Cambridge, MA 02142, USA
| | - Avtar Singh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Rebecca J Carlson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Health Sciences and Technology, MIT, Cambridge, MA 02142, USA
| | - Anja Mezger
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02142, USA; Department of Brain and Cognitive Science, MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02142, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biological Engineering, MIT, Cambridge, MA 02142, USA; Koch Institute for Integrative Cancer Research, MIT, Cambridge, MA 02142, USA.
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26
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Cho N, Seo HN, Ryu T, Kwon E, Huh S, Noh J, Yeom H, Hwang B, Ha H, Lee JH, Kwon S, Bang D. High-throughput construction of multiple cas9 gene variants via assembly of high-depth tiled and sequence-verified oligonucleotides. Nucleic Acids Res 2019. [PMID: 29529247 PMCID: PMC5961255 DOI: 10.1093/nar/gky112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Selective retrieval of sequence-verified oligonucleotides (oligos) from next-generation sequencing (NGS) flow cells, termed megacloning, promises accurate and reliable gene synthesis. However, gene assembly requires a complete collection of overlapping sense and nonsense oligos, and megacloning does not typically guarantee the complete production of sequence-verified oligos. Therefore, missing oligos must be provided via repetitive rounds of megacloning, which introduces a bottleneck for scaled-up efforts at gene assembly. Here, we introduce the concept of high-depth tiled oligo design to successfully utilize megacloned oligos for gene synthesis. Using acquired oligos from a single round of the megacloning process, we assembled 72 of 81 target Cas9-coding gene variants. We further validated 62 of these cas9 constructs, and deposited the plasmids to Addgene for subsequent functional characterization by the scientific community. This study demonstrates the utility of using sequence-verified oligos for DNA assembly and provides a practical and reliable optimized method for high-throughput gene synthesis.
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Affiliation(s)
- Namjin Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Han Na Seo
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Taehoon Ryu
- Celemics Inc., 371-17, Gasan-dong, Geumcheongu, Seoul 153-718, Republic of Korea
| | - Euijin Kwon
- Celemics Inc., 371-17, Gasan-dong, Geumcheongu, Seoul 153-718, Republic of Korea
| | - Sunghoon Huh
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Jinsung Noh
- Department of Electrical and Computer Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Huiran Yeom
- Department of Electrical and Computer Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Byungjin Hwang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Heejeong Ha
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea.,Kyung Hee Medical Science Research Institute, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sunghoon Kwon
- Department of Electrical and Computer Engineering, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Institute of Entrepreneurial Bio Convergence, Seoul National University, 1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.,Seoul National University Hospital Biomedical Research Institute, Seoul National University Hospital, 101, Daehak-ro Jongno-gu, Seoul, 03080, Republic of Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea
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27
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Lim H, Cho N, Ahn J, Park S, Jang H, Kim H, Han H, Lee JH, Bang D. Highly selective retrieval of accurate DNA utilizing a pool of in situ-replicated DNA from multiple next-generation sequencing platforms. Nucleic Acids Res 2019; 46:e40. [PMID: 29361040 PMCID: PMC6283416 DOI: 10.1093/nar/gky016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/11/2018] [Indexed: 11/13/2022] Open
Abstract
Scalable and cost-effective production of error-free DNA is critical to meet the increased demand for such DNA in the field of biological science. Methods based on ‘Dial-out PCR’ have enabled the high-throughput error-free DNA synthesis from a microarray-synthesized DNA pool by labeling with retrieval PCR tags, and retrieving error-free DNA of which the sequence is identified via next generation sequencing (NGS). However, most of the retrieved products contain byproducts due to background amplification of redundantly labeled DNAs. Here, we present a highly selective retrieval method of desired DNA from a pool of millions of DNA clones from NGS platforms. Our strategy is based on replicating entire sequence-verified DNA molecules from NGS plates to obtain population-controlled DNA pool. Using the NGS-replica pool, we could perform improved and selective retrieval of desired DNA from the replicated DNA pool compared to other dial-out PCR based methods. To evaluate the method, we tested this strategy by using 454, Illumina, and Ion Torrent platforms for producing NGS-replica pool. As a result, we observed a highly selective retrieval yield of over 95%. We anticipate that applications based on this method will enable the preparation of high-fidelity sequenced DNA from heterogeneous collections of DNA molecules.
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Affiliation(s)
- Hyeonseob Lim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Namjin Cho
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Jinwoo Ahn
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Sangun Park
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hoon Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hwangbeom Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Hyojun Han
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Ji Hyun Lee
- Department of Clinical Pharmacology and Therapeutics, College of Medicine, Kyung Hee University, Seoul 02447, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
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28
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Heckel R, Mikutis G, Grass RN. A Characterization of the DNA Data Storage Channel. Sci Rep 2019; 9:9663. [PMID: 31273225 PMCID: PMC6609604 DOI: 10.1038/s41598-019-45832-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/04/2019] [Indexed: 11/09/2022] Open
Abstract
Owing to its longevity and enormous information density, DNA, the molecule encoding biological information, has emerged as a promising archival storage medium. However, due to technological constraints, data can only be written onto many short DNA molecules that are stored in an unordered way, and can only be read by sampling from this DNA pool. Moreover, imperfections in writing (synthesis), reading (sequencing), storage, and handling of the DNA, in particular amplification via PCR, lead to a loss of DNA molecules and induce errors within the molecules. In order to design DNA storage systems, a qualitative and quantitative understanding of the errors and the loss of molecules is crucial. In this paper, we characterize those error probabilities by analyzing data from our own experiments as well as from experiments of two different groups. We find that errors within molecules are mainly due to synthesis and sequencing, while imperfections in handling and storage lead to a significant loss of sequences. The aim of our study is to help guide the design of future DNA data storage systems by providing a quantitative and qualitative understanding of the DNA data storage channel.
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Affiliation(s)
- Reinhard Heckel
- Rice University, Department of Electrical and Computer Engineering, Houston, 77005, Texas, USA.
| | - Gediminas Mikutis
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, 8093, Switzerland
| | - Robert N Grass
- ETH Zurich, Department of Chemistry and Applied Biosciences, Zurich, 8093, Switzerland
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29
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Shevelev GY, Pyshnyi DV. Modern approaches to artificial gene synthesis: aspects of oligonucleotide synthesis, enzymatic assembly, sequence verification and error correction. Vavilovskii Zhurnal Genet Selektsii 2018. [DOI: 10.18699/vj18.387] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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30
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Katz L, Chen YY, Gonzalez R, Peterson TC, Zhao H, Baltz RH. Synthetic biology advances and applications in the biotechnology industry: a perspective. ACTA ACUST UNITED AC 2018; 45:449-461. [DOI: 10.1007/s10295-018-2056-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 06/06/2018] [Indexed: 12/22/2022]
Abstract
Abstract
Synthetic biology is a logical extension of what has been called recombinant DNA (rDNA) technology or genetic engineering since the 1970s. As rDNA technology has been the driver for the development of a thriving biotechnology industry today, starting with the commercialization of biosynthetic human insulin in the early 1980s, synthetic biology has the potential to take the industry to new heights in the coming years. Synthetic biology advances have been driven by dramatic cost reductions in DNA sequencing and DNA synthesis; by the development of sophisticated tools for genome editing, such as CRISPR/Cas9; and by advances in informatics, computational tools, and infrastructure to facilitate and scale analysis and design. Synthetic biology approaches have already been applied to the metabolic engineering of microorganisms for the production of industrially important chemicals and for the engineering of human cells to treat medical disorders. It also shows great promise to accelerate the discovery and development of novel secondary metabolites from microorganisms through traditional, engineered, and combinatorial biosynthesis. We anticipate that synthetic biology will continue to have broadening impacts on the biotechnology industry to address ongoing issues of human health, world food supply, renewable energy, and industrial chemicals and enzymes.
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Affiliation(s)
- Leonard Katz
- 0000 0001 2181 7878 grid.47840.3f QB3 Institute University of California-Berkeley 5885 Hollis St., 4th Floor 94608 Emeryville CA USA
| | - Yvonne Y Chen
- 0000 0000 9632 6718 grid.19006.3e Department of Chemical and Biomolecular Engineering University of California-Los Angeles 420 Westwood Plaza, Boelter Hall 5531 90095 Los Angeles CA USA
| | - Ramon Gonzalez
- 0000 0004 1936 8278 grid.21940.3e Departments of Chemical and Biomolecular Engineering and Bioengineering Rice University 6100 Main Street 77005 Houston TX USA
| | - Todd C Peterson
- grid.427368.c Synthetic Genomics, Inc. 11149 North Torrey Pines Road 92037 La Jolla CA USA
| | - Huimin Zhao
- 0000 0004 1936 9991 grid.35403.31 Department of Chemical and Biomolecular Engineering University of Illinois 600 South Mathews Avenue 61801 Urbana IL USA
| | - Richard H Baltz
- CognoGen Biotechnology Consulting 7636 Andora Drive 34238 Sarasota FL USA
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31
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Plesa C, Sidore AM, Lubock NB, Zhang D, Kosuri S. Multiplexed gene synthesis in emulsions for exploring protein functional landscapes. Science 2018; 359:343-347. [PMID: 29301959 PMCID: PMC6261299 DOI: 10.1126/science.aao5167] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Improving our ability to construct and functionally characterize DNA sequences would broadly accelerate progress in biology. Here, we introduce DropSynth, a scalable, low-cost method to build thousands of defined gene-length constructs in a pooled (multiplexed) manner. DropSynth uses a library of barcoded beads that pull down the oligonucleotides necessary for a gene's assembly, which are then processed and assembled in water-in-oil emulsions. We used DropSynth to successfully build more than 7000 synthetic genes that encode phylogenetically diverse homologs of two essential genes in Escherichia coli We tested the ability of phosphopantetheine adenylyltransferase homologs to complement a knockout E. coli strain in multiplex, revealing core functional motifs and reasons underlying homolog incompatibility. DropSynth coupled with multiplexed functional assays allows us to rationally explore sequence-function relationships at an unprecedented scale.
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Affiliation(s)
- Calin Plesa
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Angus M. Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, California, USA
| | - Nathan B. Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
| | - Di Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- UCLA-DOE Institute for Genomics and Proteomics, Molecular Biology Institute, Quantitative and Computational Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, California, USA
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32
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Erlich Y, Zielinski D. DNA Fountain enables a robust and efficient storage architecture. Science 2017; 355:950-954. [PMID: 28254941 DOI: 10.1126/science.aaj2038] [Citation(s) in RCA: 287] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 02/09/2017] [Indexed: 12/16/2022]
Abstract
DNA is an attractive medium to store digital information. Here we report a storage strategy, called DNA Fountain, that is highly robust and approaches the information capacity per nucleotide. Using our approach, we stored a full computer operating system, movie, and other files with a total of 2.14 × 106 bytes in DNA oligonucleotides and perfectly retrieved the information from a sequencing coverage equivalent to a single tile of Illumina sequencing. We also tested a process that can allow 2.18 × 1015 retrievals using the original DNA sample and were able to perfectly decode the data. Finally, we explored the limit of our architecture in terms of bytes per molecule and obtained a perfect retrieval from a density of 215 petabytes per gram of DNA, orders of magnitude higher than previous reports.
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Affiliation(s)
- Yaniv Erlich
- New York Genome Center, New York, NY 10013, USA. .,Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY 10027, USA.,Center for Computational Biology and Bioinformatics (C2B2), Department of Systems Biology, Columbia University, New York, NY 10027, USA
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33
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Lubock NB, Zhang D, Sidore AM, Church GM, Kosuri S. A systematic comparison of error correction enzymes by next-generation sequencing. Nucleic Acids Res 2017; 45:9206-9217. [PMID: 28911123 PMCID: PMC5587813 DOI: 10.1093/nar/gkx691] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 07/14/2017] [Accepted: 07/31/2017] [Indexed: 11/13/2022] Open
Abstract
Gene synthesis, the process of assembling gene-length fragments from shorter groups of oligonucleotides (oligos), is becoming an increasingly important tool in molecular and synthetic biology. The length, quality and cost of gene synthesis are limited by errors produced during oligo synthesis and subsequent assembly. Enzymatic error correction methods are cost-effective means to ameliorate errors in gene synthesis. Previous analyses of these methods relied on cloning and Sanger sequencing to evaluate their efficiencies, limiting quantitative assessment. Here, we develop a method to quantify errors in synthetic DNA by next-generation sequencing. We analyzed errors in model gene assemblies and systematically compared six different error correction enzymes across 11 conditions. We find that ErrASE and T7 Endonuclease I are the most effective at decreasing average error rates (up to 5.8-fold relative to the input), whereas MutS is the best for increasing the number of perfect assemblies (up to 25.2-fold). We are able to quantify differential specificities such as ErrASE preferentially corrects C/G transversions whereas T7 Endonuclease I preferentially corrects A/T transversions. More generally, this experimental and computational pipeline is a fast, scalable and extensible way to analyze errors in gene assemblies, to profile error correction methods, and to benchmark DNA synthesis methods.
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Affiliation(s)
- Nathan B. Lubock
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Di Zhang
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Angus M. Sidore
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sriram Kosuri
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA
- UCLA-DOE Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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34
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Abstract
Naturally occurring DNA is encoded by the four nucleobases adenine, cytosine, guanine and thymine. Yet minor chemical modifications to these bases, such as methylation, can significantly alter DNA function, and more drastic changes, such as replacement with unnatural base pairs, could expand its function. In order to realize the full potential of DNA in therapeutic and synthetic biology applications, our ability to 'write' long modified DNA in a controlled manner must be improved. This review highlights methods currently used for the synthesis of moderately long chemically modified nucleic acids (up to 1000 bp), their limitations and areas for future expansion.
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35
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Wan W, Lu M, Wang D, Gao X, Hong J. High-fidelity de novo synthesis of pathways using microchip-synthesized oligonucleotides and general molecular biology equipment. Sci Rep 2017; 7:6119. [PMID: 28733633 PMCID: PMC5522410 DOI: 10.1038/s41598-017-06428-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/17/2017] [Indexed: 11/24/2022] Open
Abstract
Engineering and evaluation of synthetic routes for generating valuable compounds require accurate and cost-effective de novo synthesis of genetic pathways. Here, we present an economical and streamlined de novo DNA synthesis approach for engineering a synthetic pathway with microchip-synthesized oligonucleotides (oligo). The process integrates entire oligo pool amplification, error-removal, and assembly of long DNA molecules. We utilized this method to construct a functional lycopene biosynthetic pathway (11.9 kb encoding 10 genes) in Escherichia coli using a highly error-prone microchip-synthesized oligo pool (479 oligos) without pre-purification, and the error-frequency was reduced from 14.25/kb to 0.53/kb. This low-equipment-dependent and cost-effective method can be widely applied for rapid synthesis of biosynthetic pathways in general molecular biology laboratories.
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Affiliation(s)
- Wen Wan
- The Key Laboratory of Biotechnology for Medicinal Plant of Jiangsu Province, Jiangsu Normal University, Xuzhou, Jiangsu, 221116, China
| | - Min Lu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Dongmei Wang
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
| | - Xiaolian Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China
- Department of Biology and Biochemistry, University of Houston, Houston, TX77004-5001, USA
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, China.
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36
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Woodruff LBA, Gorochowski TE, Roehner N, Mikkelsen TS, Densmore D, Gordon DB, Nicol R, Voigt CA. Registry in a tube: multiplexed pools of retrievable parts for genetic design space exploration. Nucleic Acids Res 2017; 45:1553-1565. [PMID: 28007941 PMCID: PMC5388403 DOI: 10.1093/nar/gkw1226] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 11/22/2016] [Indexed: 11/14/2022] Open
Abstract
Genetic designs can consist of dozens of genes and hundreds of genetic parts. After evaluating a design, it is desirable to implement changes without the cost and burden of starting the construction process from scratch. Here, we report a two-step process where a large design space is divided into deep pools of composite parts, from which individuals are retrieved and assembled to build a final construct. The pools are built via multiplexed assembly and sequenced using next-generation sequencing. Each pool consists of ∼20 Mb of up to 5000 unique and sequence-verified composite parts that are barcoded for retrieval by PCR. This approach is applied to a 16-gene nitrogen fixation pathway, which is broken into pools containing a total of 55 848 composite parts (71.0 Mb). The pools encompass an enormous design space (1043 possible 23 kb constructs), from which an algorithm-guided 192-member 4.5 Mb library is built. Next, all 1030 possible genetic circuits based on 10 repressors (NOR/NOT gates) are encoded in pools where each repressor is fused to all permutations of input promoters. These demonstrate that multiplexing can be applied to encompass entire design spaces from which individuals can be accessed and evaluated.
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Affiliation(s)
- Lauren B A Woodruff
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas E Gorochowski
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nicholas Roehner
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Tarjei S Mikkelsen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Douglas Densmore
- Biological Design Center, Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - D Benjamin Gordon
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Nicol
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Christopher A Voigt
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.,Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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37
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Chan HF, Ma S, Tian J, Leong KW. High-throughput screening of microchip-synthesized genes in programmable double-emulsion droplets. NANOSCALE 2017; 9:3485-3495. [PMID: 28239692 PMCID: PMC5428077 DOI: 10.1039/c6nr08224f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The rapid advances in synthetic biology and biotechnology are increasingly demanding high-throughput screening technology, such as screening of the functionalities of synthetic genes for optimization of protein expression. Compartmentalization of single cells in water-in-oil (W/O) emulsion droplets allows screening of a vast number of individualized assays, and recent advances in automated microfluidic devices further help realize the potential of droplet technology for high-throughput screening. However these single-emulsion droplets are incompatible with aqueous phase analysis and the inner droplet environment cannot easily communicate with the external phase. We present a high-throughput, miniaturized screening platform for microchip-synthesized genes using microfluidics-generated water-in-oil-in-water (W/O/W) double emulsion (DE) droplets that overcome these limitations. Synthetic gene variants of fluorescent proteins are synthesized with a custom-built microarray inkjet synthesizer, which are then screened for expression in Escherichia coli (E. coli) cells. Bacteria bearing individual fluorescent gene variants are encapsulated as single cells into DE droplets where fluorescence signals are enhanced by 100 times within 24 h of proliferation. Enrichment of functionally-correct genes by employing an error correction method is demonstrated by screening DE droplets containing fluorescent clones of bacteria with the red fluorescent protein (rfp) gene. Permeation of isopropyl β-d-1-thiogalactopyranoside (IPTG) through the thin oil layer from the external solution initiates target gene expression. The induced expression of the synthetic fluorescent proteins from at least ∼100 bacteria per droplet generates detectable fluorescence signals to enable fluorescence-activated cell sorting (FACS) of the intact droplets. This technology obviates time- and labor-intensive cell culture typically required in conventional bulk experiment.
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Affiliation(s)
- H F Chan
- Department of Biomedical Engineering, Duke University, Durham, 27705, USA. and Department of Biomedical Engineering, Columbia University, New York, 10027, USA
| | - S Ma
- Department of Biomedical Engineering, Duke University, Durham, 27705, USA. and General Biosystems, Inc. Morrisville, 27560 USA
| | - J Tian
- Department of Biomedical Engineering, Duke University, Durham, 27705, USA. and General Biosystems, Inc. Morrisville, 27560 USA and Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - K W Leong
- Department of Biomedical Engineering, Duke University, Durham, 27705, USA. and Department of Biomedical Engineering, Columbia University, New York, 10027, USA and Department of Systems Biology, Columbia University, New York, 10027, USA
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38
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Smith JD, Schlecht U, Xu W, Suresh S, Horecka J, Proctor MJ, Aiyar RS, Bennett RAO, Chu A, Li YF, Roy K, Davis RW, Steinmetz LM, Hyman RW, Levy SF, St Onge RP. A method for high-throughput production of sequence-verified DNA libraries and strain collections. Mol Syst Biol 2017; 13:913. [PMID: 28193641 PMCID: PMC5327727 DOI: 10.15252/msb.20167233] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The low costs of array‐synthesized oligonucleotide libraries are empowering rapid advances in quantitative and synthetic biology. However, high synthesis error rates, uneven representation, and lack of access to individual oligonucleotides limit the true potential of these libraries. We have developed a cost‐effective method called Recombinase Directed Indexing (REDI), which involves integration of a complex library into yeast, site‐specific recombination to index library DNA, and next‐generation sequencing to identify desired clones. We used REDI to generate a library of ~3,300 DNA probes that exhibited > 96% purity and remarkable uniformity (> 95% of probes within twofold of the median abundance). Additionally, we created a collection of ~9,000 individually accessible CRISPR interference yeast strains for > 99% of genes required for either fermentative or respiratory growth, demonstrating the utility of REDI for rapid and cost‐effective creation of strain collections from oligonucleotide pools. Our approach is adaptable to any complex DNA library, and fundamentally changes how these libraries can be parsed, maintained, propagated, and characterized.
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Affiliation(s)
- Justin D Smith
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ulrich Schlecht
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Weihong Xu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Sundari Suresh
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Joe Horecka
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Proctor
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Raeka S Aiyar
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Richard A O Bennett
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Angela Chu
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Yong Fuga Li
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Kevin Roy
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ronald W Davis
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Richard W Hyman
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Sasha F Levy
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Biochemistry and Cellular Biology, Stony Brook University, Stony Brook, NY, USA
| | - Robert P St Onge
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA .,Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
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39
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Shivalingam A, Tyburn AES, El-Sagheer AH, Brown T. Molecular Requirements of High-Fidelity Replication-Competent DNA Backbones for Orthogonal Chemical Ligation. J Am Chem Soc 2017; 139:1575-1583. [PMID: 28097865 DOI: 10.1021/jacs.6b11530] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The molecular properties of the phosphodiester backbone that made it the evolutionary choice for the enzymatic replication of genetic information are not well understood. To address this, and to develop new chemical ligation strategies for assembly of biocompatible modified DNA, we have synthesized oligonucleotides containing several structurally and electronically varied artificial linkages. This has yielded a new highly promising ligation method based on amide backbone formation that is chemically orthogonal to CuAAC "click" ligation. A study of kinetics and fidelity of replication through these artificial linkages by primer extension, PCR, and deep sequencing reveals that a subtle interplay between backbone flexibility, steric factors, and ability to hydrogen bond to the polymerase modulates rapid and accurate information decoding. Even minor phosphorothioate modifications can impair the copying process, yet some radical triazole and amide DNA backbones perform surprisingly well, indicating that the phosphate group is not essential. These findings have implications in the field of synthetic biology.
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Affiliation(s)
- Arun Shivalingam
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Agnes E S Tyburn
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
| | - Afaf H El-Sagheer
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford , 12 Mansfield Road, Oxford OX1 3TA, U.K
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40
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Turchetto J, Sequeira AF, Ramond L, Peysson F, Brás JLA, Saez NJ, Duhoo Y, Blémont M, Guerreiro CIPD, Quinton L, De Pauw E, Gilles N, Darbon H, Fontes CMGA, Vincentelli R. High-throughput expression of animal venom toxins in Escherichia coli to generate a large library of oxidized disulphide-reticulated peptides for drug discovery. Microb Cell Fact 2017; 16:6. [PMID: 28095880 PMCID: PMC5242012 DOI: 10.1186/s12934-016-0617-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 12/16/2016] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Animal venoms are complex molecular cocktails containing a wide range of biologically active disulphide-reticulated peptides that target, with high selectivity and efficacy, a variety of membrane receptors. Disulphide-reticulated peptides have evolved to display improved specificity, low immunogenicity and to show much higher resistance to degradation than linear peptides. These properties make venom peptides attractive candidates for drug development. However, recombinant expression of reticulated peptides containing disulphide bonds is challenging, especially when associated with the production of large libraries of bioactive molecules for drug screening. To date, as an alternative to artificial synthetic chemical libraries, no comprehensive recombinant libraries of natural venom peptides are accessible for high-throughput screening to identify novel therapeutics. RESULTS In the accompanying paper an efficient system for the expression and purification of oxidized disulphide-reticulated venom peptides in Escherichia coli is described. Here we report the development of a high-throughput automated platform, that could be adapted to the production of other families, to generate the largest ever library of recombinant venom peptides. The peptides were produced in the periplasm of E. coli using redox-active DsbC as a fusion tag, thus allowing the efficient formation of correctly folded disulphide bridges. TEV protease was used to remove fusion tags and recover the animal venom peptides in the native state. Globally, within nine months, out of a total of 4992 synthetic genes encoding a representative diversity of venom peptides, a library containing 2736 recombinant disulphide-reticulated peptides was generated. The data revealed that the animal venom peptides produced in the bacterial host were natively folded and, thus, are putatively biologically active. CONCLUSIONS Overall this study reveals that high-throughput expression of animal venom peptides in E. coli can generate large libraries of recombinant disulphide-reticulated peptides of remarkable interest for drug discovery programs.
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Affiliation(s)
- Jeremy Turchetto
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Ana Filipa Sequeira
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
- NZYtech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, 1649-038 Lisbon, Portugal
| | - Laurie Ramond
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Fanny Peysson
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Joana L. A. Brás
- NZYtech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, 1649-038 Lisbon, Portugal
| | - Natalie J. Saez
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, 4072 Australia
| | - Yoan Duhoo
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Marilyne Blémont
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | | | - Loic Quinton
- Mass Spectrometry Laboratory, B6c University of Liège, MolSys-Quartier Agora, Allée du six Aout 11, 4000 Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, B6c University of Liège, MolSys-Quartier Agora, Allée du six Aout 11, 4000 Liège, Belgium
| | - Nicolas Gilles
- CEA/DRF/iBiTecS, Service d’Ingénierie Moléculaire des Protéines, 91191 Gif-sur-Yvette, France
| | - Hervé Darbon
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
| | - Carlos M. G. A. Fontes
- CIISA-Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, 1300-477 Lisbon, Portugal
- NZYtech Genes & Enzymes, Campus do Lumiar, Estrada do paço do Lumiar, 1649-038 Lisbon, Portugal
| | - Renaud Vincentelli
- Unité Mixte de Recherche (UMR) 7257, Centre National de la Recherche Scientifique (CNRS) Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), Marseille, France
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41
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Hughes RA, Ellington AD. Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology. Cold Spring Harb Perspect Biol 2017; 9:9/1/a023812. [PMID: 28049645 DOI: 10.1101/cshperspect.a023812] [Citation(s) in RCA: 204] [Impact Index Per Article: 29.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The chemical synthesis of DNA oligonucleotides and their assembly into synthons, genes, circuits, and even entire genomes by gene synthesis methods has become an enabling technology for modern molecular biology and enables the design, build, test, learn, and repeat cycle underpinning innovations in synthetic biology. In this perspective, we briefly review the techniques and technologies that enable the synthesis of DNA oligonucleotides and their assembly into larger DNA constructs with a focus on recent advancements that have sought to reduce synthesis cost and increase sequence fidelity. The development of lower-cost methods to produce high-quality synthetic DNA will allow for the exploration of larger biological hypotheses by lowering the cost of use and help to close the DNA read-write cost gap.
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Affiliation(s)
- Randall A Hughes
- Applied Research Laboratories, The University of Texas at Austin, Austin, Texas 78758
| | - Andrew D Ellington
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712
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42
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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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43
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Bornholt J, Lopez R, Carmean DM, Ceze L, Seelig G, Strauss K. A DNA-Based Archival Storage System. ACTA ACUST UNITED AC 2016. [DOI: 10.1145/2980024.2872397] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Demand for data storage is growing exponentially, but the capacity of existing storage media is not keeping up. Using DNA to archive data is an attractive possibility because it is extremely dense, with a raw limit of 1 exabyte/mm
3
(109 GB/mm
3
), and long-lasting, with observed half-life of over 500 years. This paper presents an architecture for a DNA-based archival storage system. It is structured as a key-value store, and leverages common biochemical techniques to provide random access. We also propose a new encoding scheme that offers controllable redundancy, trading off reliability for density. We demonstrate feasibility, random access, and robustness of the proposed encoding with wet lab experiments involving 151 kB of synthesized DNA and a 42 kB random-access subset, and simulation experiments of larger sets calibrated to the wet lab experiments. Finally, we highlight trends in biotechnology that indicate the impending practicality of DNA storage for much larger datasets.
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Affiliation(s)
| | | | | | - Luis Ceze
- University of Washington, Seattle, WA, USA
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44
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Wang F, Zhang H, Gao J, Chen F, Chen S, Zhang C, Peng G. Rapid and accurate synthesis of TALE genes from synthetic oligonucleotides. Biotechniques 2016; 60:299-305. [PMID: 27286807 DOI: 10.2144/000114422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 02/08/2016] [Indexed: 11/23/2022] Open
Abstract
Custom synthesis of transcription activator-like effector (TALE) genes has relied upon plasmid libraries of pre-fabricated TALE-repeat monomers or oligomers. Here we describe a novel synthesis method that directly incorporates annealed synthetic oligonucleotides into the TALE-repeat units. Our approach utilizes iterative sets of oligonucleotides and a translational frame check strategy to ensure the high efficiency and accuracy of TALE-gene synthesis. TALE arrays of more than 20 repeats can be constructed, and the majority of the synthesized constructs have perfect sequences. In addition, this novel oligonucleotide-based method can readily accommodate design changes to the TALE repeats. We demonstrated an increased gene targeting efficiency against a genomic site containing a potentially methylated cytosine by incorporating non-conventional repeat variable di-residue (RVD) sequences.
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Affiliation(s)
- Fenghua Wang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Hefei Zhang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Jingxia Gao
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Fengjiao Chen
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Sijie Chen
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Cuizhen Zhang
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
| | - Gang Peng
- Institutes of Brain Sciences, State Key Laboratory of Medical Neurobiology and Collaborative Innovation Center for Brain Science, Fudan University, Shanghai, China
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45
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Stone BC, Kas A, Billman ZP, Fuller DH, Fuller JT, Shendure J, Murphy SC. Complex Minigene Library Vaccination for Discovery of Pre-Erythrocytic Plasmodium T Cell Antigens. PLoS One 2016; 11:e0153449. [PMID: 27070430 PMCID: PMC4829254 DOI: 10.1371/journal.pone.0153449] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/30/2016] [Indexed: 01/15/2023] Open
Abstract
Development of a subunit vaccine targeting liver-stage Plasmodium parasites requires the identification of antigens capable of inducing protective T cell responses. However, traditional methods of antigen identification are incapable of evaluating T cell responses against large numbers of proteins expressed by these parasites. This bottleneck has limited development of subunit vaccines against Plasmodium and other complex intracellular pathogens. To address this bottleneck, we are developing a synthetic minigene technology for multi-antigen DNA vaccines. In an initial test of this approach, pools of long (150 bp) antigen-encoding oligonucleotides were synthesized and recombined into vectors by ligation-independent cloning to produce two DNA minigene library vaccines. Each vaccine encoded peptides derived from 36 (vaccine 1) and 53 (vaccine 2) secreted or transmembrane pre-erythrocytic P. yoelii proteins. BALB/cj mice were vaccinated three times with a single vaccine by biolistic particle delivery (gene gun) and screened for interferon-γ-producing T cell responses by ELISPOT. Library vaccination induced responses against four novel antigens. Naïve mice exposed to radiation-attenuated sporozoites mounted a response against only one of the four novel targets (PyMDH, malate dehydrogenase). The response to PyMDH could not be recalled by additional homologous sporozoite immunizations but could be partially recalled by heterologous cross-species sporozoite exposure. Vaccination against the dominant PyMDH epitope by DNA priming and recombinant Listeria boosting did not protect against sporozoite challenge. Improvements in library design and delivery, combined with methods promoting an increase in screening sensitivity, may enable complex minigene screening to serve as a high-throughput system for discovery of novel T cell antigens.
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Affiliation(s)
- Brad C. Stone
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- * E-mail: (BCS); (SCM)
| | - Arnold Kas
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Zachary P. Billman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Deborah H. Fuller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - James T. Fuller
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Sean C. Murphy
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Center for Emerging and Re-emerging Infectious Diseases, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Seattle Malaria Clinical Trials Center, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Human Challenge Center, Center for Infectious Disease Research, Seattle, Washington, United States of America
- * E-mail: (BCS); (SCM)
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46
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Bornholt J, Lopez R, Carmean DM, Ceze L, Seelig G, Strauss K. A DNA-Based Archival Storage System. ACTA ACUST UNITED AC 2016. [DOI: 10.1145/2954680.2872397] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | | | | | - Luis Ceze
- University of Washington, Seattle, WA, USA
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47
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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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48
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Ben Yehezkel T, Rival A, Raz O, Cohen R, Marx Z, Camara M, Dubern JF, Koch B, Heeb S, Krasnogor N, Delattre C, Shapiro E. Synthesis and cell-free cloning of DNA libraries using programmable microfluidics. Nucleic Acids Res 2015; 44:e35. [PMID: 26481354 PMCID: PMC4770201 DOI: 10.1093/nar/gkv1087] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 10/03/2015] [Indexed: 11/12/2022] Open
Abstract
Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.
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Affiliation(s)
- Tuval Ben Yehezkel
- Applied Mathematics and Computer Science and Biological Chemistry, Weizmann institute of science, Rehovot, Israel
| | | | - Ofir Raz
- Applied Mathematics and Computer Science and Biological Chemistry, Weizmann institute of science, Rehovot, Israel
| | - Rafael Cohen
- Applied Mathematics and Computer Science and Biological Chemistry, Weizmann institute of science, Rehovot, Israel
| | - Zipora Marx
- Applied Mathematics and Computer Science and Biological Chemistry, Weizmann institute of science, Rehovot, Israel
| | - Miguel Camara
- Centre for Bio-molecular Sciences, University of Nottingham, Nottingham, UK
| | | | - Birgit Koch
- School of Computing Science, Claremont Tower, Newcastle University, Newcastle, UK
| | - Stephan Heeb
- Centre for Bio-molecular Sciences, University of Nottingham, Nottingham, UK
| | - Natalio Krasnogor
- School of Computing Science, Claremont Tower, Newcastle University, Newcastle, UK
| | | | - Ehud Shapiro
- Applied Mathematics and Computer Science and Biological Chemistry, Weizmann institute of science, Rehovot, Israel
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49
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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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50
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A high-throughput optomechanical retrieval method for sequence-verified clonal DNA from the NGS platform. Nat Commun 2015; 6:6073. [PMID: 25641679 PMCID: PMC4327316 DOI: 10.1038/ncomms7073] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 12/10/2014] [Indexed: 01/29/2023] Open
Abstract
Writing DNA plays a significant role in the fields of synthetic biology, functional genomics and bioengineering. DNA clones on next-generation sequencing (NGS) platforms have the potential to be a rich and cost-effective source of sequence-verified DNAs as a precursor for DNA writing. However, it is still very challenging to retrieve target clonal DNA from high-density NGS platforms. Here we propose an enabling technology called 'Sniper Cloning' that enables the precise mapping of target clone features on NGS platforms and non-contact rapid retrieval of targets for the full utilization of DNA clones. By merging the three cutting-edge technologies of NGS, DNA microarray and our pulse laser retrieval system, Sniper Cloning is a week-long process that produces 5,188 error-free synthetic DNAs in a single run of NGS with a single microarray DNA pool. We believe that this technology has potential as a universal tool for DNA writing in biological sciences.
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