1
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Tong Y, Sun J, Chen Y, Yi C, Wang H, Li C, Dai N, Yang G. POSoligo software for in vitro gene synthesis. Sci Rep 2024; 14:11117. [PMID: 38750104 PMCID: PMC11096389 DOI: 10.1038/s41598-024-59497-3] [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: 12/16/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Oligonucleotide synthesis is vital for molecular experiments. Bioinformatics has been employed to create various algorithmic tools for the in vitro synthesis of nucleotides. The main approach to synthesizing long-chain DNA molecules involves linking short-chain oligonucleotides through ligase chain reaction (LCR) and polymerase chain reaction (PCR). Short-chain DNA molecules have low mutation rates, while LCR requires complementary interfaces at both ends of the two nucleic acid molecules or may alter the conformation of the nucleotide chain, leading to termination of amplification. Therefore, molecular melting temperature, length, and specificity must be considered during experimental design. POSoligo is a specialized offline tool for nucleotide fragment synthesis. It optimizes the oligonucleotide length and specificity based on input single-stranded DNA, producing multiple contiguous long strands (COS) and short patch strands (POS) with complementary ends. This process ensures free 5'- and 3'-ends during oligonucleotide synthesis, preventing secondary structure formation and ensuring specific binding between COS and POS without relying on stabilizing the complementary strands based on Tm values. POSoligo was used to synthesize the linear RBD sequence of SARS-CoV-2 using only one DNA strand, several POSs for LCR ligation, and two pairs of primers for PCR amplification in a time- and cost-effective manner.
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Affiliation(s)
- Yingying Tong
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Jie Sun
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Yang Chen
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Changhua Yi
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Hua Wang
- Shanghai Telebio Biomedical Technology Co., LTD, Shanghai, China
| | - Caixin Li
- Shanghai Telebio Biomedical Technology Co., LTD, Shanghai, China
| | - Nana Dai
- Anhui Health College, Chizhou, 247100, Anhui, China
| | - Guanghua Yang
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China.
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China.
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2
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Zhu R, Zhang J, Wang L, Zhang Y, Zhao Y, Han Y, Sun J, Zhang X, Dou Y, Yao H, Yan W, Luo X, Dai J, Dai Z. Engineering functional materials through bacteria-assisted living grafting. Cell Syst 2024; 15:264-274.e9. [PMID: 38460522 DOI: 10.1016/j.cels.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 09/15/2023] [Accepted: 02/22/2024] [Indexed: 03/11/2024]
Abstract
Functionalizing materials with biomacromolecules such as enzymes has broad applications in biotechnology and biomedicine. Here, we introduce a grafting method mediated by living cells to functionalize materials. We use polymeric scaffolds to trap engineered bacteria and micron-sized particles with chemical groups serving as active sites for grafting. The bacteria synthesize the desired protein for grafting and autonomously lyse to release it. The released functional moieties are locally grafted onto the active sites, generating the materials engineered by living grafting (MELGs). MELGs are resilient to perturbations because of both the bonding and the regeneration of functional domains synthesized by living cells. The programmability of the bacteria enables us to fabricate MELGs that can respond to external input, decompose a pollutant, reconstitute synthetic pathways for natural product synthesis, and purify mismatched DNA. Our work establishes a bacteria-assisted grafting strategy to functionalize materials with a broad range of biological activities in an integrated, flexible, and modular manner. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Runtao Zhu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jiao Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lin Wang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yunfeng Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yang Zhao
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ying Han
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Sun
- Soft Bio-interface Electronics Lab, Center of Neural Engineering, CAS Key Laboratory of Human-Machine Intelligence-Synergy Systems, Shenzhen Institute of Artificial Intelligence and Robotics for Society, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xi Zhang
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ying Dou
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Huaxiong Yao
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wei Yan
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaozhou Luo
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Junbiao Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhuojun Dai
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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3
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Murphy ZR, Shields DA, Evrony GD. Serial enrichment of heteroduplex DNA using a MutS-magnetic bead system. Biotechnol J 2023; 18:e2200323. [PMID: 36317440 PMCID: PMC9839629 DOI: 10.1002/biot.202200323] [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: 06/20/2022] [Revised: 10/13/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
Abstract
Numerous applications in molecular biology and genomics require characterization of mutant DNA molecules present at low levels within a larger sample of non-mutant DNA. This is often achieved either by selectively amplifying mutant DNA, or by sequencing all the DNA followed by computational identification of the mutant DNA. However, selective amplification is challenging for insertions and deletions (indels). Additionally, sequencing all the DNA in a sample may not be cost effective when only the presence of a mutation needs to be ascertained rather than its allelic fraction. The MutS protein evolved to detect DNA heteroduplexes in which the two DNA strands are mismatched. Prior methods have utilized MutS to enrich mutant DNA by hybridizing mutant to non-mutant DNA to create heteroduplexes. However, the purity of heteroduplex DNA these methods achieve is limited because they can only feasibly perform one or two enrichment cycles. We developed a MutS-magnetic bead system that enables rapid serial enrichment cycles. With six cycles, we achieve complete purification of heteroduplex indel DNA originally present at a 5% fraction and over 40-fold enrichment of heteroduplex DNA originally present at a 1% fraction. This system may enable novel approaches for enriching mutant DNA for targeted sequencing.
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Affiliation(s)
- Zachary R. Murphy
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Danielle A. Shields
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
| | - Gilad D. Evrony
- Center for Human Genetics and Genomics, Department of Pediatrics, Department of Neuroscience & Physiology, Institute for Systems Genetics, Perlmutter Cancer Center, and Neuroscience Institute, New York University Grossman School of Medicine, USA
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4
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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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Martínez MA, Jordan-Paiz A, Franco S, Nevot M. Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies. Nucleic Acids Res 2020; 47:10506-10519. [PMID: 31584076 PMCID: PMC6846928 DOI: 10.1093/nar/gkz831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022] Open
Abstract
Synthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.
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Affiliation(s)
- Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Maria Nevot
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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6
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Zhang J, Wang Y, Chai B, Wang J, Li L, Liu M, Zhao G, Yao L, Gao X, Yin Y, Xu J. Efficient and Low-Cost Error Removal in DNA Synthesis by a High-Durability MutS. ACS Synth Biol 2020; 9:940-952. [PMID: 32135061 DOI: 10.1021/acssynbio.0c00079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzyme-based error correction is a key step in de novo DNA synthesis, yet the inherent instability of error-correction enzymes such as MutS has hindered the throughput and efficiency of DNA synthesis workflows. Here we introduce a process called Improved MICC (iMICC), in which all error-correction steps of oligos and fragments within a complete gene-synthesis cycle are completed in a simple, efficient, and low-cost manner via a MutS protein engineered for high durability. By establishing a disulfide bond of L157C-G233C, full-activity shelf life of E. coli MutS (eMutS) was prolonged from 7 to 49 days and was further extended to 63 days via cellulose-bound 4 °C storage. In synthesis of 10 Cas9 homologues in-solution and 10 xylose reductase (XR) homologues on-chip, iMICC reduced error frequency to 0.64/Kb and 0.41/Kb, respectively, with 72.1% and 86.4% of assembled fragments being error-free. By elevating base accuracy by 37.6-fold while avoiding repetitive preparation of fresh enzymes, iMICC is more efficient and robust than the wild-type eMutS, and it is 6.6-fold more accurate and 26.7-fold cheaper than CorrectASE. These advantages promise its broad applications in industrial DNA synthesis.
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Affiliation(s)
- Jia Zhang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yefei Wang
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Baihui Chai
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichao Wang
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lulu Li
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
| | - Min Liu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lishan Yao
- CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolian Gao
- LC-BIO Technologies CO., LTD., Hangzhou 310018, China
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77004-5001, United States
| | - Yifeng Yin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China
- Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory of Marine Science and Technology, Qingdao, Shandong 266071, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Hao M, Qiao J, Qi H. Current and Emerging Methods for the Synthesis of Single-Stranded DNA. Genes (Basel) 2020; 11:E116. [PMID: 31973021 PMCID: PMC7073533 DOI: 10.3390/genes11020116] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 01/16/2020] [Accepted: 01/18/2020] [Indexed: 12/21/2022] Open
Abstract
Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.
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Affiliation(s)
- Min Hao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jianjun Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China; (M.H.); (J.Q.)
- Key Laboratory of Systems Bioengineering of Ministry of Education, Tianjin University, Tianjin 300072, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Tianjin University, Tianjin 300072, China
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8
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Xie Y, Yang YT, Shi W, Ai X, Xi XG. Construction, expression, and characterization of AG1 1-843 and AG1 1-1581. Protein Expr Purif 2018; 152:71-76. [PMID: 29870801 DOI: 10.1016/j.pep.2018.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/28/2018] [Accepted: 06/01/2018] [Indexed: 10/14/2022]
Abstract
AG1, a member of the DUF1220 protein family, exhibits the most extreme human lineage-specific copy number expansion of any protein-coding sequence in the genome. These variations in copy number have been linked to both brain evolution among primates and brain size in humans. Unfortunately, our current understanding of the structure and function of these proteins is limited because current cloning and expression techniques fail to consistently produce recombinant protein for in vitro studies. The present work describes a method for amino acid and DNA sequence optimization and synthesis, recombinant protein expression and analysis of two AG1 fragments, AG11-843 and AG11-1581. It was first necessary to modify the nucleotide sequence, while holding the GC content at 52.9%. The genes were then sectionally synthesized by overlap PCR. The resulting segments were cloned into the pET-15 b-sumo expression vector and subsequently transformed into BL21 (DE3) cells. After inducing their expression, the AG11-843 and AG11-1581 proteins were isolated and purified. Furthermore, using dynamic light scattering and gel filtration analysis, AG11-843 and AG11-1581 were shown to be present in tetrameric and dimeric forms in solution. To our knowledge, this is the first study to synthesize and express fragments of the DUF1220 protein family for in vitro analysis. Taken together, the proven utility and versatility of this method indicate that it can be used as an effective technique to construct and express other proteins with complicated sequences, thus providing the means to study their function and structure in vitro.
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Affiliation(s)
- Yan Xie
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yan-Tao Yang
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wei Shi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xia Ai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; Laboratoire de Biologie et Pharmacologie Appliquée, Ecole Normals Supérieure de Cachan, CNRS, 61 Avenue du Président Wilson, 94235, Cachan, France.
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9
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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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10
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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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Abstract
Efficacy of de novo gene synthesis largely depends on the quality of overlapping oligonucleotides used as template for PCR assembly. The error rate associated with current gene synthesis protocols limits the efficient and accurate production of synthetic genes, both in the small and large scales. Here, we analysed the ability of different endonuclease enzymes, which specifically recognize and cleave DNA mismatches resulting from incorrect impairments between DNA strands, to remove mutations accumulated in synthetic genes. The gfp gene, which encodes the green fluorescent protein, was artificially synthesized using an integrated protocol including an enzymatic mismatch cleavage step (EMC) following gene assembly. Functional and sequence analysis of resulting artificial genes revealed that number of deletions, insertions and substitutions was strongly reduced when T7 endonuclease I was used for mutation removal. This method diminished mutation frequency by eightfold relative to gene synthesis not incorporating an error correction step. Overall, EMC using T7 endonuclease I improved the population of error-free synthetic genes, resulting in an error frequency of 0.43 errors per 1 kb. Taken together, data presented here reveal that incorporation of a mutation-removal step including T7 endonuclease I can effectively improve the fidelity of artificial gene synthesis.
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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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13
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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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14
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Sequeira AF, Brás JLA, Guerreiro CIPD, Vincentelli R, Fontes CMGA. Development of a gene synthesis platform for the efficient large scale production of small genes encoding animal toxins. BMC Biotechnol 2016; 16:86. [PMID: 27905914 PMCID: PMC5131498 DOI: 10.1186/s12896-016-0316-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 11/23/2016] [Indexed: 11/16/2022] Open
Abstract
Background Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. Results Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides. This improved gene synthesis method uses a PCR-based protocol to assemble synthetic DNA from pools of overlapping oligonucleotides and was developed to synthesise multiples genes simultaneously. This technology incorporates an accurate, automated and cost effective ligation independent cloning step to directly integrate the synthetic genes into an effective Escherichia coli expression vector. The robustness of this technology to generate large libraries of dozens to thousands of synthetic nucleic acids was demonstrated through the parallel and simultaneous synthesis of 96 genes encoding animal toxins. Conclusions An automated platform was developed for the large-scale synthesis of small genes encoding eukaryotic toxins. Large scale recombinant expression of synthetic genes encoding eukaryotic toxins will allow exploring the extraordinary potency and pharmacological diversity of animal venoms, an increasingly valuable but unexplored source of lead molecules for drug discovery. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0316-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ana Filipa Sequeira
- Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA) - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, 1300-477, Portugal.,NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, Lisboa, 1649-038, Portugal
| | - Joana L A Brás
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, Lisboa, 1649-038, Portugal
| | - Catarina I P D Guerreiro
- NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, Lisboa, 1649-038, 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), Campus de Luminy, 163 Avenue de Luminy, Marseille, CEDEX 09, 13288, France
| | - Carlos M G A Fontes
- Centro Interdisciplinar de Investigação em Sanidade Animal (CIISA) - Faculdade de Medicina Veterinária, Universidade de Lisboa, Avenida da Universidade Técnica, Lisboa, 1300-477, Portugal. .,NZYTech Genes & Enzymes, Campus do Lumiar, Estrada do Paço do Lumiar, Edifício E, r/c, Lisboa, 1649-038, Portugal.
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15
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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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16
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Batonick M, Holland EG, Busygina V, Alderman D, Kay BK, Weiner MP, Kiss MM. Platform for high-throughput antibody selection using synthetically-designed antibody libraries. N Biotechnol 2015; 33:565-73. [PMID: 26607994 DOI: 10.1016/j.nbt.2015.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/04/2015] [Accepted: 11/09/2015] [Indexed: 11/30/2022]
Abstract
Synthetic humanized antibody libraries are frequently generated by random incorporation of changes at multiple positions in the antibody hypervariable regions. Although these libraries have very large theoretical diversities (>10(20)), the practical diversity that can be achieved by transformation of Escherichia coli is limited to about 10(10). To constrain the practical diversity to sequences that more closely mimic the diversity of natural human antibodies, we generated a scFv phage library using entirely pre-defined complementarity determining regions (CDR). We have used this library to select for novel antibodies against four human protein targets and demonstrate that identification of enriched sequences at each of the six CDRs in early selection rounds can be used to reconstruct a consensus antibody with selectivity for the target.
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Affiliation(s)
- Melissa Batonick
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States.
| | - Erika G Holland
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Valeria Busygina
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Dawn Alderman
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Brian K Kay
- University of Illinois at Chicago, 845 West Taylor Street Chicago, IL 60607, United States
| | - Michael P Weiner
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
| | - Margaret M Kiss
- AxioMx, Inc., 688 East Main Street, Branford, CT 06405, United States
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17
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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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18
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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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19
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Hu D, Hu S, Wan W, Xu M, Du R, Zhao W, Gao X, Liu J, Liu H, Hong J. Effective Optimization of Antibody Affinity by Phage Display Integrated with High-Throughput DNA Synthesis and Sequencing Technologies. PLoS One 2015; 10:e0129125. [PMID: 26046845 PMCID: PMC4457833 DOI: 10.1371/journal.pone.0129125] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 05/05/2015] [Indexed: 12/29/2022] Open
Abstract
Phage display technology has been widely used for antibody affinity maturation for decades. The limited library sequence diversity together with excessive redundancy and labour-consuming procedure for candidate identification are two major obstacles to widespread adoption of this technology. We hereby describe a novel library generation and screening approach to address the problems. The approach started with the targeted diversification of multiple complementarity determining regions (CDRs) of a humanized anti-ErbB2 antibody, HuA21, with a small perturbation mutagenesis strategy. A combination of three degenerate codons, NWG, NWC, and NSG, were chosen for amino acid saturation mutagenesis without introducing cysteine and stop residues. In total, 7,749 degenerate oligonucleotides were synthesized on two microchips and released to construct five single-chain antibody fragment (scFv) gene libraries with 4 x 106 DNA sequences. Deep sequencing of the unselected and selected phage libraries using the Illumina platform allowed for an in-depth evaluation of the enrichment landscapes in CDR sequences and amino acid substitutions. Potent candidates were identified according to their high frequencies using NGS analysis, by-passing the need for the primary screening of target-binding clones. Furthermore, a subsequent library by recombination of the 10 most abundant variants from four CDRs was constructed and screened, and a mutant with 158-fold increased affinity (Kd = 25.5 pM) was obtained. These results suggest the potential application of the developed methodology for optimizing the binding properties of other antibodies and biomolecules.
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Affiliation(s)
- Dongmei Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Siyi Hu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wen Wan
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Man Xu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Ruikai Du
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Wei Zhao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Xiaolian Gao
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Jing Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Haiyan Liu
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (JH); (HYL)
| | - Jiong Hong
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
- * E-mail: (JH); (HYL)
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20
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Hsiau THC, Sukovich D, Elms P, Prince RN, Stritmatter T, Ruan P, Curry B, Anderson P, Sampson J, Anderson JC. A method for multiplex gene synthesis employing error correction based on expression. PLoS One 2015; 10:e0119927. [PMID: 25790188 PMCID: PMC4366238 DOI: 10.1371/journal.pone.0119927] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Accepted: 01/17/2015] [Indexed: 11/18/2022] Open
Abstract
Our ability to engineer organisms with new biosynthetic pathways and genetic circuits is limited by the availability of protein characterization data and the cost of synthetic DNA. With new tools for reading and writing DNA, there are opportunities for scalable assays that more efficiently and cost effectively mine for biochemical protein characteristics. To that end, we have developed the Multiplex Library Synthesis and Expression Correction (MuLSEC) method for rapid assembly, error correction, and expression characterization of many genes as a pooled library. This methodology enables gene synthesis from microarray-synthesized oligonucleotide pools with a one-pot technique, eliminating the need for robotic liquid handling. Post assembly, the gene library is subjected to an ampicillin based quality control selection, which serves as both an error correction step and a selection for proteins that are properly expressed and folded in E. coli. Next generation sequencing of post selection DNA enables quantitative analysis of gene expression characteristics. We demonstrate the feasibility of this approach by building and testing over 90 genes for empirical evidence of soluble expression. This technique reduces the problem of part characterization to multiplex oligonucleotide synthesis and deep sequencing, two technologies under extensive development with projected cost reduction.
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Affiliation(s)
- Timothy H.-C. Hsiau
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - David Sukovich
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Phillip Elms
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Robin N. Prince
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Tobias Stritmatter
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
| | - Paul Ruan
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, CA, United States of America
| | - Bo Curry
- Agilent Technologies, Santa Clara, CA, United States of America
| | - Paige Anderson
- Agilent Technologies, Santa Clara, CA, United States of America
| | - Jeff Sampson
- Agilent Technologies, Santa Clara, CA, United States of America
| | - J. Christopher Anderson
- Department of Bioengineering, University of California, Berkeley, CA, United States of America
- Synthetic Biology Institute, University of California, Berkeley, CA, United States of America
- * E-mail:
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