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Wang B, Liu Y, Bai X, Tian H, Wang L, Feng M, Xia H. In vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis. Commun Biol 2024; 7:628. [PMID: 38789612 PMCID: PMC11126579 DOI: 10.1038/s42003-024-06340-0] [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: 10/22/2023] [Accepted: 05/15/2024] [Indexed: 05/26/2024] Open
Abstract
Generating genetic diversity lies at the heart of directed evolution which has been widely used to engineer genetic parts and gene circuits in synthetic biology. With the ever-expanding application of directed evolution, different approaches of generating genetic diversity are required to enrich the traditional toolbox. Here we show in vitro generation of genetic diversity for directed evolution by error-prone artificial DNA synthesis (epADS). This approach comprises a three-step process which incorporates base errors randomly generated during chemical synthesis of oligonucleotides under specific conditions into the target DNA. Through this method, 200 ~ 4000 folds of diversification in fluorescent strength have been achieved in genes encoding fluorescent proteins. EpADS has also been successfully used to diversify regulatory genetic parts, synthetic gene circuits and even increase microbial tolerance to carbenicillin in a short time period. EpADS would be an alternative tool for directed evolution which may have useful applications in synthetic biology.
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Affiliation(s)
- Baowei Wang
- Department of Strategic and Integrative Research, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
| | - Yang Liu
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xuelian Bai
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huijuan Tian
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lina Wang
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Miao Feng
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China.
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Hairong Xia
- National Center of Technology Innovation for Synthetic Biology, Tianjin, 300308, China
- Technique Support and Core Facility Center, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
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2
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Schaudy E, Ibañez-Redín G, Parlar E, Somoza MM, Lietard J. Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates. Anal Chem 2024; 96:2378-2386. [PMID: 38285499 PMCID: PMC10867803 DOI: 10.1021/acs.analchem.3c04166] [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: 09/15/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.
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Affiliation(s)
- Erika Schaudy
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Gisela Ibañez-Redín
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Etkin Parlar
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Mark M. Somoza
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, Freising 85354, Germany
- Chair
of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, Freising 85354, Germany
| | - Jory Lietard
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
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3
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Yin Y, Arneson R, Apostle A, Eriyagama AMDN, Chillar K, Burke E, Jahfetson M, Yuan Y, Fang S. Long oligodeoxynucleotides: chemical synthesis, isolation via catching-by-polymerization, verification via sequencing, and gene expression demonstration. Beilstein J Org Chem 2023; 19:1957-1965. [PMID: 38170048 PMCID: PMC10760481 DOI: 10.3762/bjoc.19.146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Long oligodeoxynucleotides (ODNs) are segments of DNAs having over one hundred nucleotides (nt). They are typically assembled using enzymatic methods such as PCR and ligation from shorter 20 to 60 nt ODNs produced by automated de novo chemical synthesis. While these methods have made many projects in areas such as synthetic biology and protein engineering possible, they have various drawbacks. For example, they cannot produce genes and genomes with long repeats and have difficulty to produce sequences containing stable secondary structures. Here, we report a direct de novo chemical synthesis of 400 nt ODNs, and their isolation from the complex reaction mixture using the catching-by-polymerization (CBP) method. To determine the authenticity of the ODNs, 399 and 401 nt ODNs were synthesized and purified with CBP. The two were joined together using Gibson assembly to give the 800 nt green fluorescent protein (GFP) gene construct. The sequence of the construct was verified via Sanger sequencing. To demonstrate the potential use of the long ODN synthesis method, the GFP gene was expressed in E. coli. The long ODN synthesis and isolation method presented here provides a pathway to the production of genes and genomes containing long repeats or stable secondary structures that cannot be produced or are highly challenging to produce using existing technologies.
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Affiliation(s)
- Yipeng Yin
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Reed Arneson
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Alexander Apostle
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Adikari M D N Eriyagama
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Komal Chillar
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Emma Burke
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Martina Jahfetson
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
| | - Yinan Yuan
- College of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA
| | - Shiyue Fang
- Department of Chemistry and Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI 49931, USA,
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4
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Yeom H, Kim N, Lee AC, Kim J, Kim H, Choi H, Song SW, Kwon S, Choi Y. Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing. ACS Synth Biol 2023; 12:3567-3577. [PMID: 37961855 PMCID: PMC10729760 DOI: 10.1021/acssynbio.3c00308] [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: 05/15/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
A comprehensive error analysis of DNA-stored data during processing, such as DNA synthesis and sequencing, is crucial for reliable DNA data storage. Both synthesis and sequencing errors depend on the sequence and the transition of bases of nucleotides; ignoring either one of the error sources leads to technical challenges in minimizing the error rate. Here, we present a methodology and toolkit that utilizes an oligonucleotide library generated from a 10-base-shifted sequence array, which is individually labeled with unique molecular identifiers, to delineate and profile DNA synthesis and sequencing errors simultaneously. This methodology enables position- and sequence-independent error profiling of both DNA synthesis and sequencing. Using this toolkit, we report base transitional errors in both synthesis and sequencing in general DNA data storage as well as degenerate-base-augmented DNA data storage. The methodology and data presented will contribute to the development of DNA sequence designs with minimal error.
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Affiliation(s)
- Huiran Yeom
- Division
of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong 18323, Republic of Korea
| | - Namphil Kim
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | | | - Jinhyun Kim
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | - Hamin Kim
- Department
of Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, South Korea
| | - Hansol Choi
- Bio-MAX
Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Seo Woo Song
- Basic Science
and Engineering Initiative, Children’s Heart Center, Stanford University, Stanford, California 94304, United States
| | - Sunghoon Kwon
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
- Department
of Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, South Korea
- Bio-MAX
Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeongjae Choi
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju 61105, Republic of Korea
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5
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Simmons BL, McDonald ND, Robinett NG. Assessment of enzymatically synthesized DNA for gene assembly. Front Bioeng Biotechnol 2023; 11:1208784. [PMID: 37476479 PMCID: PMC10354541 DOI: 10.3389/fbioe.2023.1208784] [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: 04/19/2023] [Accepted: 06/20/2023] [Indexed: 07/22/2023] Open
Abstract
Phosphoramidite chemical DNA synthesis technology is utilized for creating de novo ssDNA building blocks and is widely used by commercial vendors. Recent advances in enzymatic DNA synthesis (EDS), including engineered enzymes and reversibly terminated nucleotides, bring EDS technology into competition with traditional chemical methods. In this short study, we evaluate oligos produced using a benchtop EDS instrument alongside chemically produced commercial oligonucleotides to assemble a synthetic gene encoding green fluorescent protein (GFP). While enzymatic synthesis produced lower concentrations of individual oligonucleotides, these were available in half the time of commercially produced oligonucleotides and were sufficient to assemble functional GFP sequences without producing hazardous organic chemical waste.
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Affiliation(s)
- Brooke L. Simmons
- U.S. Army Combat Capabilities Development Command (DEVCOM) Chemical Biological Center, Gunpowder, MD, United States
- Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States
| | - Nathan D. McDonald
- U.S. Army Combat Capabilities Development Command (DEVCOM) Chemical Biological Center, Gunpowder, MD, United States
| | - Natalie G. Robinett
- U.S. Army Combat Capabilities Development Command (DEVCOM) Chemical Biological Center, Gunpowder, MD, United States
- Excet, Inc., Springfield, VA, United States
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Sabat N, Katkevica D, Pajuste K, Flamme M, Stämpfli A, Katkevics M, Hanlon S, Bisagni S, Püntener K, Sladojevich F, Hollenstein M. Towards the controlled enzymatic synthesis of LNA containing oligonucleotides. Front Chem 2023; 11:1161462. [PMID: 37179777 PMCID: PMC10172484 DOI: 10.3389/fchem.2023.1161462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/15/2023] Open
Abstract
Enzymatic, de novo XNA synthesis represents an alternative method for the production of long oligonucleotides containing chemical modifications at distinct locations. While such an approach is currently developed for DNA, controlled enzymatic synthesis of XNA remains at a relative state of infancy. In order to protect the masking groups of 3'-O-modified LNA and DNA nucleotides against removal caused by phosphatase and esterase activities of polymerases, we report the synthesis and biochemical characterization of nucleotides equipped with ether and robust ester moieties. While the resulting ester-modified nucleotides appear to be poor substrates for polymerases, ether-blocked LNA and DNA nucleotides are readily incorporated into DNA. However, removal of the protecting groups and modest incorporation yields represent obstacles for LNA synthesis via this route. On the other hand, we have also shown that the template-independent RNA polymerase PUP represents a valid alternative to the TdT and we have also explored the possibility of using engineered DNA polymerases to increase substrate tolerance for such heavily modified nucleotide analogs.
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Affiliation(s)
- Nazarii Sabat
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
| | | | | | - Marie Flamme
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
| | - Andreas Stämpfli
- Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | | | - Steven Hanlon
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Serena Bisagni
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Kurt Püntener
- Pharmaceutical Division, Synthetic Molecules Technical Development, Process Development and Catalysis, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Filippo Sladojevich
- Pharma Research and Early Development, Roche Innovation Center Basel, F Hoffmann-La Roche Ltd., Basel, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Université de Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, Paris, France
- *Correspondence: Marcel Hollenstein,
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