1
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Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [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: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
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Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
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2
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Van Deuren V, Plessers S, Lavigne R, Robben J. Application of Deep Sequencing in Phage Display. Methods Mol Biol 2024; 2738:333-345. [PMID: 37966608 DOI: 10.1007/978-1-0716-3549-0_20] [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] [Indexed: 11/16/2023]
Abstract
This chapter describes the workflow to implement deep sequencing into standard phage display experiments on protein libraries. By harvesting the power of high throughput of these techniques, it allows for comprehensive analysis of the naïve library and library evolution in response to selection by ligand binding. The mutagenized target region of the protein variants encoded by the phage pool is analyzed by Illumina paired-end sequencing. Sequence data are processed to extract selection-enriched amino acid motifs. In addition, a complementary long-read sequencing approach is proposed enabling the monitoring of display vector stability.
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Affiliation(s)
- Vincent Van Deuren
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Sander Plessers
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium
| | - Rob Lavigne
- Animal and Human Health Engineering (A2H), Leuven (Arenberg), KU Leuven, Leuven, Belgium
| | - Johan Robben
- Department of Biochemistry, Molecular and Structural Biology, KU Leuven, Leuven, Belgium.
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3
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Huber LB, Betz K, Marx A. Reverse Transcriptases: From Discovery and Applications to Xenobiology. Chembiochem 2023; 24:e202200521. [PMID: 36354312 DOI: 10.1002/cbic.202200521] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/09/2022] [Indexed: 11/12/2022]
Abstract
Reverse transcriptases are DNA polymerases that can use RNA as a template for DNA synthesis. They thus catalyze the reverse of transcription. Although discovered in 1970, reverse transcriptases are still of great interest and are constantly being further developed for numerous modern research approaches. They are frequently used in biotechnological and molecular diagnostic applications. In this review, we describe the discovery of these fascinating enzymes and summarize research results and applications ranging from molecular cloning, direct virus detection, and modern sequencing methods to xenobiology.
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Affiliation(s)
- Luisa B Huber
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78464, Konstanz, Germany
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4
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Aggarwal N, Liang Y, Foo JL, Ling H, Hwang IY, Chang MW. FELICX: A robust nucleic acid detection method using flap endonuclease and CRISPR-Cas12. Biosens Bioelectron 2023; 222:115002. [PMID: 36527830 DOI: 10.1016/j.bios.2022.115002] [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: 10/11/2022] [Revised: 11/26/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Nucleic acid detection is crucial for monitoring diseases for which rapid, sensitive, and easy-to-deploy diagnostic tools are needed. CRISPR-based technologies can potentially fulfill this need for nucleic acid detection. However, their widespread use has been restricted by the requirement of a protospacer adjacent motif in the target and extensive guide RNA optimization. In this study, we developed FELICX, a technique that can overcome these limitations and provide a useful alternative to existing technologies. FELICX comprises flap endonuclease, Taq ligase and CRISPR-Cas for diagnostics (X) and can be used for detecting nucleic acids and single-nucleotide polymorphisms. This method can be deployed as a point-of-care test, as only two temperatures are needed without thermocycling for its functionality, with the result generated on lateral flow strips. As a proof-of-concept, we showed that up to 0.6 copies/μL of DNA and RNA could be detected by FELICX in 60 min and 90 min, respectively, using simulated samples. Additionally, FELICX could be used to probe any base pair, unlike other CRISPR-based technologies. Finally, we demonstrated the versatility of FELICX by employing it for virus detection in infected human cells, the identification of antibiotic-resistant bacteria, and cancer diagnostics using simulated samples. Based on its unique advantages, we envision the use of FELICX as a next-generation CRISPR-based technology in nucleic acid diagnostics.
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Affiliation(s)
- Nikhil Aggarwal
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yuanmei Liang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jee Loon Foo
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - In Young Hwang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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5
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Graczyk A, Radzikowska-Cieciura E, Kaczmarek R, Pawlowska R, Chworos A. Modified Nucleotides for Chemical and Enzymatic Synthesis of Therapeutic RNA. Curr Med Chem 2023; 30:1320-1347. [PMID: 36239720 DOI: 10.2174/0929867330666221014111403] [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: 03/02/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022]
Abstract
In recent years, RNA has emerged as a medium with a broad spectrum of therapeutic potential, however, for years, a group of short RNA fragments was studied and considered therapeutic molecules. In nature, RNA plays both functions, with coding and non-coding potential. For RNA, like any other therapeutic, to be used clinically, certain barriers must be crossed. Among them, there are biocompatibility, relatively low toxicity, bioavailability, increased stability, target efficiency and low off-target effects. In the case of RNA, most of these obstacles can be overcome by incorporating modified nucleotides into its structure. This may be achieved by both, in vitro and in vivo biosynthetic methods, as well as chemical synthesis. Some advantages and disadvantages of each approach are summarized here. The wide range of nucleotide analogues has been tested for their utility as monomers for RNA synthesis. Many of them have been successfully implemented, and a lot of pre-clinical and clinical studies involving modified RNA have been carried out. Some of these medications have already been introduced into clinics. After the huge success of RNA-based vaccines that were introduced into widespread use in 2020, and the introduction to the market of some RNA-based drugs, RNA therapeutics containing modified nucleotides appear to be the future of medicine.
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Affiliation(s)
- Anna Graczyk
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Ewa Radzikowska-Cieciura
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Renata Kaczmarek
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Roza Pawlowska
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Arkadiusz Chworos
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
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6
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Sun L, Ma X, Zhang B, Qin Y, Ma J, Du Y, Chen T. From polymerase engineering to semi-synthetic life: artificial expansion of the central dogma. RSC Chem Biol 2022; 3:1173-1197. [PMID: 36320892 PMCID: PMC9533422 DOI: 10.1039/d2cb00116k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/08/2022] [Indexed: 11/21/2022] Open
Abstract
Nucleic acids have been extensively modified in different moieties to expand the scope of genetic materials in the past few decades. While the development of unnatural base pairs (UBPs) has expanded the genetic information capacity of nucleic acids, the production of synthetic alternatives of DNA and RNA has increased the types of genetic information carriers and introduced novel properties and functionalities into nucleic acids. Moreover, the efforts of tailoring DNA polymerases (DNAPs) and RNA polymerases (RNAPs) to be efficient unnatural nucleic acid polymerases have enabled broad application of these unnatural nucleic acids, ranging from production of stable aptamers to evolution of novel catalysts. The introduction of unnatural nucleic acids into living organisms has also started expanding the central dogma in vivo. In this article, we first summarize the development of unnatural nucleic acids with modifications or alterations in different moieties. The strategies for engineering DNAPs and RNAPs are then extensively reviewed, followed by summarization of predominant polymerase mutants with good activities for synthesizing, reverse transcribing, or even amplifying unnatural nucleic acids. Some recent application examples of unnatural nucleic acids with their polymerases are then introduced. At the end, the approaches of introducing UBPs and synthetic genetic polymers into living organisms for the creation of semi-synthetic organisms are reviewed and discussed.
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Affiliation(s)
- Leping Sun
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Binliang Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Jiezhao Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology 510006 Guangzhou China
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7
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Jácome R, Campillo-Balderas JA, Becerra A, Lazcano A. Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited. J Mol Evol 2022; 90:283-295. [PMID: 35639164 PMCID: PMC9153872 DOI: 10.1007/s00239-022-10059-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 05/11/2022] [Indexed: 12/24/2022]
Abstract
In the past few years, our understanding of the RNA virosphere has changed dramatically due to the growth and spurt of metagenomics, exponentially increasing the number of RNA viral sequences, and providing a better understanding of their range of potential hosts. As of today, the only conserved protein among RNA viruses appears to be the monomeric RNA-dependent RNA polymerase. This enzyme belongs to the right-hand DNA-and RNA polymerases, which also includes reverse transcriptases and eukaryotic replicative DNA polymerases. The ubiquity of this protein in RNA viruses makes it a unique evolutionary marker and an appealing broad-spectrum antiviral target. In this work pairwise structural comparisons of viral RdRps and RTs were performed, including tertiary structures that have been obtained in the last few years. The resulting phylogenetic tree shows that the RdRps from (+)ss- and dsRNA viruses might have been recruited several times throughout the evolution of mobile genetic elements. RTs also display multiple evolutionary routes. We have identified a structural core comprising the entire palm, a large moiety of the fingers and the N-terminal helices of the thumb domain, comprising over 300 conserved residues, including two regions that we have named the “knuckles” and the “hypothenar eminence”. The conservation of an helix bundle in the region preceding the polymerase domain confirms that (−)ss and dsRNA Reoviruses’ polymerases share a recent ancestor. Finally, the inclusion of DNA polymerases into our structural analyses suggests that monomeric RNA-dependent polymerases might have diverged from B-family polymerases.
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Affiliation(s)
- Rodrigo Jácome
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico
| | | | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico
| | - Antonio Lazcano
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico, Mexico.
- Miembro de El Colegio Nacional, Mexico, Mexico.
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8
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Xue Y, Braslavsky I, Quake SR. Temperature effect on polymerase fidelity. J Biol Chem 2021; 297:101270. [PMID: 34695416 PMCID: PMC8592868 DOI: 10.1016/j.jbc.2021.101270] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/24/2021] [Accepted: 09/29/2021] [Indexed: 11/21/2022] Open
Abstract
The discovery of extremophiles helped enable the development of groundbreaking technology such as PCR. Temperature variation is often an essential step of these technology platforms, but the effect of temperature on the error rate of polymerases from different origins is underexplored. Here, we applied high-throughput sequencing to profile the error rates of DNA polymerases from psychrophilic, mesophilic, and thermophilic origins with single-molecule resolution. We found that the reaction temperature substantially increases substitution and deletion error rates of psychrophilic and mesophilic DNA polymerases. Our motif analysis shows that the substitution error profiles cluster according to phylogenetic similarity of polymerases, not the reaction temperature, thus suggesting that the reaction temperature increases the global error rate of polymerases independent of the sequence context. Intriguingly, we also found that the DNA polymerase I of psychrophilic bacteria exhibits higher polymerization activity than its mesophilic ortholog across all temperature ranges, including down to -19 °C, which is well below the freezing temperature of water. Our results provide a useful reference for how the reaction temperature, a crucial parameter of biochemistry, can affect DNA polymerase fidelity in organisms adapted to a wide range of thermal environments.
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Affiliation(s)
- Yuan Xue
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Ido Braslavsky
- The Robert H. Smith Faculty of Agriculture, Food and Environment, Institute of Biochemistry, Food Science and Nutrition, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Applied Physics, Stanford University, Stanford, California, USA; Chan Zuckerberg Biohub, Mission Bay, California, USA.
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9
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Dutta K, Shityakov S, Khalifa I. New Trends in Bioremediation Technologies Toward Environment-Friendly Society: A Mini-Review. Front Bioeng Biotechnol 2021; 9:666858. [PMID: 34409018 PMCID: PMC8365754 DOI: 10.3389/fbioe.2021.666858] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/26/2021] [Indexed: 01/29/2023] Open
Abstract
Today's environmental balance has been compromised by the unreasonable and sometimes dangerous actions committed by humans to maintain their dominance over the Earth's natural resources. As a result, oceans are contaminated by the different types of plastic trash, crude oil coming from mismanagement of transporting ships spilling it in the water, and air pollution due to increasing production of greenhouse gases, such as CO2 and CH4 etc., into the atmosphere. The lands, agricultural fields, and groundwater are also contaminated by the infamous chemicals viz., polycyclic aromatic hydrocarbons, pyrethroids pesticides, bisphenol-A, and dioxanes. Therefore, bioremediation might function as a convenient alternative to restore a clean environment. However, at present, the majority of bioremediation reports are limited to the natural capabilities of microbial enzymes. Synthetic biology with uncompromised supervision of ethical standards could help to outsmart nature's engineering, such as the CETCH cycle for improved CO2 fixation. Additionally, a blend of synthetic biology with machine learning algorithms could expand the possibilities of bioengineering. This review summarized current state-of-the-art knowledge of the data-assisted enzyme redesigning to actively promote new research on important enzymes to ameliorate the environment.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Medinipur, India
| | - Sergey Shityakov
- Department of Chemoinformatics, Infochemistry Scientific Center, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Saint-Petersburg, Russia
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Benha University, Moshtohor, Egypt
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10
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Sung JY, Lee YJ, Cho YJ, Shin MN, Lee SJ, Lee HS, Koh H, Bae JW, Shin JH, Kim HJ, Lee DW. A large-scale metagenomic study for enzyme profiles using the focused identification of the NGS-based definitive enzyme research (FINDER) strategy. Biotechnol Bioeng 2021; 118:4360-4374. [PMID: 34309016 DOI: 10.1002/bit.27904] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 04/23/2021] [Accepted: 07/23/2021] [Indexed: 11/09/2022]
Abstract
Excavating the molecular details of many diverse enzymes from metagenomes remains challenging in agriculture, food, health, and environmental fields. We present a versatile method that accelerates metabolic enzyme discovery for highly selective gene capture in metagenomes using next-generation sequencing. Culture-independent enzyme mining of environmental DNA is based on a set of short identifying degenerate sequences specific for a wide range of enzyme superfamilies, followed by multiplexed DNA barcode sequencing. A strategy of 'focused identification of next-generation sequencing-based definitive enzyme research' enabled us to generate targeted enzyme datasets from metagenomes, resulting in minimal hands-on obtention of high-throughput biological diversity and potential function profiles, without being time-consuming. This method also provided a targeted inventory of predicted proteins and molecular features of metabolic activities from several metagenomic samples. We suggest that the efficiency and sensitivity of this method will accelerate the decryption of microbial diversity and the signature of proteins and their metabolism from environmental samples.
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Affiliation(s)
- Jae-Yoon Sung
- Department of Biotechnology, Yonsei University, Seoul, South Korea
| | - Yong-Jik Lee
- Department of Bio-Cosmetics, Seowon University, Chung-Ju, South Korea
| | - Yong-Joon Cho
- Department of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Myeong-Na Shin
- Department of Central Area Crop Science, NICS, RDA, Suwon, South Korea
| | - Sang-Jae Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Han-Seung Lee
- Major in Food Biotechnology, Silla University, Busan, South Korea
| | - Hong Koh
- Department of Pediatrics, Yonsei University, Seoul, South Korea
| | - Jin-Woo Bae
- Department of Biology, Kyung Hee University, Seoul, South Korea
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, South Korea
| | - Hyun Jung Kim
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas, USA
| | - Dong-Woo Lee
- Department of Biotechnology, Yonsei University, Seoul, South Korea
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11
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Lindenburg L, Hollfelder F. “NAD‐display”: Ultrahigh‐Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
- Current address: Genmab Uppsalalaan 15 3584 CT Utrecht The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry University of Cambridge Tennis Court Road Cambridge CB2 1GA UK
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12
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Lindenburg L, Hollfelder F. "NAD-display": Ultrahigh-Throughput in Vitro Screening of NAD(H) Dehydrogenases Using Bead Display and Flow Cytometry. Angew Chem Int Ed Engl 2021; 60:9015-9021. [PMID: 33470025 PMCID: PMC8048591 DOI: 10.1002/anie.202013486] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Indexed: 12/25/2022]
Abstract
NAD(H)‐utiliing enzymes have been the subject of directed evolution campaigns to improve their function. To enable access to a larger swath of sequence space, we demonstrate the utility of a cell‐free, ultrahigh‐throughput directed evolution platform for dehydrogenases. Microbeads (1.5 million per sample) carrying both variant DNA and an immobilised analogue of NAD+ were compartmentalised in water‐in‐oil emulsion droplets, together with cell‐free expression mixture and enzyme substrate, resulting in the recording of the phenotype on each bead. The beads’ phenotype could be read out and sorted for on a flow cytometer by using a highly sensitive fluorescent protein‐based sensor of the NAD+:NADH ratio. Integration of this “NAD‐display” approach with our previously described Split & Mix (SpliMLiB) method for generating large site‐saturation libraries allowed straightforward screening of fully balanced site saturation libraries of formate dehydrogenase, with diversities of 2×104. Based on modular design principles of synthetic biology NAD‐display offers access to sophisticated in vitro selections, avoiding complex technology platforms.
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Affiliation(s)
- Laurens Lindenburg
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK.,Current address: Genmab, Uppsalalaan 15, 3584 CT, Utrecht, The Netherlands
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
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13
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Dong H, Zhang W, Zhou S, Huang J, Wang P. Engineering bioscaffolds for enzyme assembly. Biotechnol Adv 2021; 53:107721. [PMID: 33631185 DOI: 10.1016/j.biotechadv.2021.107721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 02/04/2021] [Accepted: 02/14/2021] [Indexed: 12/27/2022]
Abstract
With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Wenxue Zhang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Shengmin Zhou
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Jiaofang Huang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Ping Wang
- Department of Bioproducts and Biosystems Engineering, University of Minnesota, St Paul, MN 55108, USA.
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14
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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15
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Duffy K, Arangundy-Franklin S, Holliger P. Modified nucleic acids: replication, evolution, and next-generation therapeutics. BMC Biol 2020; 18:112. [PMID: 32878624 PMCID: PMC7469316 DOI: 10.1186/s12915-020-00803-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.
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Affiliation(s)
- Karen Duffy
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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16
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Chung ME, Goroncy K, Kolesnikova A, Schönauer D, Schwaneberg U. Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution. Biotechnol Bioeng 2020; 117:3699-3711. [PMID: 32827316 DOI: 10.1002/bit.27542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 12/29/2022]
Abstract
We report a first of its kind functional cell surface display of nucleic acid polymerase and its directed evolution to efficiently incorporate 2'-O-methyl nucleotide triphosphates (2'-OMe-NTPs). In the development of polymerase cell surface display, two autotransporter proteins (Escherichia coli adhesin involved in diffuse adherence and Pseudomonas aeruginosa esterase A [EstA]) were employed to transport and anchor the 68-kDa Klenow fragment (KF) of E. coli DNA polymerase I on the surface of E. coli. The localization and function of the displayed KF were verified by analysis of cell outer membrane fractions, immunostaining, and fluorometric detection of synthesized DNA products. The EstA cell surface display system was applied to evolve KF for the incorporation of 2'-OMe-NTPs and a KF variant with a 50.7-fold increased ability to successively incorporate 2'-OMe-NTPs was discovered. Expanding the scope of cell-surface displayable proteins to the realm of polymerases provides a novel screening tool for tailoring polymerases to diverse application demands in a polymerase chain reaction and sequencing-based biotechnological and medical applications. Especially, cell surface display enables novel polymerase screening strategies in which the heat-lysis step is bypassed and thus allows the screening of mesophilic polymerases with broad application potentials ranging from diagnostics and DNA sequencing to replication of synthetic genetic polymers.
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Affiliation(s)
- Mu-En Chung
- SeSaM-Biotech GmbH, Aachen, Germany.,Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | | | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials, Aachen, Germany
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17
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Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
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18
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Kimoto M, Hirao I. New Research Area, Xenobiology, by Integrating Chemistry and Biology. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR
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19
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Zhukov SA, Fokina AA, Stetsenko DA, Vasilyeva SV. Methods for Molecular Evolution of Polymerases. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2019. [DOI: 10.1134/s1068162019060426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Nikoomanzar A, Vallejo D, Chaput JC. Elucidating the Determinants of Polymerase Specificity by Microfluidic-Based Deep Mutational Scanning. ACS Synth Biol 2019; 8:1421-1429. [PMID: 31081325 DOI: 10.1021/acssynbio.9b00104] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Engineering polymerases to synthesize artificial genetic polymers with unique backbone structures is limited by a general lack of understanding about the structural determinants that govern substrate specificity. Here, we report a high-throughput microfluidic-based approach for mapping sequence-function relationships that combines droplet-based optical polymerase sorting with deep mutational scanning. We applied this strategy to map the finger subdomain of a replicative DNA polymerase isolated from Thermococcus kodakarensis (Kod). The enrichment profile provides an unbiased view of the ability of each mutant to synthesize threose nucleic acid, which was used as a model non-natural genetic polymer. From a single round of sorting, we discovered two cases of positive epistasis and demonstrate the near inversion of substrate specificity from a double mutant variant. This effort indicates that polymerase specificity may be governed by a small number of highly specific residues that can be elucidated by deep mutational scanning without the need for iterative rounds of directed evolution.
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Affiliation(s)
- Ali Nikoomanzar
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - Derek Vallejo
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
| | - John C Chaput
- Departments of Pharmaceutical Sciences, Chemistry, and Molecular Biology and Biochemistry , University of California , Irvine , California 92697-3958 , United States
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21
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Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
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Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
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22
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Palikša S, Alzbutas G, Skirgaila R. Decreased Km to dNTPs is an essential M-MuLV reverse transcriptase adoption required to perform efficient cDNA synthesis in One-Step RT-PCR assay. Protein Eng Des Sel 2019; 31:79-89. [PMID: 29608777 DOI: 10.1093/protein/gzy003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 02/05/2018] [Indexed: 01/27/2023] Open
Abstract
Personalized medicine and advanced diagnostic tools based on RNA analysis are focusing on fast and direct One-Step RT-PCR assays. First strand complementary DNA (cDNA) synthesized by the reverse transcriptase (RT) is exponentially amplified in the end-point or real-time PCR. Even a minor discrepancy in PCR conditions would result in big deviations during the data analysis. Thus, One-Step RT-PCR composition is typically based on the PCR buffer. In this study, we have used compartmentalized ribosome display technique for in vitro evolution of the Moloney Murine Leukemia Virus reverse transcriptase (M-MuLV RT) that would be able to perform efficient full-length cDNA synthesis in PCR buffer optimized for Thermus aquaticus DNA polymerase. The most frequent mutations found in a selected library were analyzed. Aside from the mutations, which switch off RNase H activity of RT and are beneficial for the full-length cDNA synthesis, we have identified several mutations in the active center of the enzyme (Q221R and V223A/M), which result in 4-5-fold decrease of Km for dNTPs (<0.2 mM). The selected mutations are in surprising agreement with the natural evolution process because they transformed the active center from the oncoretroviral M-MuLV RT-type to the lenitiviral enzyme-type. We believe that this was the major and essential phenotypic adjustment required to perform fast and efficient cDNA synthesis in PCR buffer at 0.2-mM concentration of each dNTP.
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Affiliation(s)
- S Palikša
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania.,JSC Diagnolita, LT-10257 Vilnius, Lithuania
| | - G Alzbutas
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania
| | - R Skirgaila
- Thermo Fisher Scientific Baltics, UAB, LT-02241 Vilnius, Lithuania
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23
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Engineering-driven biological insights into DNA polymerase mechanism. Curr Opin Biotechnol 2018; 60:9-16. [PMID: 30502514 DOI: 10.1016/j.copbio.2018.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/11/2022]
Abstract
DNA-dependent DNA polymerases have been extensively studied for over 60 years and lie at the core of multiple biotechnological and diagnostic applications. Nevertheless, these complex molecular machines remain only partially understood. Here we present some evidence on how polymerase engineering for the synthesis and replication of xenobiotic nucleic acids (XNAs) have improved our understanding of these enzymes and how that can be used to gain further insight into their mechanism. Better understanding of the mechanisms of DNA polymerases can accelerate their engineering and we highlight how it is now feasible to use structure-based and function-based approaches to systematically and iteratively develop XNA polymerases for increasingly divergent chemistries.
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24
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Abil Z, Ellington AD. Compartmentalized Self-Replication for Evolution of a DNA Polymerase. ACTA ACUST UNITED AC 2018; 10:1-17. [DOI: 10.1002/cpch.34] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Zhanar Abil
- Center for Systems and Synthetic Biology University of Texas at Austin; Austin Texas
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology University of Texas at Austin; Austin Texas
- Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin; Austin Texas
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25
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Agudo R, Calvo PA, Martínez-Jiménez MI, Blanco L. Engineering human PrimPol into an efficient RNA-dependent-DNA primase/polymerase. Nucleic Acids Res 2017; 45:9046-9058. [PMID: 28911121 PMCID: PMC5587808 DOI: 10.1093/nar/gkx633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 07/12/2017] [Indexed: 02/01/2023] Open
Abstract
We have developed a straightforward fluorometric assay to measure primase-polymerase activity of human PrimPol (HsPrimPol). The sensitivity of this procedure uncovered a novel RNA-dependent DNA priming-polymerization activity (RdDP) of this enzyme. In an attempt to enhance HsPrimPol RdDP activity, we constructed a smart mutant library guided by prior sequence-function analysis, and tested this library in an adapted screening platform of our fluorometric assay. After screening less than 500 variants, we found a specific HsPrimPol mutant, Y89R, which displays 10-fold higher RdDP activity than the wild-type enzyme. The improvement of RdDP activity in the Y89R variant was due mainly to an increased in the stabilization of the preternary complex (protein:template:incoming nucleotide), a specific step preceding dimer formation. Finally, in support of the biotechnological potential of PrimPol as a DNA primer maker during reverse transcription, mutant Y89R HsPrimPol rendered up to 17-fold more DNA than with random hexamer primers.
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Affiliation(s)
- Rubén Agudo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
| | - Patricia A. Calvo
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
| | | | - Luis Blanco
- Centro de Biología Molecular ‘Severo Ochoa’ (CSIC-UAM), Cantoblanco, E-28049 Madrid, Spain
- To whom correspondence should be addressed. Tel: +34 91 196 46 85; Fax: +34 91 196 44 20; . Correspondence may also be addressed to Rubén Agudo. Tel: +34 91 196 46 86; Fax: +34 91 196 44 20;
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26
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Lewis EL, Leconte AM. DNA Polymerase Activity Assay Using Near-infrared Fluorescent Labeled DNA Visualized by Acrylamide Gel Electrophoresis. J Vis Exp 2017. [PMID: 29053685 DOI: 10.3791/56228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
For any enzyme, robust, quantitative methods are required for characterization of both native and engineered enzymes. For DNA polymerases, DNA synthesis can be characterized using an in vitro DNA synthesis assay followed by polyacrylamide gel electrophoresis. The goal of this assay is to quantify synthesis of both natural DNA and modified DNA (M-DNA). These approaches are particularly useful for resolving oligonucleotides with single nucleotide resolution, enabling observation of individual steps during enzymatic oligonucleotide synthesis. These methods have been applied to the evaluation of an array of biochemical and biophysical properties such as the measurement of steady-state rate constants of individual steps of DNA synthesis, the error rate of DNA synthesis, and DNA binding affinity. By using modified components including, but not limited to, modified nucleoside triphosphates (NTP), M-DNA, and/or mutant DNA polymerases, the relative utility of substrate-DNA polymerase pairs can be effectively evaluated. Here, we detail the assay itself, including the changes that must be made to accommodate nontraditional primer DNA labeling strategies such as near-infrared fluorescently labeled DNA. Additionally, we have detailed crucial technical steps for acrylamide gel pouring and running, which can often be technically challenging.
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Affiliation(s)
- Eliza L Lewis
- Department of Chemistry, W.M. Keck Science Department of Claremont Mckenna, Pitzer, and Scripps College
| | - Aaron M Leconte
- Department of Chemistry, W.M. Keck Science Department of Claremont Mckenna, Pitzer, and Scripps College;
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27
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Wu WJ, Yang W, Tsai MD. How DNA polymerases catalyse replication and repair with contrasting fidelity. Nat Rev Chem 2017. [DOI: 10.1038/s41570-017-0068] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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28
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Abstract
Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code.
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29
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Levin M, Udi Y, Solomonov I, Sagi I. Next generation matrix metalloproteinase inhibitors - Novel strategies bring new prospects. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017. [PMID: 28636874 DOI: 10.1016/j.bbamcr.2017.06.009] [Citation(s) in RCA: 120] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymatic proteolysis of cell surface proteins and extracellular matrix (ECM) is critical for tissue homeostasis and cell signaling. These proteolytic activities are mediated predominantly by a family of proteases termed matrix metalloproteinases (MMPs). The growing evidence in recent years that ECM and non-ECM bioactive molecules (e.g., growth factors, cytokines, chemokines, on top of matrikines and matricryptins) have versatile functions redefines our view on the roles matrix remodeling enzymes play in many physiological and pathological processes, and underscores the notion that ECM proteolytic reaction mechanisms represent master switches in the regulation of critical biological processes and govern cell behavior. Accordingly, MMPs are not only responsible for direct degradation of ECM molecules but are also key modulators of cardinal bioactive factors. Many attempts were made to manipulate ECM degradation by targeting MMPs using small peptidic and organic inhibitors. However, due to the high structural homology shared by these enzymes, the majority of the developed compounds are broad-spectrum inhibitors affecting the proteolytic activity of various MMPs and other zinc-related proteases. These inhibitors, in many cases, failed as therapeutic agents, mainly due to the bilateral role of MMPs in pathological conditions such as cancer, in which MMPs have both pro- and anti-tumorigenic effects. Despite the important role of MMPs in many human diseases, none of the broad-range synthetic MMP inhibitors that were designed have successfully passed clinical trials. It appears that, designing highly selective MMP inhibitors that are also effective in vivo, is not trivial. The challenges related to designing selective and effective metalloprotease inhibitors, are associated in part with the aforesaid high structural homology and the dynamic nature of their protein scaffolds. Great progress was achieved in the last decade in understanding the biochemistry and biology of MMPs activity. This knowledge, combined with lessons from the past has drawn new "boundaries" for the development of the next-generation MMP inhibitors. These novel agents are currently designed to be highly specific, capable to discriminate between the homologous MMPs and ideally administered as a short-term topical treatment. In this review we discuss the latest progress in the fields of MMP inhibitors in terms of structure, function and their specific activity. The development of novel highly specific inhibitors targeting MMPs paves the path to study complex biological processes associated with ECM proteolysis in health and disease. This article is part of a Special Issue entitled: Matrix Metalloproteinases edited by Rafael Fridman.
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Affiliation(s)
- Maxim Levin
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yael Udi
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10065, USA
| | - Inna Solomonov
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Irit Sagi
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel.
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30
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Houlihan G, Arangundy-Franklin S, Holliger P. Engineering and application of polymerases for synthetic genetics. Curr Opin Biotechnol 2017; 48:168-179. [PMID: 28601700 DOI: 10.1016/j.copbio.2017.04.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 11/26/2022]
Abstract
Organic chemistry has systematically probed the chemical determinants of function in nucleic acids by variation to the nucleobase, sugar ring and backbone moieties to build synthetic genetic polymers. Concomitantly, protein engineering has advanced to allow the discovery of polymerases capable of utilizing modified nucleotide analogs. A conjunction of these two lines of investigation in nucleotide chemistry and molecular biology has given rise to a new field of synthetic genetics dedicated to the exploration of the capacity of these novel, synthetic nucleic acids for the storage and propagation of genetic information, for evolution and for crosstalk, that is, information exchange with the natural genetic system. Here we summarize recent progress in synthetic genetics, specifically in the design of novel unnatural basepairs to expand the genetic alphabet as well as progress in engineering polymerases capable of templated synthesis, reverse transcription and evolution of synthetic genetic polymers.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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31
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Aioub AG, Dahora L, Gamble K, Finn MG. Selection of Natural Peptide Ligands for Copper-Catalyzed Azide–Alkyne Cycloaddition Catalysis. Bioconjug Chem 2017; 28:1693-1701. [DOI: 10.1021/acs.bioconjchem.7b00161] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Allison G. Aioub
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Lindsay Dahora
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - Kelly Gamble
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
| | - M. G. Finn
- School
of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332, United States
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32
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Rosenblum SL, Weiden AG, Lewis EL, Ogonowsky AL, Chia HE, Barrett SE, Liu MD, Leconte AM. Design and Discovery of New Combinations of Mutant DNA Polymerases and Modified DNA Substrates. Chembiochem 2017; 18:816-823. [PMID: 28160372 DOI: 10.1002/cbic.201600701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/06/2022]
Abstract
Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more-diverse physical structures. However, native DNA polymerases generally cannot synthesize significant lengths of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2'-modified DNAs; however, it is limited in the length of the products it can synthesize. Here, we rationally designed and characterized ten mutants of SFM19. From this, we identified enzymes with substantially improved activity for the synthesis of 2'F-, 2'OH-, 2'OMe-, and 3'OMe-modified DNA as well as for reverse transcription of 2'OMe DNA. We also evaluated mutant DNA polymerases previously only tested for synthesis for 2'OMe DNA and showed that they are capable of an expanded range of modified DNA synthesis. This work significantly expands the known combinations of modified DNA and Taq DNA polymerase mutants.
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Affiliation(s)
- Sydney L Rosenblum
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aurora G Weiden
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Eliza L Lewis
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Alexie L Ogonowsky
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Hannah E Chia
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Susanna E Barrett
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Mira D Liu
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aaron M Leconte
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
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33
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Dellafiore MA, Montserrat JM, Iribarren AM. Modified Nucleoside Triphosphates for In-vitro Selection Techniques. Front Chem 2016; 4:18. [PMID: 27200340 PMCID: PMC4854868 DOI: 10.3389/fchem.2016.00018] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 04/05/2016] [Indexed: 12/22/2022] Open
Abstract
The development of SELEX (Selective Enhancement of Ligands by Exponential Enrichment) provides a powerful tool for the search of functional oligonucleotides with the ability to bind ligands with high affinity and selectivity (aptamers) and for the discovery of nucleic acid sequences with diverse enzymatic activities (ribozymes and DNAzymes). This technique has been extensively applied to the selection of natural DNA or RNA molecules but, in order to improve chemical and structural diversity as well as for particular applications where further chemical or biological stability is necessary, the extension of this strategy to modified oligonucleotides is desirable. Taking into account these needs, this review intends to collect the research carried out during the past years, focusing mainly on the use of modified nucleotides in SELEX and the development of mutant enzymes for broadening nucleoside triphosphates acceptance. In addition, comments regarding the synthesis of modified nucleoside triphosphate will be briefly discussed.
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Affiliation(s)
- María A Dellafiore
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET) Ciudad Autónoma de Buenos Aires, Argentina
| | - Javier M Montserrat
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Instituto de Ciencias, Universidad Nacional de General SarmientoLos Polvorines, Argentina
| | - Adolfo M Iribarren
- Laboratorio de Química de Ácidos Nucleicos, INGEBI (CONICET)Ciudad Autónoma de Buenos Aires, Argentina; Laboratorio de Biotransformaciones, Universidad Nacional de QuilmesBernal, Argentina
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Chen T, Hongdilokkul N, Liu Z, Adhikary R, Tsuen SS, Romesberg FE. Evolution of thermophilic DNA polymerases for the recognition and amplification of C2'-modified DNA. Nat Chem 2016; 8:556-62. [PMID: 27219699 PMCID: PMC4880425 DOI: 10.1038/nchem.2493] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
The PCR amplification of oligonucleotides enables the evolution of sequences called aptamers that bind specific targets with antibody-like affinity. However, the use of these aptamers is limited in many applications by nuclease-mediated degradation. In contrast, oligonucleotides that are modified at their sugar C2' positions with methoxy or fluorine substituents are stable to nucleases but cannot be synthesized by natural polymerases. Here, we report the development of a polymerase evolution system and its use to evolve thermostable polymerases that efficiently interconvert C2'-OMe modified oligonucleotides and their DNA counterparts via “transcription” and “reverse transcription,” or more importantly, PCR amplify partially C2'-OMe or C2'-F modified oligonucleotides. A mechanistic analysis demonstrates that the ability to amplify the modified oligonucleotides was evolved by optimizing interdomain interactions that stabilize the catalytically competent closed conformation of the polymerase. The evolved polymerases should find practical applications and the developed evolution system should be a powerful tool for the tailoring of polymerases to have other types of novel function.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Narupat Hongdilokkul
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Zhixia Liu
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Shujian S Tsuen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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35
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Schultz HJ, Gochi AM, Chia HE, Ogonowsky AL, Chiang S, Filipovic N, Weiden AG, Hadley EE, Gabriel SE, Leconte AM. Taq DNA Polymerase Mutants and 2'-Modified Sugar Recognition. Biochemistry 2015; 54:5999-6008. [PMID: 26334839 DOI: 10.1021/acs.biochem.5b00689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical modifications to DNA, such as 2' modifications, are expected to increase the biotechnological utility of DNA; however, these modified forms of DNA are limited by their inability to be effectively synthesized by DNA polymerase enzymes. Previous efforts have identified mutant Thermus aquaticus DNA polymerase I (Taq) enzymes capable of recognizing 2'-modified DNA nucleotides. While these mutant enzymes recognize these modified nucleotides, they are not capable of synthesizing full length modified DNA; thus, further engineering is required for these enzymes. Here, we describe comparative biochemical studies that identify useful, but previously uncharacterized, properties of these enzymes; one enzyme, SFM19, is able to recognize a range of 2'-modified nucleotides much wider than that previously examined, including fluoro, azido, and amino modifications. To understand the molecular origins of these differences, we also identify specific amino acids and combinations of amino acids that contribute most to the previously evolved unnatural activity. Our data suggest that a negatively charged amino acid at 614 and mutation of the steric gate residue, E615, to glycine make up the optimal combination for modified oligonucleotide synthesis. These studies yield an improved understanding of the mutational origins of 2'-modified substrate recognition as well as identify SFM19 as the best candidate for further engineering, whether via rational design or directed evolution.
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Affiliation(s)
- Hayley J Schultz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Andrea M Gochi
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Hannah E Chia
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Alexie L Ogonowsky
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Sharon Chiang
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Nedim Filipovic
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Aurora G Weiden
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Emma E Hadley
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Sara E Gabriel
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Aaron M Leconte
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
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36
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Delespaul W, Peeters Y, Herdewijn P, Robben J. A novel helper phage for HaloTag-mediated co-display of enzyme and substrate on phage. Biochem Biophys Res Commun 2015; 460:245-9. [PMID: 25772618 DOI: 10.1016/j.bbrc.2015.03.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 03/04/2015] [Indexed: 10/23/2022]
Abstract
Phage display is an established technique for the molecular evolution of peptides and proteins. For the selection of enzymes based on catalytic activity however, simultaneous coupling of an enzyme and its substrate to the phage surface is required. To facilitate this process of co-display, we developed a new helper phage displaying HaloTag, a modified haloalkane dehalogenase that binds specifically and covalently to functionalized haloalkane ligands. The display of functional HaloTag was demonstrated by capture on streptavidin-coated magnetic beads, after coupling a biotinylated haloalkane ligand, or after on-phage extension of a DNA oligonucleotide primer with a biotinylated nucleotide by phi29 DNA polymerase. We also achieved co-display of HaloTag and phi29 DNA polymerase, thereby opening perspectives for the molecular evolution of this enzyme (and others) towards new substrate specificities.
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Affiliation(s)
- Wouter Delespaul
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium.
| | - Yves Peeters
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium.
| | - Piet Herdewijn
- Rega Institute for Medicinal Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium.
| | - Johan Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001 Heverlee, Belgium.
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37
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Laos R, Thomson JM, Benner SA. DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides. Front Microbiol 2014; 5:565. [PMID: 25400626 PMCID: PMC4215692 DOI: 10.3389/fmicb.2014.00565] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 10/07/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. The focus of this review is on non-standard nucleotides that expand the genetic "alphabet." This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution.
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
| | | | - Steven A Benner
- Foundation for Applied Molecular Evolution Gainesville, FL, USA
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38
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Chen T, Romesberg FE. Directed polymerase evolution. FEBS Lett 2013; 588:219-29. [PMID: 24211837 DOI: 10.1016/j.febslet.2013.10.040] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 12/23/2022]
Abstract
Polymerases evolved in nature to synthesize DNA and RNA, and they underlie the storage and flow of genetic information in all cells. The availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. To circumvent these limitations, researchers have turned to directed evolution to tailor the properties and/or substrate repertoire of polymerases for different applications, and several systems have been developed for this purpose. These systems draw on different methods of creating a pool of randomly mutated polymerases and are differentiated by the process used to isolate the most fit members. A variety of polymerases have been evolved, providing new or improved functionality, as well as interesting new insight into the factors governing activity.
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Affiliation(s)
- Tingjian Chen
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States
| | - Floyd E Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, United States.
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39
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Blatter N, Bergen K, Nolte O, Welte W, Diederichs K, Mayer J, Wieland M, Marx A. Structure and function of an RNA-reading thermostable DNA polymerase. Angew Chem Int Ed Engl 2013; 52:11935-9. [PMID: 24106012 DOI: 10.1002/anie.201306655] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 08/16/2013] [Indexed: 12/30/2022]
Affiliation(s)
- Nina Blatter
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz (Germany)
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40
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Blatter N, Bergen K, Nolte O, Welte W, Diederichs K, Mayer J, Wieland M, Marx A. Struktur und Funktion einer RNA-lesenden thermostabilen DNA-Polymerase. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306655] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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41
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Uzawa T, Tada S, Wang W, Ito Y. Expansion of the aptamer library from a "natural soup" to an "unnatural soup". Chem Commun (Camb) 2013; 49:1786-95. [PMID: 23283144 DOI: 10.1039/c2cc36348h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The possibility of evolving a commonly existing biomolecule into a variety of functional biomolecules has now been realized in the form of aptamers through the development of in vitro selection. In addition to their high affinity and high specificity for the desired targets, aptamers are easily synthesized chemically and can be modified for downstream applications. Although aptamers were originally selected from a library containing only natural components, the past decade has seen a wealth of new aptamers selected from libraries containing unnatural components to provide new aptamer functions artificially. In this review, we highlight this transition (the shift between selection from natural components and selection from unnatural components) and the applications of selected aptamers.
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Affiliation(s)
- Takanori Uzawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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42
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Bazan J, Całkosiński I, Gamian A. Phage display--a powerful technique for immunotherapy: 2. Vaccine delivery. Hum Vaccin Immunother 2012; 8:1829-35. [PMID: 22906938 DOI: 10.4161/hv.21704] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phage display is a powerful technique in medical and health biotechnology. This technology has led to formation of antibody libraries and has provided techniques for fast and efficient search of these libraries. The phage display technique has been used in studying the protein-protein or protein-ligand interactions, constructing of the antibody and antibody fragments and improving the affinity of proteins to receptors. Recently phage display has been widely used to study immunization process, develop novel vaccines and investigate allergen-antibody interactions. This technology can provide new tools for protection against viral, fungal and bacterial infections. It may become a valuable tool in cancer therapies, abuse and allergies treatment. This review presents the recent advancements in diagnostic and therapeutic applications of phage display. In particular the applicability of this technology to study the immunization process, construction of new vaccines and development of safer and more efficient delivery strategies has been described.
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Affiliation(s)
- Justyna Bazan
- Department of Medical Biochemistry; Wroclaw Medical University; Wroclaw, Poland
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43
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Pinheiro VB, Holliger P. The XNA world: progress towards replication and evolution of synthetic genetic polymers. Curr Opin Chem Biol 2012; 16:245-52. [PMID: 22704981 DOI: 10.1016/j.cbpa.2012.05.198] [Citation(s) in RCA: 144] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/16/2012] [Accepted: 05/21/2012] [Indexed: 01/25/2023]
Abstract
Life's diversity is built on the wide range of properties and functions that can be encoded in natural biopolymers such as polypeptides and nucleic acids. However, despite their versatility, the range of chemical functionalities is limited, particularly in the case of nucleic acids. Chemical modification of nucleic acids can greatly increase their functional diversity but access to the full phenotypic potential of such polymers requires a system of replication. Here we review progress in the chemical and enzymatic synthesis, replication and evolution of unnatural nucleic acid polymers, which promises to enable the exploration of a vast sequence space not accessible to nature and deliver ligands, catalysts and materials based on this new class of biopolymers.
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Affiliation(s)
- Vitor B Pinheiro
- Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 0QH, UK
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44
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Baranauskas A, Paliksa S, Alzbutas G, Vaitkevicius M, Lubiene J, Letukiene V, Burinskas S, Sasnauskas G, Skirgaila R. Generation and characterization of new highly thermostable and processive M-MuLV reverse transcriptase variants. Protein Eng Des Sel 2012; 25:657-68. [PMID: 22691702 DOI: 10.1093/protein/gzs034] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In vitro synthesis of cDNA is one of the most important techniques in present molecular biology. Faithful synthesis of long cDNA on highly structured RNA templates requires thermostable and processive reverse transcriptases. In a recent attempt to increase the thermostability of the wt Moloney Murine leukemia virus reverse transcriptase (M-MuLV RT), we have employed the compartmentalized ribosome display (CRD) evolution in vitro technique and identified a large set of previously unknown mutations that enabled cDNA synthesis at elevated temperatures. In this study, we have characterized a group of the M-MuLV RT variants (28 novel amino acid positions, 84 point mutants) carrying the individual mutations. The performance of point mutants (thermal inactivation rate, substrate-binding affinity and processivity) correlated remarkably well with the mutation selection frequency in the CRD experiment. By combining the best-performing mutations D200N, L603W, T330P, L139P and E607K, we have generated highly processive and thermostable multiply-mutated M-MuLV RT variants. The processivity of the best-performing multiple mutant increased to 1500 nt (65-fold improvement in comparison to the wt enzyme), and the maximum temperature of the full-length 7.5-kb cDNA synthesis was raised to 62°C (17° higher in comparison with the wt enzyme).
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45
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Abstract
DNA polymerase substrate specificity is fundamental to genome integrity and to polymerase applications in biotechnology. In the current paradigm, active site geometry is the main site of specificity control. Here, we describe the discovery of a distinct specificity checkpoint located over 25 Å from the active site in the polymerase thumb subdomain. In Tgo, the replicative DNA polymerase from Thermococcus gorgonarius, we identify a single mutation (E664K) within this region that enables translesion synthesis across a template abasic site or a cyclobutane thymidine dimer. In conjunction with a classic "steric-gate" mutation (Y409G) in the active site, E664K transforms Tgo DNA polymerase into an RNA polymerase capable of synthesizing RNAs up to 1.7 kb long as well as fully pseudouridine-, 5-methyl-C-, 2'-fluoro-, or 2'-azido-modified RNAs primed from a wide range of primer chemistries comprising DNA, RNA, locked nucleic acid (LNA), or 2'O-methyl-DNA. We find that E664K enables RNA synthesis by selectively increasing polymerase affinity for the noncognate RNA/DNA duplex as well as lowering the K(m) for ribonucleotide triphosphate incorporation. This gatekeeper mutation therefore identifies a key missing step in the adaptive path from DNA to RNA polymerases and defines a previously unknown postsynthetic determinant of polymerase substrate specificity with implications for the synthesis and replication of noncognate nucleic acid polymers.
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46
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Vaisman A, Kuban W, McDonald JP, Karata K, Yang W, Goodman MF, Woodgate R. Critical amino acids in Escherichia coli UmuC responsible for sugar discrimination and base-substitution fidelity. Nucleic Acids Res 2012; 40:6144-57. [PMID: 22422840 PMCID: PMC3401427 DOI: 10.1093/nar/gks233] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The active form of Escherichia coli DNA polymerase V responsible for damage-induced mutagenesis is a multiprotein complex (UmuD′2C-RecA-ATP), called pol V Mut. Optimal activity of pol V Mut in vitro is observed on an SSB-coated single-stranded circular DNA template in the presence of the β/γ complex and a transactivated RecA nucleoprotein filament, RecA*. Remarkably, under these conditions, wild-type pol V Mut efficiently incorporates ribonucleotides into DNA. A Y11A substitution in the ‘steric gate’ of UmuC further reduces pol V sugar selectivity and converts pol V Mut into a primer-dependent RNA polymerase that is capable of synthesizing long RNAs with a processivity comparable to that of DNA synthesis. Despite such properties, Y11A only promotes low levels of spontaneous mutagenesis in vivo. While the Y11F substitution has a minimal effect on sugar selectivity, it results in an increase in spontaneous mutagenesis. In comparison, an F10L substitution increases sugar selectivity and the overall fidelity of pol V Mut. Molecular modeling analysis reveals that the branched side-chain of L10 impinges on the benzene ring of Y11 so as to constrict its movement and as a consequence, firmly closes the steric gate, which in wild-type enzyme fails to guard against ribonucleoside triphosphates incorporation with sufficient stringency.
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Affiliation(s)
- Alexandra Vaisman
- Laboratory of Genomic Integrity, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892-3371, USA
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47
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Hirao I, Kimoto M. Unnatural base pair systems toward the expansion of the genetic alphabet in the central dogma. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2012; 88:345-67. [PMID: 22850726 PMCID: PMC3422687 DOI: 10.2183/pjab.88.345] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 06/01/2012] [Indexed: 05/30/2023]
Abstract
Toward the expansion of the genetic alphabet of DNA, several artificial third base pairs (unnatural base pairs) have been created. Synthetic DNAs containing the unnatural base pairs can be amplified faithfully by PCR, along with the natural A-T and G-C pairs, and transcribed into RNA. The unnatural base pair systems now have high potential to open the door to next generation biotechnology. The creation of unnatural base pairs is a consequence of repeating "proof of concept" experiments. In the process, initially designed base pairs were modified to address their weak points. Some of them were artificially evolved to ones with higher efficiency and selectivity in polymerase reactions, while others were eliminated from the analysis. Here, we describe the process of unnatural base pair development, as well as the tests of their applications.
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Affiliation(s)
- Ichiro Hirao
- RIKEN Systems and Structural Biology Center (SSBC), Yokohama, Japan.
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48
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Affiliation(s)
- Ramon Kranaster
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
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49
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Abstract
To maintain genomic stability, ribonucleotide incorporation during DNA synthesis is controlled predominantly at the DNA polymerase level. A steric clash between the 2'-hydroxyl of an incoming ribonucleotide and a bulky active site residue, known as the "steric gate", establishes an effective mechanism for most DNA polymerases to selectively insert deoxyribonucleotides. Recent kinetic, structural, and in vivo studies have illuminated novel features about ribonucleotide exclusion and the mechanistic consequences of ribonucleotide misincorporation on downstream events, such as the bypass of a ribonucleotide in a DNA template and the subsequent extension of the DNA lesion bypass product. These important findings are summarized in this review.
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Affiliation(s)
- Jessica A Brown
- Department of Biochemistry, Ohio State University, Columbus, Ohio 43210, United States
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50
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Staiger N, Marx A. A DNA polymerase with increased reactivity for ribonucleotides and C5-modified deoxyribonucleotides. Chembiochem 2011; 11:1963-6. [PMID: 20734370 DOI: 10.1002/cbic.201000384] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Nadine Staiger
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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