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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Sett A, Gadewar M, Babu MA, Panja A, Sachdeva P, Almutary AG, Upadhye V, Jha SK, Jha NK. Orchestration and theranostic applications of synthetic genome with Hachimoji bases/building blocks. Chem Biol Drug Des 2024; 103:e14378. [PMID: 38230795 DOI: 10.1111/cbdd.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 01/18/2024]
Abstract
Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its in vitro and in vivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology.
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Affiliation(s)
- Arghya Sett
- ERIN Department, Luxembourg Institute of Science and Technology, 5 Av. des Hauts-Fourneaux, Belval, 4362, Esch, Luxembourg
| | - Manoj Gadewar
- Department of Pharmacology, School of Medical and Allied Sciences, K R Mangalam University, Gurgaon, India
| | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA University, Mathura, India
| | | | | | - Abdulmajeed G Almutary
- Department of Biomedical Sciences, College of Health Sciences, Abu Dhabi University, Abu Dhabi, United Arab Emirates
| | - Vijay Upadhye
- Centre of Research for Development (CR4D) and Department of Microbiology, Parul University, Vadodara, Gujarat, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering and Technology, Sharda University, Greater Noida, India
| | - Niraj Kumar Jha
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
- Centre of Research Impact and Outreach, Chitkara University Institute of Engineering and Technology, Chitkara University, Punjab, India
- School of Bioengineering & Biosciences, Lovely Professional University, Phagwara, 144411, India
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Mohali, 140413, India
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3
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Qin Y, Ma X, Tao R, Du Y, Chen T. Synthesis, Reverse Transcription, Replication, and Inter-Transcription of 2'-Modified Nucleic Acids with Evolved Thermophilic Polymerases: Efforts toward Multidimensional Expansion of the Central Dogma. ACS Synth Biol 2023; 12:2616-2631. [PMID: 37646406 DOI: 10.1021/acssynbio.3c00213] [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: 09/01/2023]
Abstract
In the past decades, various xenobiotic nucleic acids (XNAs), including 2'-modified nucleic acids, have been developed as novel genetic materials and demonstrated great potential in synthetic biology and biotechnology. Enzymatic polymerization and replication of these artificial polymers are obviously the prerequisite to make full use of them, and DNA and RNA polymerases from different families have thus been extensively engineered for these purposes. However, the performance of engineered XNA polymerases is still far from satisfactory, especially in terms of the efficiency of synthesizing XNA with bigger lengths and the capability of directly replicating XNAs or transcribing one XNA to another. In this work, we tailored a mutant of Stoffel fragment of Taq DNA polymerase, SFM4-3, by engineering a key residue pair on the surfaces of fingers and thumb domains, and successfully obtained mutants with significantly enhanced efficiency for the synthesis of fully 2'-OMe-modified DNA with bigger lengths. Remarkably, we also found that these polymerase mutants are capable of synthesizing, reverse transcribing, and even replicating RNA and different fully 2'-modified XNAs, as well as transcribing one of these nucleic acids to another, with varied efficiencies. The application of these activities for producing DNA strands end-protected by XNA duplexes was then demonstrated. These results clearly suggest that the genetic information can be stored in and transmitted among DNA, RNA, and different 2'-modified XNAs with the assistance of polymerase mutants, and the central dogma of life can be expanded to higher dimensions via the development of XNAs together with engineering their polymerases.
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Affiliation(s)
- Yanjia Qin
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Xingyun Ma
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Rui Tao
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Yuhui Du
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Tingjian Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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4
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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5
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Wang G, Du Y, Ma X, Ye F, Qin Y, Wang Y, Xiang Y, Tao R, Chen T. Thermophilic Nucleic Acid Polymerases and Their Application in Xenobiology. Int J Mol Sci 2022; 23:ijms232314969. [PMID: 36499296 PMCID: PMC9738464 DOI: 10.3390/ijms232314969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/22/2022] [Accepted: 11/27/2022] [Indexed: 12/02/2022] Open
Abstract
Thermophilic nucleic acid polymerases, isolated from organisms that thrive in extremely hot environments, possess great DNA/RNA synthesis activities under high temperatures. These enzymes play indispensable roles in central life activities involved in DNA replication and repair, as well as RNA transcription, and have already been widely used in bioengineering, biotechnology, and biomedicine. Xeno nucleic acids (XNAs), which are analogs of DNA/RNA with unnatural moieties, have been developed as new carriers of genetic information in the past decades, which contributed to the fast development of a field called xenobiology. The broad application of these XNA molecules in the production of novel drugs, materials, and catalysts greatly relies on the capability of enzymatic synthesis, reverse transcription, and amplification of them, which have been partially achieved with natural or artificially tailored thermophilic nucleic acid polymerases. In this review, we first systematically summarize representative thermophilic and hyperthermophilic polymerases that have been extensively studied and utilized, followed by the introduction of methods and approaches in the engineering of these polymerases for the efficient synthesis, reverse transcription, and amplification of XNAs. The application of XNAs facilitated by these polymerases and their mutants is then discussed. In the end, a perspective for the future direction of further development and application of unnatural nucleic acid polymerases is provided.
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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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Molecular and thermodynamic mechanisms for protein adaptation. EUROPEAN BIOPHYSICS JOURNAL 2022; 51:519-534. [DOI: 10.1007/s00249-022-01618-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022]
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8
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Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
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Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
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9
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Laos R, Benner S. Fluorinated oil-surfactant mixtures with the density of water: Artificial cells for synthetic biology. PLoS One 2022; 17:e0252361. [PMID: 35051170 PMCID: PMC8775225 DOI: 10.1371/journal.pone.0252361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 12/20/2021] [Indexed: 11/20/2022] Open
Abstract
There is a rising interest in biotechnology for the compartmentalization of biochemical reactions in water droplets. Several applications, such as the widely used digital PCR, seek to encapsulate a single molecule in a droplet to be amplified. Directed evolution, another technology with growing popularity, seeks to replicate what happens in nature by encapsulating a single gene and the protein encoded by this gene, linking genotype with phenotype. Compartmentalizing reactions in droplets also allows the experimentalist to run millions of different reactions in parallel. Compartmentalization requires a fluid that is immiscible with water and a surfactant to stabilize the droplets. While there are fluids and surfactants on the market that have been used to accomplish encapsulation, there are reported concerns with these. Span® 80, for example, a commonly used surfactant, has contaminants that interfere with various biochemical reactions. Similarly, synthetic fluids distributed by the cosmetic industry allow some researchers to produce experimental results that can be published, but then other researchers fail to reproduce some of these protocols due to the unreliable nature of these products, which are not manufactured with the intent of being used in biotechnology. The most reliable fluids, immiscible with water and suitable for biochemical reactions, are fluorinated fluids. Fluorinated compounds have the peculiar characteristic of being immiscible with water while at the same time not mixing with hydrophobic molecules. This peculiar characteristic has made fluorinated fluids attractive because it seems to be the basis of their being biologically inert. However, commercially available fluorinated fluids have densities between 1.4 to 1.6 g/mL. The higher-than-water density of fluorinated oils complicates handling of the droplets since these would float on the fluid since the water droplets would be less dense. This can cause aggregation and coalescence of the droplets. Here, we report the synthesis, characterization, and use of fluorinated polysiloxane oils that have densities similar to the one of water at room temperature, and when mixed with non-ionic fluorinated surfactants, can produce droplets encapsulating biochemical reactions. We show how droplets in these emulsions can host many biological processes, including PCR, DNA origami, rolling circle amplification (RCA), and Taqman® assays. Some of these use unnatural DNA built from an Artificially Expanded Genetic Information System (AEGIS) with six nucleotide "letters".
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Affiliation(s)
- Roberto Laos
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
- Panamerican Biolabs LLC, Gainesville, Florida, United States of America
| | - Steven Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, United States of America
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10
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Wu S, Liu X, Ye S, Liu J, Zheng W, Dong X, Yin X. Colorimetric isothermal nucleic acid detection of SARS-CoV-2 with dye combination. Heliyon 2021; 7:e06886. [PMID: 33903853 PMCID: PMC8059943 DOI: 10.1016/j.heliyon.2021.e06886] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/19/2021] [Accepted: 04/19/2021] [Indexed: 12/21/2022] Open
Abstract
RT-LAMP detection of SARS-CoV-2 has been demonstrated to be a valuable diagnostic method for the diagnosis of COVID-191,2, which can rapidly screen carriers of the virus to effectively control the spread of the SARS-CoV-2. Here, we present a combination of dyes for isothermal detection of SARS-CoV-2 as a commercial alternative, with expanded colorimetric spectrum. We compared them with commercial reagents and proved their suitability and sensitivity through clinical RNA samples. In addition, together with commercial single dye indicators, we believe the expanded color spectrum developed here as an indicator of rapid detection will promote the diagnosis of COVID-19.
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Affiliation(s)
- Shanshan Wu
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, 110142, Shenyang, China
| | - Xiyang Liu
- Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Shenglong Ye
- Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
| | - Jianmin Liu
- Shenyang Center for Disease Control and Prevention, 110031, Shenyang, Liaoning, China
| | - Wei Zheng
- Liaoning Cancer Hospital and Institute, No. 44 Xiaoheyan Rd, Dadong District, ShenYang, 110042 China
| | - Xue Dong
- Shenyang Center for Disease Control and Prevention, 110031, Shenyang, Liaoning, China
- Corresponding author.
| | - Xiushan Yin
- Applied Biology Laboratory, College of Pharmaceutical and Biological Engineering, Shenyang University of Chemical Technology, 110142, Shenyang, China
- Biotech & Biomedicine Science (Shenyang) Co. Ltd, Shenyang, 110000, China
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology. Karolinska Institutet, Solna 17165, Sweden
- Pluri Biotech Co.Ltd, Xuzhou, 221001, China
- Nanog Biotech Co.Ltd, Shanghai, 200000, China
- Biotech & Biomedicine Science (Jiangxi) Co. Ltd, Ganzhou, 341000, China
- Department of Respiratory and Critical Care Medicine, Central Hospital Affiliated to Shenyang Medical College, Shenyang 110024, People's Republic of China
- Corresponding author.
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11
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Siau JW, Nonis S, Chee S, Koh LQ, Ferrer FJ, Brown CJ, Ghadessy FJ. Directed co-evolution of interacting protein-peptide pairs by compartmentalized two-hybrid replication (C2HR). Nucleic Acids Res 2021; 48:e128. [PMID: 33104786 PMCID: PMC7736784 DOI: 10.1093/nar/gkaa933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 10/02/2020] [Accepted: 10/07/2020] [Indexed: 12/21/2022] Open
Abstract
Directed evolution methodologies benefit from read-outs quantitatively linking genotype to phenotype. We therefore devised a method that couples protein–peptide interactions to the dynamic read-out provided by an engineered DNA polymerase. Fusion of a processivity clamp protein to a thermostable nucleic acid polymerase enables polymerase activity and DNA amplification in otherwise prohibitive high-salt buffers. Here, we recapitulate this phenotype by indirectly coupling the Sso7d processivity clamp to Taq DNA polymerase via respective fusion to a high affinity and thermostable interacting protein–peptide pair. Escherichia coli cells co-expressing protein–peptide pairs can directly be used in polymerase chain reactions to determine relative interaction strengths by the measurement of amplicon yields. Conditional polymerase activity is further used to link genotype to phenotype of interacting protein–peptide pairs co-expressed in E. coli using the compartmentalized self-replication directed evolution platform. We validate this approach, termed compartmentalized two-hybrid replication, by selecting for high-affinity peptides that bind two model protein partners: SpyCatcher and the large fragment of NanoLuc luciferase. We further demonstrate directed co-evolution by randomizing both protein and peptide components of the SpyCatcher–SpyTag pair and co-selecting for functionally interacting variants.
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Affiliation(s)
- Jia Wei Siau
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Samuel Nonis
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Sharon Chee
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Li Quan Koh
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Fernando J Ferrer
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Christopher J Brown
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
| | - Farid J Ghadessy
- p53 Laboratory, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, 138648, Singapore
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12
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Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ. Building better polymerases: Engineering the replication of expanded genetic alphabets. J Biol Chem 2020; 295:17046-17059. [PMID: 33004440 PMCID: PMC7863901 DOI: 10.1074/jbc.rev120.013745] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 09/30/2020] [Indexed: 11/30/2022] Open
Abstract
DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the "performance specifications" needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.
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Affiliation(s)
- Zahra Ouaray
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Alachua, Florida, USA
| | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA.
| | - Nigel G J Richards
- School of Chemistry, Cardiff University, Park Place, Cardiff, United Kingdom; Foundation for Applied Molecular Evolution, Alachua, Florida, USA.
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13
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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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14
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Nie P, Bai Y, Mei H. Synthetic Life with Alternative Nucleic Acids as Genetic Materials. Molecules 2020; 25:molecules25153483. [PMID: 32751873 PMCID: PMC7435384 DOI: 10.3390/molecules25153483] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 12/20/2022] Open
Abstract
DNA, the fundamental genetic polymer of all living organisms on Earth, can be chemically modified to embrace novel functions that do not exist in nature. The key chemical and structural parameters for genetic information storage, heredity, and evolution have been elucidated, and many xenobiotic nucleic acids (XNAs) with non-canonical structures are developed as alternative genetic materials in vitro. However, it is still particularly challenging to replace DNAs with XNAs in living cells. This review outlines some recent studies in which the storage and propagation of genetic information are achieved in vivo by expanding genetic systems with XNAs.
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15
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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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16
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Markel U, Essani KD, Besirlioglu V, Schiffels J, Streit WR, Schwaneberg U. Advances in ultrahigh-throughput screening for directed enzyme evolution. Chem Soc Rev 2020; 49:233-262. [PMID: 31815263 DOI: 10.1039/c8cs00981c] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Enzymes are versatile catalysts and their synthetic potential has been recognized for a long time. In order to exploit their full potential, enzymes often need to be re-engineered or optimized for a given application. (Semi-) rational design has emerged as a powerful means to engineer proteins, but requires detailed knowledge about structure function relationships. In turn, directed evolution methodologies, which consist of iterative rounds of diversity generation and screening, can improve an enzyme's properties with virtually no structural knowledge. Current diversity generation methods grant us access to a vast sequence space (libraries of >1012 enzyme variants) that may hide yet unexplored catalytic activities and selectivity. However, the time investment for conventional agar plate or microtiter plate-based screening assays represents a major bottleneck in directed evolution and limits the improvements that are obtainable in reasonable time. Ultrahigh-throughput screening (uHTS) methods dramatically increase the number of screening events per time, which is crucial to speed up biocatalyst design, and to widen our knowledge about sequence function relationships. In this review, we summarize recent advances in uHTS for directed enzyme evolution. We shed light on the importance of compartmentalization to preserve the essential link between genotype and phenotype and discuss how cells and biomimetic compartments can be applied to serve this function. Finally, we discuss how uHTS can inspire novel functional metagenomics approaches to identify natural biocatalysts for novel chemical transformations.
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Affiliation(s)
- Ulrich Markel
- Institute of Biotechnology, RWTH Aachen University, Worringer Weg 3, 52074 Aachen, Germany.
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17
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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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18
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Santín O, Galié S, Moncalián G. Directed evolution of a bacterial WS/DGAT acyltransferase: improving tDGAT from Thermomonospora curvata. Protein Eng Des Sel 2019; 32:25-32. [PMID: 31251342 DOI: 10.1093/protein/gzz011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 05/08/2019] [Accepted: 06/04/2019] [Indexed: 11/12/2022] Open
Abstract
Some bacteria belonging to the actinobacteria and proteobacteria groups can accumulate neutral lipids expressing enzymes of the wax ester synthase/acyl coenzyme A: diacylglycerol acyltransferase (WS/DGAT) family. tDGAT is a WS/DGAT-like enzyme from Thermomonospora curvata able to produce TAGs and WEs when heterologously expressed in Escherichia coli. In this study, a protocol for the directed evolution of bacterial lipid-producing enzymes based on fluorimetry is developed and tested. tDGAT has been successfully evolved towards the improvement of TAG production with an up to 2.5 times increase in TAG accumulation. Mutants with no ability to produce TAGs but able to accumulate waxes were also selected during the screening. The localization of the mutations that enhance TAG production in the outer surface of tDGAT points out possible new mechanisms that contribute to the activity of this family of enzymes. This Nile red-based high throughput screening provides an evolution platform for other WS/DGAT-like enzymes.
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Affiliation(s)
- Omar Santín
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - Serena Galié
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
| | - Gabriel Moncalián
- Departamento de Biología Molecular, Universidad de Cantabria and Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), CSIC-Universidad de Cantabria, Santander, Spain
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19
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Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM. Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. Nucleic Acids Res 2019; 46:7977-7988. [PMID: 29986111 PMCID: PMC6125688 DOI: 10.1093/nar/gky552] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/15/2018] [Indexed: 01/20/2023] Open
Abstract
The next challenge in synthetic biology is to be able to replicate synthetic nucleic acid sequences efficiently. The synthetic pair, 2-amino-8-(1-beta-d-2′- deoxyribofuranosyl) imidazo [1,2-a]-1,3,5-triazin-[8H]-4-one (trivially designated P) with 6-amino-3-(2′-deoxyribofuranosyl)-5-nitro-1H-pyridin-2-one (trivially designated Z), is replicated by certain Family A polymerases, albeit with lower efficiency. Through directed evolution, we identified a variant KlenTaq polymerase (M444V, P527A, D551E, E832V) that incorporates dZTP opposite P more efficiently than the wild-type enzyme. Here, we report two crystal structures of this variant KlenTaq, a post-incorporation complex that includes a template-primer with P:Z trapped in the active site (binary complex) and a pre-incorporation complex with dZTP paired to template P in the active site (ternary complex). In forming the ternary complex, the fingers domain exhibits a larger closure angle than in natural complexes but engages the template-primer and incoming dNTP through similar interactions. In the binary complex, although many of the interactions found in the natural complexes are retained, there is increased relative motion of the thumb domain. Collectively, our analyses suggest that it is the post-incorporation complex for unnatural substrates that presents a challenge to the natural enzyme and that more efficient replication of P:Z pairs requires a more flexible polymerase.
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Affiliation(s)
- Isha Singh
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Roberto Laos
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA
| | - Millie M Georgiadis
- Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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20
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Arangundy-Franklin S, Taylor AI, Porebski BT, Genna V, Peak-Chew S, Vaisman A, Woodgate R, Orozco M, Holliger P. A synthetic genetic polymer with an uncharged backbone chemistry based on alkyl phosphonate nucleic acids. Nat Chem 2019; 11:533-542. [PMID: 31011171 DOI: 10.1038/s41557-019-0255-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 03/15/2019] [Indexed: 12/24/2022]
Abstract
The physicochemical properties of nucleic acids are dominated by their highly charged phosphodiester backbone chemistry. This polyelectrolyte structure decouples information content (base sequence) from bulk properties, such as solubility, and has been proposed as a defining trait of all informational polymers. However, this conjecture has not been tested experimentally. Here, we describe the encoded synthesis of a genetic polymer with an uncharged backbone chemistry: alkyl phosphonate nucleic acids (phNAs) in which the canonical, negatively charged phosphodiester is replaced by an uncharged P-alkyl phosphonodiester backbone. Using synthetic chemistry and polymerase engineering, we describe the enzymatic, DNA-templated synthesis of P-methyl and P-ethyl phNAs, and the directed evolution of specific streptavidin-binding phNA aptamer ligands directly from random-sequence mixed P-methyl/P-ethyl phNA repertoires. Our results establish an example of the DNA-templated enzymatic synthesis and evolution of an uncharged genetic polymer and provide a foundational methodology for their exploration as a source of novel functional molecules.
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Affiliation(s)
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Benjamin T Porebski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vito Genna
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Sew Peak-Chew
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexandra Vaisman
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Roger Woodgate
- Section on DNA Replication, Repair and Mutagenesis, Bethesda, MD, USA
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Biochemistry and Biomedicine, University of Barcelona, Barcelona, Spain
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK.
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21
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Huy Le B, Nguyen VT, Seo YJ. Site-specific incorporation of multiple units of functional nucleotides into DNA using a step-wise approach with polymerase and its application to monitoring DNA structural changes. Chem Commun (Camb) 2019; 55:2158-2161. [PMID: 30675606 DOI: 10.1039/c8cc09444f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have developed a new method, a step-wise approach with polymerase, for site-specific incorporation of multiple units of functional nucleotides into DNA to form hairpin secondary structures. The fluorescence of the resulting DNA incorporating the functional nucleotides varied upon transitioning from single-strand to hairpin and duplex structures.
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Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, South Korea
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22
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Abstract
Measuring biological data across time and space is critical for understanding complex biological processes and for various biosurveillance applications. However, such data are often inaccessible or difficult to directly obtain. Less invasive, more robust and higher-throughput biological recording tools are needed to profile cells and their environments. DNA-based cellular recording is an emerging and powerful framework for tracking intracellular and extracellular biological events over time across living cells and populations. Here, we review and assess DNA recorders that utilize CRISPR nucleases, integrases and base-editing strategies, as well as recombinase and polymerase-based methods. Quantitative characterization, modelling and evaluation of these DNA-recording modalities can guide their design and implementation for specific application areas.
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Affiliation(s)
- Ravi U Sheth
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Integrated Program in Cellular, Molecular and Biomedical Studies, Columbia University, New York, NY, USA
| | - Harris H Wang
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA.
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23
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Affiliation(s)
- Vito Genna
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Elisa Donati
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy
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24
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Torres LL, Pinheiro VB. Xenobiotic Nucleic Acid (XNA) Synthesis by Phi29 DNA Polymerase. ACTA ACUST UNITED AC 2018; 10:e41. [PMID: 29927114 DOI: 10.1002/cpch.41] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phi29 DNA polymerase (DNAP) is the replicative enzyme of the Bacillus subtilis bacteriophage Phi29. Its extraordinary processivity and its ability to perform isothermal amplification of DNA are central to many molecular biology applications, including high-sensitivity detection and large-scale production of DNA. We present here Phi29 DNAP as an efficient catalyst for the production of various artificial nucleic acids (XNAs) carrying backbone modifications such as 1,5-anhydrohexitol nucleic acid (HNA), 2'-deoxy-2'-fluoro-arabinonucleic acid (FANA), and 2'-fluoro-2'-deoxyribonucleic acid (2'-fluoro-DNA). A full protocol for the synthesis of HNA polymers by an exonuclease-deficient variant (D12A) of Phi29 DNAP plus a detailed guide for the design and test of novel XNA synthetase reactions performed by Phi29 DNAP are provided. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Leticia L Torres
- Department of Structural and Molecular Biology, University College London, London, United Kingdom
| | - Vitor B Pinheiro
- Department of Structural and Molecular Biology, University College London, London, United Kingdom.,Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, United Kingdom
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25
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Milligan JN, Shroff R, Garry DJ, Ellington AD. Evolution of a Thermophilic Strand-Displacing Polymerase Using High-Temperature Isothermal Compartmentalized Self-Replication. Biochemistry 2018; 57:4607-4619. [PMID: 29629759 DOI: 10.1021/acs.biochem.8b00200] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Strand-displacing polymerases are a crucial component of isothermal amplification (IA) reactions, where the lack of thermal cycling reduces equipment needs and improves the time to answer, especially for point-of-care applications. In order to improve the function of strand-displacing polymerases, we have developed an emulsion-based directed evolution scheme, high-temperature isothermal compartmentalized self-replication (HTI-CSR) that does not rely on thermal cycling. Starting from an algorithm-optimized shuffled library of exonuclease-deficient Family A polymerases from Geobacillus stearothermophilus (Bst LF) and Thermus aquaticus (Klentaq), we have applied HTI-CSR to generate a more thermostable strand-displacing polymerase variant that performs well in loop-mediated isothermal amplification and rolling circle amplification, even after thermal challenges of up to 95 °C that lead to better primer annealing. The new enzyme (v5.9) is also capable of a variety of new reactions, including isothermal hyperbranched rolling circle amplification. The HTI-CSR method should now prove useful for evolving additional beneficial phenotypes in strand-displacing polymerases.
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Affiliation(s)
- John N Milligan
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Raghav Shroff
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Daniel J Garry
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
| | - Andrew D Ellington
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Department of Molecular Biosciences , University of Texas , 2500 Speedway , Austin , Texas 78712 , United States
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26
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Röthlisberger P, Gasse C, Hollenstein M. Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery. Int J Mol Sci 2017; 18:E2430. [PMID: 29144411 PMCID: PMC5713398 DOI: 10.3390/ijms18112430] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/25/2022] Open
Abstract
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.
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Affiliation(s)
- Pascal Röthlisberger
- 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.
| | - Cécile Gasse
- Institute of Systems & Synthetic Biology, Xenome Team, 5 rue Henri Desbruères Genopole Campus 1, University of Evry, F-91030 Evry, 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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27
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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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28
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Variants of sequence family B Thermococcus kodakaraensis DNA polymerase with increased mismatch extension selectivity. PLoS One 2017; 12:e0183623. [PMID: 28832623 PMCID: PMC5568139 DOI: 10.1371/journal.pone.0183623] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/08/2017] [Indexed: 12/01/2022] Open
Abstract
Fidelity and selectivity of DNA polymerases are critical determinants for the biology of life, as well as important tools for biotechnological applications. DNA polymerases catalyze the formation of DNA strands by adding deoxynucleotides to a primer, which is complementarily bound to a template. To ensure the integrity of the genome, DNA polymerases select the correct nucleotide and further extend the nascent DNA strand. Thus, DNA polymerase fidelity is pivotal for ensuring that cells can replicate their genome with minimal error. DNA polymerases are, however, further optimized for more specific biotechnological or diagnostic applications. Here we report on the semi-rational design of mutant libraries derived by saturation mutagenesis at single sites of a 3’-5’-exonuclease deficient variant of Thermococcus kodakaraensis DNA polymerase (KOD pol) and the discovery for variants with enhanced mismatch extension selectivity by screening. Sites of potential interest for saturation mutagenesis were selected by their proximity to primer or template strands. The resulting libraries were screened via quantitative real-time PCR. We identified three variants with single amino acid exchanges—R501C, R606Q, and R606W—which exhibited increased mismatch extension selectivity. These variants were further characterized towards their potential in mismatch discrimination. Additionally, the identified enzymes were also able to differentiate between cytosine and 5-methylcytosine. Our results demonstrate the potential in characterizing and developing DNA polymerases for specific PCR based applications in DNA biotechnology and diagnostics.
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29
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Eremeeva E, Abramov M, Margamuljana L, Herdewijn P. Base-Modified Nucleic Acids as a Powerful Tool for Synthetic Biology and Biotechnology. Chemistry 2017; 23:9560-9576. [PMID: 28513881 DOI: 10.1002/chem.201700679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 11/10/2022]
Abstract
The ability of various nucleoside triphosphate analogues of deoxyguanosine and deoxycytidine with 7-deazadeoxyadenosine (A1 ) and 5-chlorodeoxyuridine (T1 ) to serve as substrates for Taq DNA polymerase was evaluated. The triphosphate set composed of A1 , T1 , and 7-deazadeoxyguanosine with either 5-methyldeoxycytidine or 5-fluorodeoxycytidine was successfully employed in the polymerase chain reaction (PCR) of 1.5 kb fragments as well as random oligonucleotide libraries. Another effective combination of triphosphates for the synthesis of a 1 kb PCR product was A1 , T1 , deoxyinosine, and 5-bromodeoxycytidine. In vivo experiments using an antibiotic-resistant gene containing the latter set demonstrated that the bacterial machinery accepts fully modified sequences as genetic templates. Moreover, the ability of the base-modified segments to selectively protect DNA from cleavage by restriction endonucleases was shown. This approach can be used to regulate the endonuclease cleavage pattern.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Michail Abramov
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Lia Margamuljana
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49 box 1041, 3000, Leuven, Belgium.,Université d'évry, CNRS-UMR8030/ Laboratoire iSSB, CEA, DRF, IG, Genoscope, Université Paris-Saclay, évry, 91000, Paris, France
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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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Houlihan G, Arangundy-Franklin S, Holliger P. Exploring the Chemistry of Genetic Information Storage and Propagation through Polymerase Engineering. Acc Chem Res 2017; 50:1079-1087. [PMID: 28383245 PMCID: PMC5406124 DOI: 10.1021/acs.accounts.7b00056] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Nucleic
acids are a distinct form of sequence-defined biopolymer.
What sets them apart from other biopolymers such as polypeptides or
polysaccharides is their unique capacity to encode, store, and propagate
genetic information (molecular heredity). In nature, just two closely
related nucleic acids, DNA and RNA, function as repositories and carriers
of genetic information. They therefore are the molecular embodiment
of biological information. This naturally leads to questions regarding
the degree of variation from this seemingly ideal “Goldilocks”
chemistry that would still be compatible with the fundamental property
of molecular heredity. To address this question, chemists have
created a panoply of synthetic
nucleic acids comprising unnatural sugar ring congeners, backbone
linkages, and nucleobases in order to establish the molecular parameters
for encoding genetic information and its emergence at the origin of
life. A deeper analysis of the potential of these synthetic genetic
polymers for molecular heredity requires a means of replication and
a determination of the fidelity of information transfer. While non-enzymatic
synthesis is an increasingly powerful method, it currently remains
restricted to short polymers. Here we discuss efforts toward establishing
enzymatic synthesis, replication, and evolution of synthetic genetic
polymers through the engineering of polymerase enzymes found in nature. To endow natural polymerases with the ability to efficiently utilize
non-cognate nucleotide substrates, novel strategies for the screening
and directed evolution of polymerase function have been realized.
High throughput plate-based screens, phage display, and water-in-oil
emulsion technology based methods have yielded a number of engineered
polymerases, some of which can synthesize and reverse transcribe synthetic
genetic polymers with good efficiency and fidelity. The inception
of such polymerases demonstrates that, at a basic
level at least, molecular heredity is not restricted to the natural
nucleic acids DNA and RNA, but may be found in a large (if finite)
number of synthetic genetic polymers. And it has opened up these novel
sequence spaces for investigation. Although largely unexplored, first
tentative forays have yielded ligands (aptamers) against a range of
targets and several catalysts elaborated in a range of different chemistries.
Finally, taking the lead from established DNA designs, simple polyhedron
nanostructures have been described. We anticipate that further
progress in this area will expand the
range of synthetic genetic polymers that can be synthesized, replicated,
and evolved providing access to a rich sequence, structure, and phenotypic
space. “Synthetic genetics”, that is, the exploration
of these spaces, will illuminate the chemical parameter range for
en- and decoding information, 3D folding, and catalysis and yield
novel ligands, catalysts, and nanostructures and devices for applications
in biotechnology and medicine.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick
Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, U.K
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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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Povilaitis T, Alzbutas G, Sukackaite R, Siurkus J, Skirgaila R. In vitroevolution of phi29 DNA polymerase using isothermal compartmentalized self replication technique. Protein Eng Des Sel 2016; 29:617-628. [DOI: 10.1093/protein/gzw052] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/18/2016] [Accepted: 09/05/2016] [Indexed: 02/06/2023] Open
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Kaltenbach M, Emond S, Hollfelder F, Tokuriki N. Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity. PLoS Genet 2016; 12:e1006305. [PMID: 27716796 PMCID: PMC5065130 DOI: 10.1371/journal.pgen.1006305] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/17/2016] [Indexed: 11/19/2022] Open
Abstract
The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution. Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new, promiscuous activity is often accompanied by only a mild reduction of the native, original activity. A model that associates weak trade-offs with “evolvability” was put forward, which proposed that enzymes possess mutational robustness in the native activity and plasticity in promiscuous activities. This would enable the acquisition of a new function without compromising the original one, reducing the benefit of early gene duplication and therefore the selection pressure thereon. Yet, to date, no experimental study has examined this hypothesis directly. Here, we investigate the causes of weak trade-offs by systematically characterizing adaptive mutations that occurred in two cases of evolutionary transitions in enzyme function: (1) from phosphotriesterase to arylesterase, and (2) from atrazine chlorohydrolase to melamine deaminase. Mutational analyses in various genetic backgrounds revealed that, in contrast to the prevailing model, the native activity is less robust to mutations than the promiscuous activity. For example, in phosphotriesterase, the deleterious effect of individual mutations on the native phosphotriesterase activity is much larger than their positive effect on the promiscuous arylesterase activity. Our observations suggest a revision of the established model: weak trade-offs are not caused by an intrinsic robustness of the native activity and plasticity of the promiscuous activity. We propose that upon strong adaptive pressure for the new activity without selection against the original one, selected mutations will lead to the largest possible increases in the new function, but whether and to what extent they decrease the old function is irrelevant, creating a bias towards initially weak trade-offs and the emergence of generalist enzymes. Understanding how enzymes evolve is a fundamental question that can help us decipher not only the mechanisms of evolution on a higher level, i.e., whole organisms, but also advances our knowledge of sequence-structure-function relationships as a guide to artificial evolution in the test tube. An important yet unexplained phenomenon occurs during the evolution of a new enzymatic function; it has been observed that new and ancestral functions often trade-off only weakly, meaning the original native activity is initially maintained at a high level despite drastic improvement of the new promiscuous activity. It has previously been proposed that weak trade-offs occur because the native activity is robust to mutations while the promiscuous activity is not. However, the present work contradicts this hypothesis, based on the detailed characterization of mutational effects on both activities in two examples of enzyme evolution. We propose an alternative explanation: the weak activity trade-off is consistent with being a by-product of strong selection for the new activity rather than an intrinsic property of the native activity.
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Affiliation(s)
- Miriam Kaltenbach
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
| | - Stephane Emond
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories, University of British Columbia, Vancouver, Canada
- * E-mail:
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016; 55:7515-9. [PMID: 27159019 DOI: 10.1002/anie.201601529] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 01/04/2023]
Abstract
The ability of alternative nucleic acids, in which all four nucleobases are substituted, to replicate in vitro and to serve as genetic templates in vivo was evaluated. A nucleotide triphosphate set of 5-chloro-2'-deoxyuridine, 7-deaza-2'-deoxyadenosine, 5-fluoro-2'-deoxycytidine, and 7-deaza-2'deoxyguanosine successfully underwent polymerase chain reaction (PCR) amplification using templates of different lengths (57 or 525mer) and Taq or Vent (exo-) DNA polymerases as catalysts. Furthermore, a fully morphed gene encoding a dihydrofolate reductase was generated by PCR using these fully substituted nucleotides and was shown to transform and confer trimethoprim resistance to E. coli. These results demonstrated that fully modified templates were accurately read by the bacterial replication machinery and provide the first example of a long fully modified DNA molecule being functional in vivo.
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Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium
| | - Valerie Pezo
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Philippe Marlière
- ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega, Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000, Leuven, Belgium. .,ISSB, Génopole, Genavenir 6, Equipe Xénome, 5 rue Henri Desbruères, 91030, Evry Cedex, France.
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Eremeeva E, Abramov M, Margamuljana L, Rozenski J, Pezo V, Marlière P, Herdewijn P. Chemical Morphing of DNA Containing Four Noncanonical Bases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601529] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Elena Eremeeva
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Michail Abramov
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Lia Margamuljana
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Jef Rozenski
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
| | - Valerie Pezo
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Philippe Marlière
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
| | - Piet Herdewijn
- Laboratory of Medicinal Chemistry, Rega; Institute for Medical Research; KU Leuven; Minderbroedersstraat 10 3000 Leuven Belgium
- ISSB; Génopole; Genavenir 6; Equipe Xénome; 5 rue Henri Desbruères 91030 Evry Cedex France
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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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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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40
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Glasscock C, Lucks J, DeLisa M. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chem Biol 2016; 23:45-56. [DOI: 10.1016/j.chembiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 12/01/2015] [Accepted: 12/01/2015] [Indexed: 11/25/2022]
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Yamagami T, Matsukawa H, Tsunekawa S, Kawarabayasi Y, Ishino S, Ishino Y. A longer finger-subdomain of family A DNA polymerases found by metagenomic analysis strengthens DNA binding and primer extension abilities. Gene 2015; 576:690-5. [PMID: 26476294 DOI: 10.1016/j.gene.2015.10.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The family A DNA polymerases from thermophilic bacteria are useful for PCR. The DNA polymerase from Thermus aquaticus (Taq polymerase) was the original enzyme used when practical PCR was developed, and it has remained the standard enzyme for PCR to date. Knowledge gained from structure-function relationship studies of Taq polymerase is applicable to create PCR enzymes with enhanced performance. We collected the deduced amino acid sequences of the regions from motif A to motif C in the family A DNA polymerases from metagenomic sequence data, obtained by sequencing DNAs from microorganisms isolated from various hot spring areas in Japan. The corresponding regions of the polA gene for Taq polymerase were substituted with the metagenomic DNA gene fragments, and various chimeric DNA polymerases were prepared. Based on the properties of these chimeric enzymes and their sequences, we found an insertion sequence that affects the primer extension ability of the family A DNA polymerases. The insertion sequence is located in the finger subdomain, and it may enhance the affinity of the enzyme to DNA. Mutant Taq polymerases with the corresponding 9 amino acid insertion displayed enhanced PCR performance.
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Affiliation(s)
- Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan
| | - Hiroaki Matsukawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sae Tsunekawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Kawarabayasi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan.
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan.
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42
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Meyer AJ, Ellefson JW, Ellington AD. Directed Evolution of a Panel of Orthogonal T7 RNA Polymerase Variants for in Vivo or in Vitro Synthetic Circuitry. ACS Synth Biol 2015; 4:1070-6. [PMID: 25279711 DOI: 10.1021/sb500299c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
T7 RNA polymerase is the foundation of synthetic biological circuitry both in vivo and in vitro due to its robust and specific control of transcription from its cognate promoter. Here we present the directed evolution of a panel of orthogonal T7 RNA polymerase:promoter pairs that each specifically recognizes a synthetic promoter. These newly described pairs can be used to independently control up to six circuits in parallel.
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Affiliation(s)
- Adam J. Meyer
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jared W. Ellefson
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
| | - Andrew D. Ellington
- Institute for Cellular and Molecular Biology, ‡Department of Chemistry and Biochemistry, and §Center for Systems & Synthetic Biology, University of Texas at Austin, Austin, Texas 78712, United States
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43
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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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44
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DNA sequencing using polymerase substrate-binding kinetics. Nat Commun 2015; 6:5936. [PMID: 25612848 PMCID: PMC4354037 DOI: 10.1038/ncomms6936] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 11/21/2014] [Indexed: 02/08/2023] Open
Abstract
Next-generation sequencing (NGS) has transformed genomic research by decreasing the cost of sequencing. However, whole-genome sequencing is still costly and complex for diagnostics purposes. In the clinical space, targeted sequencing has the advantage of allowing researchers to focus on specific genes of interest. Routine clinical use of targeted NGS mandates inexpensive instruments, fast turnaround time and an integrated and robust workflow. Here we demonstrate a version of the Sequencing by Synthesis (SBS) chemistry that potentially can become a preferred targeted sequencing method in the clinical space. This sequencing chemistry uses natural nucleotides and is based on real-time recording of the differential polymerase/DNA-binding kinetics in the presence of correct or mismatch nucleotides. This ensemble SBS chemistry has been implemented on an existing Illumina sequencing platform with integrated cluster amplification. We discuss the advantages of this sequencing chemistry for targeted sequencing as well as its limitations for other applications. Next-generation sequencing technologies vary in performance, which is often measured by metrics such as sequencing speed, accuracy and read length. Here, the authors present a new sequencing by synthesis method that monitors polymerase binding to DNA, and suggest that this method has the potential to generate longer and faster reads.
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45
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Joshi S, Satyanarayana T. In vitro engineering of microbial enzymes with multifarious applications: prospects and perspectives. BIORESOURCE TECHNOLOGY 2015; 176:273-283. [PMID: 25435065 DOI: 10.1016/j.biortech.2014.10.151] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 10/28/2014] [Accepted: 10/29/2014] [Indexed: 06/04/2023]
Abstract
The discovery of a novel enzyme from a microbial source takes anywhere between months to years, and therefore, there has been an immense interest in modifying the existing microbial enzymes to suit the present day needs of the industry. The redesigning of industrially useful enzymes for improving their performance has become a challenge because bioinformatics databases have been revealing new facts on a day-to-day basis. Modification of the existing enzymes has become a trend for fine tuning of biocatalysts in the biotech industry. Hydrolases are employed in pharmaceutical, biofuel, detergent, food and feed industries that significantly contribute to the global annual revenue, and therefore, the emphasis has been on engineering them. Although a large data is accumulating on making alterations in microbial enzymes, there is a lack of definite information on redesigning industrial enzymes. This review focuses on the recent developments in improving the characteristics of various biotechnologically important enzymes.
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Affiliation(s)
- Swati Joshi
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India
| | - Tulasi Satyanarayana
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110 021, India.
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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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Yamagami T, Ishino S, Kawarabayasi Y, Ishino Y. Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering. Front Microbiol 2014; 5:461. [PMID: 25232352 PMCID: PMC4153296 DOI: 10.3389/fmicb.2014.00461] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/14/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, DNA labeling, mutagenesis, and other experiments. Thermostable DNA polymerases are especially useful and became quite valuable after the development of PCR technology. A DNA polymerase from Thermus aquaticus (Taq polymerase) is the most famous DNA polymerase as a PCR enzyme, and has been widely used all over the world. In this study, the gene fragments of the family A DNA polymerases were amplified by PCR from the DNAs from microorganisms within environmental soil samples, using a primer set for the two conserved regions. The corresponding region of the pol gene for Taq polymerase was substituted with the amplified gene fragments, and various chimeric DNA polymerases were prepared. Based on the properties of these chimeric enzymes and their sequences, two residues, E742 and A743, in Taq polymerase were found to be critical for its elongation ability. Taq polymerases with mutations at 742 and 743 actually showed higher DNA affinity and faster primer extension ability. These factors also affected the PCR performance of the DNA polymerase, and improved PCR results were observed with the mutant Taq polymerase.
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Affiliation(s)
- Takeshi Yamagami
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Sonoko Ishino
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Yutaka Kawarabayasi
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan ; Health Research Institute, National Institute of Advanced Industrial Science and Technology Amagasaki, Japan
| | - Yoshizumi Ishino
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
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48
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Ishino S, Ishino Y. DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field. Front Microbiol 2014; 5:465. [PMID: 25221550 PMCID: PMC4148896 DOI: 10.3389/fmicb.2014.00465] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/15/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase is a ubiquitous enzyme that synthesizes complementary DNA strands according to the template DNA in living cells. Multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, labeling, mutagenesis, and other purposes. The fundamental ability of DNA polymerases to synthesize a deoxyribonucleotide chain is conserved. However, the more specific properties, including processivity, fidelity (synthesis accuracy), and substrate nucleotide selectivity, differ among the enzymes. The distinctive properties of each DNA polymerase may lead to the potential development of unique reagents, and therefore searching for novel DNA polymerase has been one of the major focuses in this research field. In addition, protein engineering techniques to create mutant or artificial DNA polymerases have been successfully developing powerful DNA polymerases, suitable for specific purposes among the many kinds of DNA manipulations. Thermostable DNA polymerases are especially important for PCR-related techniques in molecular biology. In this review, we summarize the history of the research on developing thermostable DNA polymerases as reagents for genetic manipulation and discuss the future of this research field.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
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Pinheiro VB, Arangundy‐Franklin S, Holliger P. Compartmentalized Self‐Tagging for In Vitro‐Directed Evolution of XNA Polymerases. ACTA ACUST UNITED AC 2014; 57:9.9.1-18. [DOI: 10.1002/0471142700.nc0909s57] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Vitor B. Pinheiro
- Institute of Structural and Molecular Biology, University College, University of London London United Kingdom
- Birkbeck College, University of London London United Kingdom
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50
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Pinheiro VB, Holliger P. Towards XNA nanotechnology: new materials from synthetic genetic polymers. Trends Biotechnol 2014; 32:321-8. [PMID: 24745974 PMCID: PMC4039137 DOI: 10.1016/j.tibtech.2014.03.010] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 03/17/2014] [Accepted: 03/18/2014] [Indexed: 12/21/2022]
Abstract
Nucleic acids display remarkable properties beyond information storage and propagation. The well-understood base pairing rules have enabled nucleic acids to be assembled into nanostructures of ever increasing complexity. Although nanostructures can be constructed using other building blocks, including peptides and lipids, it is the capacity to evolve that sets nucleic acids apart from all other nanoscale building materials. Nonetheless, the poor chemical and biological stability of DNA and RNA constrain their applications. Recent advances in nucleic acid chemistry and polymerase engineering enable the synthesis, replication, and evolution of a range of synthetic genetic polymers (XNAs) with improved chemical and biological stability. We discuss the impact of this technology on the generation of XNA ligands, enzymes, and nanostructures with tailor-made chemistry.
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Affiliation(s)
- Vitor B Pinheiro
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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