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Pichon M, Hollenstein M. Controlled enzymatic synthesis of oligonucleotides. Commun Chem 2024; 7:138. [PMID: 38890393 PMCID: PMC11189433 DOI: 10.1038/s42004-024-01216-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/24/2024] [Indexed: 06/20/2024] Open
Abstract
Oligonucleotides are advancing as essential materials for the development of new therapeutics, artificial genes, or in storage of information applications. Hitherto, our capacity to write (i.e., synthesize) oligonucleotides is not as efficient as that to read (i.e., sequencing) DNA/RNA. Alternative, biocatalytic methods for the de novo synthesis of natural or modified oligonucleotides are in dire need to circumvent the limitations of traditional synthetic approaches. This Perspective article summarizes recent progress made in controlled enzymatic synthesis, where temporary blocked nucleotides are incorporated into immobilized primers by polymerases. While robust protocols have been established for DNA, RNA or XNA synthesis is more challenging. Nevertheless, using a suitable combination of protected nucleotides and polymerase has shown promises to produce RNA oligonucleotides even though the production of long DNA/RNA/XNA sequences (>1000 nt) remains challenging. We surmise that merging ligase- and polymerase-based synthesis would help to circumvent the current shortcomings of controlled enzymatic synthesis.
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Affiliation(s)
- Maëva Pichon
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Université Paris Cité, CNRS UMR3523, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, 28, Rue du Docteur Roux, 75724, Paris Cedex 15, France.
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2
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Mahjoubin-Tehran M, Rezaei S, Santos RD, Jamialahmadi T, Almahmeed W, Sahebkar A. Targeting PCSK9 as a key player in lipid metabolism: exploiting the therapeutic and biosensing potential of aptamers. Lipids Health Dis 2024; 23:156. [PMID: 38796450 PMCID: PMC11128129 DOI: 10.1186/s12944-024-02151-8] [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: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
The degradation of low-density lipoprotein receptor (LDLR) is induced by proprotein convertase subtilisin/kexin type 9 (PCSK9), resulting in elevated plasma concentrations of LDL cholesterol. Therefore, inhibiting the interactions between PCSK9 and LDLR is a desirable therapeutic goal for managing hypercholesterolemia. Aptamers, which are RNA or single-stranded DNA sequences, can recognize their targets based on their secondary structure. Aptamers exhibit high selectivity and affinity for binding to target molecules. The systematic evolution of ligands by exponential enrichment (SELEX), a combination of biological approaches, is used to screen most aptamers in vitro. Due to their unique advantages, aptamers have garnered significant interest since their discovery and have found extensive applications in various fields. Aptamers have been increasingly utilized in the development of biosensors for sensitive detection of pathogens, analytes, toxins, drug residues, and malignant cells. Furthermore, similar to monoclonal antibodies, aptamers can serve as therapeutic tools. Unlike certain protein therapeutics, aptamers do not elicit antibody responses, and their modified sugars at the 2'-positions generally prevent toll-like receptor-mediated innate immune responses. The focus of this review is on aptamer-based targeting of PCSK9 and the application of aptamers both as biosensors and therapeutic agents.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Raul D Santos
- Lipid Clinic Heart Institute (Incor), University of São Paulo, Medical School Hospital, São Paulo, Brazil
| | - Tannaz Jamialahmadi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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3
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Hoshino H, Kasahara Y, Obika S. Polyamines promote xenobiotic nucleic acid synthesis by modified thermophilic polymerase mutants. RSC Chem Biol 2024; 5:467-472. [PMID: 38725908 PMCID: PMC11078213 DOI: 10.1039/d4cb00017j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
The enzymatic synthesis of xenobiotic nucleic acids (XNA), which are artificially sugar-modified nucleic acids, is essential for the preparation of XNA libraries. XNA libraries are used in the in vitro selection of XNA aptamers and enzymes (XNAzymes). Efficient enzymatic synthesis of various XNAs can enable the screening of high-quality XNA aptamers and XNAzymes by expanding the diversity of XNA libraries and adding a variety of properties to XNA aptamers and XNAzymes. However, XNAs that form unstable duplexes with DNA, such as arabino nucleic acid (ANA), may dissociate during enzyme synthesis at temperatures suitable for thermophilic polymerases. Thus, such XNAs are not efficiently synthesised by the thermophilic polymerase mutants at the end of the sequence. This undesirable bias reduces the possibility of generating high-quality XNA aptamers and XNAzymes. Here, we demonstrate that polyamine-induced DNA/ANA duplex stabilisation promotes ANA synthesis that is catalysed by thermophilic polymerase mutants. Several polyamines, including spermine, spermidine, cadaverine, and putrescine promote ANA synthesis. The negative effect of polyamines on the fidelity of ANA synthesis was negligible. We also showed that polyamines promote the synthesis of other XNAs, including 2'-amino-RNA/2'-fluoro-RNA mixture and 2'-O-methyl-RNA. In addition, we found that polyamine promotes DNA synthesis from the 2'-O-methyl-RNA template. Polyamines, with the use of thermophilic polymerase mutants, may allow further development of XNA aptamers and XNAzymes by promoting the transcription and reverse transcription of XNAs.
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Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN) 7-6-8 Saito-Asagi Ibaraki 567-0085 Osaka Japan
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka Suita 565-0871 Osaka Japan
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Brunderová M, Havlíček V, Matyašovský J, Pohl R, Poštová Slavětínská L, Krömer M, Hocek M. Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases. Nat Commun 2024; 15:3054. [PMID: 38594306 PMCID: PMC11004144 DOI: 10.1038/s41467-024-47444-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 03/26/2024] [Indexed: 04/11/2024] Open
Abstract
Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases - SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics.
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Affiliation(s)
- Mária Brunderová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, UK
| | - Vojtěch Havlíček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic
| | - Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- The Rosalind Franklin Institute, Harwell Campus, Didcot, Oxfordshire, UK.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16000, Prague, 6, Czech Republic.
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843, Prague, 2, Czech Republic.
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Ishida K, Kasahara Y, Hoshino H, Okuda T, Obika S. Systematic Analysis of 2'- O-Alkyl Modified Analogs for Enzymatic Synthesis and Their Oligonucleotide Properties. Molecules 2023; 28:7911. [PMID: 38067640 PMCID: PMC10708256 DOI: 10.3390/molecules28237911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Enzymatic oligonucleotide synthesis is used for the development of functional oligonucleotides selected by in vitro selection. Expanding available sugar modifications for in vitro selection helps the functional oligonucleotides to be used as therapeutics reagents. We previously developed a KOD DNA polymerase mutant, KOD DGLNK, that enzymatically synthesized fully-LNA- or 2'-O-methyl-modified oligonucleotides. Here, we report a further expansion of the available 2'-O-alkyl-modified nucleotide for enzymatic synthesis by KOD DGLNK. We chemically synthesized five 2'-O-alkyl-5-methyluridine triphosphates and incorporated them into the oligonucleotides. We also enzymatically synthesized a 2'-O-alkyl-modified oligonucleotide with a random region (oligonucleotide libraries). The 2'-O-alkyl-modified oligonucleotide libraries showed high nuclease resistance and a wide range of hydrophobicity. Our synthesized 2'-O-alkyl-modified oligonucleotide libraries provide novel possibilities that can promote the development of functional molecules for therapeutic use.
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Affiliation(s)
- Kenta Ishida
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
| | - Takumi Okuda
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), 7-6-8 Saito-Asagi, Ibaraki 567-0085, Osaka, Japan; (K.I.); (H.H.)
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita 565-0871, Osaka, Japan
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Elias M, Guan X, Hudson D, Bose R, Kwak J, Petrounia I, Touah K, Mansour S, Yue P, Errasti G, Delacroix T, Ghosh A, Chakrabarti R. Evolution of Organic Solvent-Resistant DNA Polymerases. ACS Synth Biol 2023; 12:3170-3188. [PMID: 37611245 DOI: 10.1021/acssynbio.2c00515] [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: 08/25/2023]
Abstract
The introduction of thermostable polymerases revolutionized the polymerase chain reaction (PCR) and biotechnology. However, many GC-rich genes cannot be PCR-amplified with high efficiency in water, irrespective of temperature. Although polar organic cosolvents can enhance nucleic acid polymerization and amplification by destabilizing duplex DNA and secondary structures, nature has not selected for the evolution of solvent-tolerant polymerase enzymes. Here, we used ultrahigh-throughput droplet-based selection and deep sequencing along with computational free-energy and binding affinity calculations to evolve Taq polymerase to generate enzymes that are both stable and highly active in the presence of organic cosolvents, resulting in up to 10% solvent resistance and over 100-fold increase in stability at 97.5 °C in the presence of 1,4-butanediol, as well as tolerance to up to 10 times higher concentrations of the potent cosolvents sulfolane and 2-pyrrolidone. Using these polymerases, we successfully amplified a broad spectrum of GC-rich templates containing regions with over 90% GC content, including templates recalcitrant to amplification with existing polymerases, even in the presence of cosolvents. We also demonstrated dramatically reduced GC bias in the amplification of genes with widely varying GC content in quantitative polymerase chain reaction (qPCR). By expanding the scope of solvent systems compatible with nucleic acid polymerization, these organic solvent-resistant polymerases enable a dramatic reduction of sequence bias not achievable through thermal resistance alone, with significant implications for a wide range of applications including sequencing and synthetic biology in mixed aqueous-organic media.
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Affiliation(s)
- Mohammed Elias
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Xiangying Guan
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Devin Hudson
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Rahul Bose
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Joon Kwak
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Ioanna Petrounia
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Kenza Touah
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Sourour Mansour
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Peng Yue
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
| | - Gauthier Errasti
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Thomas Delacroix
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
| | - Anisha Ghosh
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- McGill University, 845 Rue Sherbrooke Ouest, Montreal, QC H3A 0G4, Canada
| | - Raj Chakrabarti
- Chakrabarti Advanced Technology, LLC, PMC Group Building, 1288 Route 73, Suite 110, Mount Laurel, New Jersey 08054, United States
- Center for Protein Engineering & Drug Discovery, PMC Isochem SAS, 32 Rue Lavoisier, Vert-Le-Petit 91710, France
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7
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Li D, Su Y, Li J, Liu R, Fang B, He J, Xu W, Zhu L. Applications and Challenges of Bacteriostatic Aptamers in the Treatment of Common Pathogenic Bacteria Infections. Biomacromolecules 2023; 24:4568-4586. [PMID: 37728999 DOI: 10.1021/acs.biomac.3c00634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
The continuous evolution and spread of common pathogenic bacteria is a major challenge in diagnosis and treatment with current biotechnology and modern molecular medicine. To confront this challenge, scientists urgently need to find alternatives for traditional antimicrobial agents. Various bacteriostatic aptamers obtained through SELEX screening are one of the most promising strategies. These bacteriostatic aptamers can reduce bacterial infection by blocking bacterial toxin infiltration, inhibiting biofilm formation, preventing bacterial invasion of immune cells, interfering with essential biochemical processes, and other mechanisms. In addition, aptamers may also help enhance the function of other antibacterial materials/drugs when used in combination. This paper has reviewed the bacteriostatic aptamers in the treatment of common pathogenic bacteria infections. For this aspect, first, bacteriostatic aptamers and their screening strategies are summarized. Then, the effect of molecular tailoring and modification on the performance of the bacteriostatic aptamer is analyzed, and the antibacterial mechanism and antibacterial strategy based on aptamers are introduced. Finally, the key technical challenges and their development prospects in clinical treatment are also carefully discussed.
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Affiliation(s)
- Diandian Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yuan Su
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Rong Liu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Bing Fang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jingjing He
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
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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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9
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Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
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Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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10
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Moody ER, Obexer R, Nickl F, Spiess R, Lovelock SL. An enzyme cascade enables production of therapeutic oligonucleotides in a single operation. Science 2023; 380:1150-1154. [PMID: 37319201 DOI: 10.1126/science.add5892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 05/12/2023] [Indexed: 06/17/2023]
Abstract
Therapeutic oligonucleotides have emerged as a powerful drug modality with the potential to treat a wide range of diseases; however, the rising number of therapies poses a manufacturing challenge. Existing synthetic methods use stepwise extension of sequences immobilized on solid supports and are limited by their scalability and sustainability. We report a biocatalytic approach to efficiently produce oligonucleotides in a single operation where polymerases and endonucleases work in synergy to amplify complementary sequences embedded within catalytic self-priming templates. This approach uses unprotected building blocks and aqueous conditions. We demonstrate the versatility of this methodology through the synthesis of clinically relevant oligonucleotide sequences containing diverse modifications.
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Affiliation(s)
- E R Moody
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Obexer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - F Nickl
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - R Spiess
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - S L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
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11
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Akram F, Shah FI, Ibrar R, Fatima T, Haq IU, Naseem W, Gul MA, Tehreem L, Haider G. Bacterial thermophilic DNA polymerases: A focus on prominent biotechnological applications. Anal Biochem 2023; 671:115150. [PMID: 37054862 DOI: 10.1016/j.ab.2023.115150] [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: 01/14/2023] [Revised: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 04/15/2023]
Abstract
DNA polymerases are the enzymes able to replicate the genetic information in nucleic acid. As a result, they are necessary to copy the complete genome of every living creature before cell division and sustain the integrity of the genetic information throughout the life of each cell. Any organism that uses DNA as its genetic information, whether unicellular or multicellular, requires one or more thermostable DNA polymerases to thrive. Thermostable DNA polymerase is important in modern biotechnology and molecular biology because it results in methods such as DNA cloning, DNA sequencing, whole genome amplification, molecular diagnostics, polymerase chain reaction, synthetic biology, and single nucleotide polymorphism detection. There are at least 14 DNA-dependent DNA polymerases in the human genome, which is remarkable. These include the widely accepted, high-fidelity enzymes responsible for replicating the vast majority of genomic DNA and eight or more specialized DNA polymerases discovered in the last decade. The newly discovered polymerases' functions are still being elucidated. Still, one of its crucial tasks is to permit synthesis to resume despite the DNA damage that stops the progression of replication-fork. One of the primary areas of interest in the research field has been the quest for novel DNA polymerase since the unique features of each thermostable DNA polymerase may lead to the prospective creation of novel reagents. Furthermore, protein engineering strategies for generating mutant or artificial DNA polymerases have successfully generated potent DNA polymerases for various applications. In molecular biology, thermostable DNA polymerases are extremely useful for PCR-related methods. This article examines the role and importance of DNA polymerase in a variety of techniques.
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Affiliation(s)
- Fatima Akram
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan.
| | - Fatima Iftikhar Shah
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan; The University of Lahore, Pakistan
| | - Ramesha Ibrar
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Taseer Fatima
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ikram Ul Haq
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan; Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Waqas Naseem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Mahmood Ayaz Gul
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Laiba Tehreem
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
| | - Ghanoor Haider
- Institute of Industrial Biotechnology, Government College University, Lahore, 54000, Pakistan
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12
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Díaz-Perlas C, Escobar-Rosales M, Morgan CW, Oller-Salvia B. Encoding Noncanonical Amino Acids into Phage Displayed Proteins. Methods Mol Biol 2023; 2676:117-129. [PMID: 37277628 DOI: 10.1007/978-1-0716-3251-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phage display facilitates the evolution of peptides and proteins for affinity selection against targets, but it is mostly limited to the chemical diversity provided by the naturally encoded amino acids. The combination of phage display with genetic code expansion allows the incorporation of noncanonical amino acids (ncAAs) into proteins expressed on the phage. In this method, we describe incorporation of one or two ncAAs in a single-chain fragment variable (scFv) antibody in response to amber or quadruplet codon. We take advantage of the pyrrolysyl-tRNA synthetase/tRNA pair to incorporate a lysine derivative and an orthogonal tyrosyl-tRNA synthetase/tRNA pair to incorporate a phenylalanine derivative. The encoding of novel chemical functionalities and building blocks in proteins displayed on phage provides the foundation for further phage display applications in fields such as imaging, protein targeting, and the production of new materials.
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Affiliation(s)
| | | | - Charles W Morgan
- Research School of Biology, The Australian National University, Canberra, Australia
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13
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Freund N, Taylor AI, Arangundy-Franklin S, Subramanian N, Peak-Chew SY, Whitaker AM, Freudenthal BD, Abramov M, Herdewijn P, Holliger P. A two-residue nascent-strand steric gate controls synthesis of 2'-O-methyl- and 2'-O-(2-methoxyethyl)-RNA. Nat Chem 2023; 15:91-100. [PMID: 36229679 PMCID: PMC7614059 DOI: 10.1038/s41557-022-01050-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 08/29/2022] [Indexed: 01/17/2023]
Abstract
Steric exclusion is a key element of enzyme substrate specificity, including in polymerases. Such substrate specificity restricts the enzymatic synthesis of 2'-modified nucleic acids, which are of interest in nucleic-acid-based drug development. Here we describe the discovery of a two-residue, nascent-strand, steric control 'gate' in an archaeal DNA polymerase. We show that engineering of the gate to reduce steric bulk in the context of a previously described RNA polymerase activity unlocks the synthesis of 2'-modified RNA oligomers, specifically the efficient synthesis of both defined and random-sequence 2'-O-methyl-RNA (2'OMe-RNA) and 2'-O-(2-methoxyethyl)-RNA (MOE-RNA) oligomers up to 750 nt. This enabled the discovery of RNA endonuclease catalysts entirely composed of 2'OMe-RNA (2'OMezymes) for the allele-specific cleavage of oncogenic KRAS (G12D) and β-catenin CTNNB1 (S33Y) mRNAs, and the elaboration of mixed 2'OMe-/MOE-RNA aptamers with high affinity for vascular endothelial growth factor. Our results open up these 2'-modified RNAs-used in several approved nucleic acid therapeutics-for enzymatic synthesis and a wider exploration in directed evolution and nanotechnology.
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Affiliation(s)
- Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
| | | | - Nithya Subramanian
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Sew-Yeu Peak-Chew
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Amy M Whitaker
- Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Bret D Freudenthal
- Laboratory of Genome Maintenance and Structural Biology, Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Mikhail Abramov
- Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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14
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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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15
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Cai R, Chen X, Zhang Y, Wang X, Zhou N. Systematic bio-fabrication of aptamers and their applications in engineering biology. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:223-245. [PMID: 38013802 PMCID: PMC9550155 DOI: 10.1007/s43393-022-00140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 10/27/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.
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Affiliation(s)
- Rongfeng Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xin Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Yuting Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Xiaoli Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 China
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16
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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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17
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Aggarwal T, Hansen WA, Hong J, Ganguly A, York DM, Khare SD, Izgu EC. Introducing a New Bond-Forming Activity in an Archaeal DNA Polymerase by Structure-Guided Enzyme Redesign. ACS Chem Biol 2022; 17:1924-1936. [PMID: 35776893 DOI: 10.1021/acschembio.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerases have evolved to feature a highly conserved activity across the tree of life: formation of, without exception, internucleotidyl O-P linkages. Can this linkage selectivity be overcome by design to produce xenonucleic acids? Here, we report that the structure-guided redesign of an archaeal DNA polymerase, 9°N, exhibits a new activity undetectable in the wild-type enzyme: catalyzing the formation of internucleotidyl N-P linkages using 3'-NH2-ddNTPs. Replacing a metal-binding aspartate in the 9°N active site with asparagine was key to the emergence of this unnatural enzyme activity. MD simulations provided insights into how a single substitution enhances the productive positioning of a 3'-amino nucleophile in the active site. Further remodeling of the protein-nucleic acid interface in the finger subdomain yielded a quadruple-mutant variant (9°N-NRQS) displaying DNA-dependent NP-DNA polymerase activity. In addition, the engineered promiscuity of 9°N-NRQS was leveraged for one-pot synthesis of DNA─NP-DNA copolymers. This work sheds light on the molecular basis of substrate fidelity and latent promiscuity in enzymes.
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Affiliation(s)
- Tushar Aggarwal
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - William A Hansen
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Jonathan Hong
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States
| | - Darrin M York
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Laboratory for Biomolecular Simulation Research, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Sagar D Khare
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Institute for Quantitative Biomedicine, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - Enver Cagri Izgu
- Department of Chemistry and Chemical Biology, Rutgers University, New Brunswick, New Jersey 08854, United States.,Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08901, United States.,Rutgers Center for Lipid Research and New Jersey Institute for Food, Nutrition, and Health, Rutgers University, New Brunswick, New Jersey 08901, United States
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18
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Shroff R, Ellefson JW, Wang SS, Boulgakov AA, Hughes RA, Ellington AD. Recovery of Information Stored in Modified DNA with an Evolved Polymerase. ACS Synth Biol 2022; 11:554-561. [PMID: 35113518 DOI: 10.1021/acssynbio.1c00575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA is increasingly being explored as an alternative medium for digital information storage, but the potential information loss from degradation and associated issues with error during reading challenge its wide-scale implementation. To address this, we propose an atomic-scale encoding standard for DNA, where information is encoded in degradation-resistant analogues of natural nucleic acids (xNAs). To better enable this approach, we used directed evolution to create a polymerase capable of transforming 2'-O-methyl templates into double-stranded DNA. Starting from a thermophilic, error-correcting reverse transcriptase, RTX, we evolved an enzyme (RTX-Ome v6) that relies on a fully functional proofreading domain to correct mismatches on DNA, RNA, and 2'-O-methyl templates. In addition, we implemented a downstream analysis strategy that accommodates deletions that arise during phosphoramidite synthesis, the most common type of synthesis error. By coupling and integrating new chemistries, enzymes, and algorithms, we further enable the large-scale use of nucleic acids for information storage.
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Affiliation(s)
- Raghav Shroff
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
| | - Jared W. Ellefson
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
| | - Siyuan S. Wang
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
| | - Alexander A. Boulgakov
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
| | - Randall A. Hughes
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
| | - Andrew D. Ellington
- Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712, United States
- Army Research Laboratory, Biotechnology Branch, Adelphi, Maryland 20783, United States
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19
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Wang F, Li P, Chu HC, Lo PK. Nucleic Acids and Their Analogues for Biomedical Applications. BIOSENSORS 2022; 12:bios12020093. [PMID: 35200353 PMCID: PMC8869748 DOI: 10.3390/bios12020093] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/20/2022] [Accepted: 01/25/2022] [Indexed: 05/07/2023]
Abstract
Nucleic acids are emerging as powerful and functional biomaterials due to their molecular recognition ability, programmability, and ease of synthesis and chemical modification. Various types of nucleic acids have been used as gene regulation tools or therapeutic agents for the treatment of human diseases with genetic disorders. Nucleic acids can also be used to develop sensing platforms for detecting ions, small molecules, proteins, and cells. Their performance can be improved through integration with other organic or inorganic nanomaterials. To further enhance their biological properties, various chemically modified nucleic acid analogues can be generated by modifying their phosphodiester backbone, sugar moiety, nucleobase, or combined sites. Alternatively, using nucleic acids as building blocks for self-assembly of highly ordered nanostructures would enhance their biological stability and cellular uptake efficiency. In this review, we will focus on the development and biomedical applications of structural and functional natural nucleic acids, as well as the chemically modified nucleic acid analogues over the past ten years. The recent progress in the development of functional nanomaterials based on self-assembled DNA-based platforms for gene regulation, biosensing, drug delivery, and therapy will also be presented. We will then summarize with a discussion on the advanced development of nucleic acid research, highlight some of the challenges faced and propose suggestions for further improvement.
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Affiliation(s)
- Fei Wang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pan Li
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Hoi Ching Chu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
| | - Pik Kwan Lo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China; (F.W.); (P.L.); (H.C.C.)
- Key Laboratory of Biochip Technology, Biotech and Health Care, Shenzhen Research Institute of City University of Hong Kong, Shenzhen 518057, China
- Correspondence:
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20
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Zhu G, Song P, Wu J, Luo M, Chen Z, Chen T. Application of Nucleic Acid Frameworks in the Construction of Nanostructures and Cascade Biocatalysts: Recent Progress and Perspective. Front Bioeng Biotechnol 2022; 9:792489. [PMID: 35071205 PMCID: PMC8777461 DOI: 10.3389/fbioe.2021.792489] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 12/10/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids underlie the storage and retrieval of genetic information literally in all living organisms, and also provide us excellent materials for making artificial nanostructures and scaffolds for constructing multi-enzyme systems with outstanding performance in catalyzing various cascade reactions, due to their highly diverse and yet controllable structures, which are well determined by their sequences. The introduction of unnatural moieties into nucleic acids dramatically increased the diversity of sequences, structures, and properties of the nucleic acids, which undoubtedly expanded the toolbox for making nanomaterials and scaffolds of multi-enzyme systems. In this article, we first introduce the molecular structures and properties of nucleic acids and their unnatural derivatives. Then we summarized representative artificial nanomaterials made of nucleic acids, as well as their properties, functions, and application. We next review recent progress on constructing multi-enzyme systems with nucleic acid structures as scaffolds for cascade biocatalyst. Finally, we discuss the future direction of applying nucleic acid frameworks in the construction of nanomaterials and multi-enzyme molecular machines, with the potential contribution that unnatural nucleic acids may make to this field highlighted.
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Affiliation(s)
- Gan Zhu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jing Wu
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Minglan Luo
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhipeng Chen
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, 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, Guangzhou, China
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21
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Wang Y, Zhang Y, Li PC, Guo J, Huo F, Yang J, Jia R, Wang J, Huang Q, Theodorescu D, Yu H, Yan C. Development of novel aptamer-based targeted chemotherapy for bladder cancer. Cancer Res 2022; 82:1128-1139. [DOI: 10.1158/0008-5472.can-21-2691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 12/08/2021] [Accepted: 01/18/2022] [Indexed: 12/24/2022]
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22
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Levi-Acobas F, McKenzie LK, Hollenstein M. Towards polymerase-mediated synthesis of artificial RNA–DNA metal base pairs. NEW J CHEM 2022. [DOI: 10.1039/d2nj00427e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Polymerase-mediated synthesis of RNA-DNA metal base pairs.
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Affiliation(s)
- Fabienne Levi-Acobas
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Luke K. McKenzie
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
- Chimie ParisTech, PSL University, CNRS, Institute of Chemistry for Life and Health Sciences, Laboratory for Inorganic Chemical Biology, 75005 Paris, France
| | - Marcel Hollenstein
- Institut Pasteur, Université de Paris, CNRS UMR3523, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
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23
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Christensen TA, Lee KY, Gottlieb SZP, Carrier MB, Leconte AM. Mutant polymerases capable of 2′ fluoro-modified nucleic acid synthesis and amplification with improved accuracy. RSC Chem Biol 2022; 3:1044-1051. [PMID: 35975008 PMCID: PMC9347352 DOI: 10.1039/d2cb00064d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/16/2022] [Indexed: 11/21/2022] Open
Abstract
Nonnatural nucleic acids (xeno nucleic acids, XNA) can possess several useful properties such as expanded reactivity and nuclease resistance, which can enhance the utility of DNA as a biotechnological tool. Native DNA polymerases are unable to synthesize XNA, so, in recent years mutant XNA polymerases have been engineered with sufficient activity for use in processes such as PCR. While substantial improvements have been made, accuracy still needs to be increased by orders of magnitude to approach natural error rates and make XNA polymerases useful for applications that require high fidelity. Here, we systematically evaluate leading Taq DNA polymerase mutants for their fidelity during synthesis of 2′F XNA. To further improve their accuracy, we add mutations that have been shown to increase the fidelity of wild-type Taq polymerases, to some of the best current XNA polymerases (SFM4–3, SFM4–6, and SFP1). The resulting polymerases show significant improvements in synthesis accuracy. In addition to generating more accurate XNA polymerases, this study also informs future polymerase engineering efforts by demonstrating that mutations that improve the accuracy of DNA synthesis may also have utility in improving the accuracy of XNA synthesis. Polymerases that have been evolved to synthesize 2′F XNA are often inaccurate. Here, we show that you can improve the accuracy of 2′F XNA polymerase synthesis by adding mutations previously found to improve the accuracy of natural DNA synthesis.![]()
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Affiliation(s)
- Trevor A. Christensen
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Kristi Y. Lee
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Simone Z. P. Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Mikayla B. Carrier
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
| | - Aaron M. Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, USA
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24
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Ishaqat A, Herrmann A. Polymers Strive for Accuracy: From Sequence-Defined Polymers to mRNA Vaccines against COVID-19 and Polymers in Nucleic Acid Therapeutics. J Am Chem Soc 2021; 143:20529-20545. [PMID: 34841867 DOI: 10.1021/jacs.1c08484] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Unquestionably, polymers have influenced the world over the past 100 years. They are now more crucial than ever since the COVID-19 pandemic outbreak. The pandemic paved the way for certain polymers to be in the spotlight, namely sequence-defined polymers such as messenger ribonucleic acid (mRNA), which was the first type of vaccine to be authorized in the U.S. and Europe to protect against the SARS-CoV-2 virus. This rise of mRNA will probably influence scientific research concerning nucleic acids in general and RNA therapeutics in specific. In this Perspective, we highlight the recent trends in sequence-controlled and sequence-defined polymers. Then we discuss mRNA vaccines as an example to illustrate the need of ultimate sequence control to achieve complex functions such as specific activation of the immune system. We briefly present how mRNA vaccines are produced, the importance of modified nucleotides, the characteristic features, and the advantages and challenges associated with this class of vaccines. Finally, we discuss the chances and opportunities for polymer chemistry to provide solutions and contribute to the future progress of RNA-based therapeutics. We highlight two particular roles of polymers in this context. One represents conjugation of polymers to nucleic acids to form biohybrids. The other is concerned with advanced polymer-based carrier systems for nucleic acids. We believe that polymers can help to address present problems of RNA-based therapeutic technologies and impact the field beyond the COVID-19 pandemic.
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Affiliation(s)
- Aman Ishaqat
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
| | - Andreas Herrmann
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstraße 50, 52074 Aachen, Germany.,Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074 Aachen, Germany
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25
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Oliveira R, Pinho E, Sousa AL, DeStefano JJ, Azevedo NF, Almeida C. Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches. Trends Biotechnol 2021; 40:549-563. [PMID: 34756455 DOI: 10.1016/j.tibtech.2021.09.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/29/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022]
Abstract
Aptamers are structural single-stranded oligonucleotides generated in vitro to bind to a specific target molecule. Aptamers' versatility can be enhanced with nucleic acid mimics (NAMs) during or after a selection process, also known as systematic evolution of ligands by exponential enrichment (SELEX). We address advantages and limitations of the technologies used to generate NAM aptamers, especially the applicability of existing engineered polymerases to replicate NAMs and methodologies to improve aptamers after SELEX. We also discuss the limitations of existing methods for sequencing NAM sequences and bioinformatic tools to predict NAM aptamer structures. As a conclusion, we suggest that NAM aptamers might successfully compete with molecular tools based on proteins such as antibodies for future application.
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Affiliation(s)
- Ricardo Oliveira
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Eva Pinho
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal
| | - Ana Luísa Sousa
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA
| | - Nuno Filipe Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, 4485-655 Vairão, Vila do Conde, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology, and Energy, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal; Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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26
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Directed Evolution Methods for Enzyme Engineering. Molecules 2021; 26:molecules26185599. [PMID: 34577070 PMCID: PMC8470892 DOI: 10.3390/molecules26185599] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 11/22/2022] Open
Abstract
Enzymes underpin the processes required for most biotransformations. However, natural enzymes are often not optimal for biotechnological uses and must be engineered for improved activity, specificity and stability. A rich and growing variety of wet-lab methods have been developed by researchers over decades to accomplish this goal. In this review such methods and their specific attributes are examined.
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27
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Song P, Zhang R, He C, Chen T. Transcription, Reverse Transcription, and Amplification of Backbone-Modified Nucleic Acids with Laboratory-Evolved Thermophilic DNA Polymerases. Curr Protoc 2021; 1:e188. [PMID: 34232574 DOI: 10.1002/cpz1.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Backbone-modified nucleic acids are usually more stable enzymatically than their natural counterparts, enabling their broad application as potential diagnostic or therapeutic agents. Moreover, the development of nucleic acids with unnatural backbones has expanded the pool of genetic information carriers and paved the way toward synthetic xenobiology. However, synthesizing these molecules remains very challenging due to the requirement for harsh reaction conditions and the low coupling efficiency during their traditional solid-phase synthesis. Although enzymatic synthesis provides an attractive alternative that also allows the replication and artificial evolution of these molecules, it is crucially dependent on the availability of polymerases capable of synthesizing these backbone-modified nucleotides. Previously, a series of thermostable polymerases that can efficiently synthesize or even amplify backbone-modified DNA or RNA have been evolved through a polymerase evolution method based on phage display. Herein we summarize protocols to use these evolved polymerase mutants to transcribe, reverse transcribe, and PCR amplify backbone-modified nucleic acids. We also outline the polymerase chain transcription method, developed later for the rapid production of RNA or backbone-modified RNA with one of these evolved polymerases, SFM4-3. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Transcription/synthesis of modified DNA/RNA from DNA templates with evolved polymerases SFM4-3 or SFM4-6 Basic Protocol 2: Reverse transcription of modified DNA/RNA with evolved polymerase SFM4-9 Basic Protocol 3: PCR amplification of modified DNA with evolved polymerase SFM4-3 Basic Protocol 4: Polymerase chain transcription for the production of RNA/modified RNA oligonucleotides with evolved polymerase SFM4-3.
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Affiliation(s)
- Ping Song
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Rujie Zhang
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, P. R. China
| | - Chuanping He
- MOE International Joint Research Laboratory on Synthetic Biology and Medicines, School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 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, P. R. China
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28
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Ohashi S, Hashiya F, Abe H. Variety of Nucleotide Polymerase Mutants Aiming to Synthesize Modified RNA. Chembiochem 2021; 22:2398-2406. [PMID: 33822453 DOI: 10.1002/cbic.202100004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/01/2021] [Indexed: 01/09/2023]
Abstract
Significant efforts have been made to develop therapeutic RNA aptamers that exploit synthetic RNA to capture target molecules. However, ensuring RNA aptamers are resistant against intrinsic nucleases remains an issue and restricts their use as therapeutics. Introduction of chemical modifications to the 2' sugar moiety of RNA improves their stability effectively and can be achieved by chemical synthesis using modified phosphoramidites; however, this approach is not suitable for preparing long RNA molecules. Although recombinant nucleotide polymerases can transcribe RNA, these polymerases cannot synthesize modified RNA because they do not recognize 2' modified nucleoside triphosphates. In this review, we focus on several polymerase mutants that tolerate substrates containing modifications of the 2' sugar moiety to synthesize RNA, and the problems that must be overcome to prepare chemically modified RNA with high efficacy by in vitro transcription.
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Affiliation(s)
- Sana Ohashi
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Fumitaka Hashiya
- Research Center for Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Hiroshi Abe
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,Research Center for Material Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.,CREST, Japan Science and Technology Agency, 7, Gobancho, Chiyoda-ku, Tokyo, 102-0076, Japan.,Institute for Glyco-core Research (iGCORE), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
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29
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Hoshino H, Kasahara Y, Kuwahara M, Obika S. DNA Polymerase Variants with High Processivity and Accuracy for Encoding and Decoding Locked Nucleic Acid Sequences. J Am Chem Soc 2020; 142:21530-21537. [PMID: 33306372 DOI: 10.1021/jacs.0c10902] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Xenobiotic nucleic acids (XNAs) are chemically modified nucleic acid analogues with potential applications in nucleic acid-based therapeutics including nucleic acid aptamers, ribozymes, small interfering RNAs, and antisense oligonucleotides. We have developed a promising XNA for therapeutic uses, 2',4'-bridged nucleic acid (2',4'-BNA), also known as locked nucleic acid (LNA). Unlike the rational design of small interfering and antisense oligonucleotides, the development of LNA aptamers and catalysts requires genetically engineered polymerases that enable the synthesis of LNA from DNA and the converse reverse transcription. However, no LNA decoders or encoders with sufficient performance have been developed. In this study, we developed variants of KOD DNA polymerase, a family B DNA polymerase derived from Thermococcus kodakarensis KOD1, which are effective LNA decoders and encoders, via structural analyses. KOD DGLNK (KOD: N210D/Y409G/A485L/D614N/E664K) enabled LNA synthesis from DNA (DNA → LNA), and KOD DLK (KOD: N210D/A485L/E664K) enabled LNA reverse transcription to DNA (LNA → DNA). Both variants exhibited greatly improved efficiency and accuracy. Notably, we synthesized LNAs longer than one kilobase using KOD DGLNK. We also showed that these variants can accept 2'-O-methyl (2'-OMe), a common modification for therapeutic uses. Here, we also show that LNA and 2'-OMe mix aptamer can be practically obtained via SELEX. The variants can be used as powerful tools for creating XNA aptamers and catalysts to completely eliminate the natural species, DNA and RNA.
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Affiliation(s)
- Hidekazu Hoshino
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuuya Kasahara
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Masayasu Kuwahara
- Graduate School of Integrated Basic Sciences, Nihon University, 3-25-40 Sakurajosui, Setagaya-ku, Tokyo 156-8550, Japan
| | - Satoshi Obika
- National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.,Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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30
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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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31
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Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
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Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
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32
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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: 61] [Impact Index Per Article: 15.3] [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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33
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Matyašovský J, Hocek M. 2-Substituted 2'-deoxyinosine 5'-triphosphates as substrates for polymerase synthesis of minor-groove-modified DNA and effects on restriction endonuclease cleavage. Org Biomol Chem 2020; 18:255-262. [PMID: 31815989 DOI: 10.1039/c9ob02502b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Five 2-substituted 2'-deoxyinosine triphosphates (dRITP) were synthesized and tested as substrates in enzymatic synthesis of minor-groove base-modified DNA. Only 2-methyl and 2-vinyl derivatives proved to be good substrates for Therminator DNA polymerase, whilst all other dRITPs and other tested DNA polymerases did not give full length products in primer extension. The DNA containing 2-vinylhypoxanthine was then further modified through thiol-ene reactions with thiols. Cross-linking reaction between cysteine-containing minor-groove binding dodecapeptide and DNA proceeded thanks to the proximity effect between thiol and vinyl groups inside the minor groove. 2-Substituted dIRTPs and also previously prepared 2-substituted 2'-deoxyadenosine triphosphates (dRATP) were then used for enzymatic synthesis of minor-groove modified DNA to study the effect of minor-groove modifications on cleavage of DNA by type II restriction endonucleases (REs). Although the REs should recognize the sequence through H-bonds in the major groove, some minor-groove modifications also had an inhibiting effect on the cleavage.
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Affiliation(s)
- Ján Matyašovský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo namesti 2, CZ-16610 Prague 6, Czech Republic.
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34
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Chung ME, Goroncy K, Kolesnikova A, Schönauer D, Schwaneberg U. Display of functional nucleic acid polymerase on Escherichia coli surface and its application in directed polymerase evolution. Biotechnol Bioeng 2020; 117:3699-3711. [PMID: 32827316 DOI: 10.1002/bit.27542] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/30/2020] [Accepted: 08/09/2020] [Indexed: 12/29/2022]
Abstract
We report a first of its kind functional cell surface display of nucleic acid polymerase and its directed evolution to efficiently incorporate 2'-O-methyl nucleotide triphosphates (2'-OMe-NTPs). In the development of polymerase cell surface display, two autotransporter proteins (Escherichia coli adhesin involved in diffuse adherence and Pseudomonas aeruginosa esterase A [EstA]) were employed to transport and anchor the 68-kDa Klenow fragment (KF) of E. coli DNA polymerase I on the surface of E. coli. The localization and function of the displayed KF were verified by analysis of cell outer membrane fractions, immunostaining, and fluorometric detection of synthesized DNA products. The EstA cell surface display system was applied to evolve KF for the incorporation of 2'-OMe-NTPs and a KF variant with a 50.7-fold increased ability to successively incorporate 2'-OMe-NTPs was discovered. Expanding the scope of cell-surface displayable proteins to the realm of polymerases provides a novel screening tool for tailoring polymerases to diverse application demands in a polymerase chain reaction and sequencing-based biotechnological and medical applications. Especially, cell surface display enables novel polymerase screening strategies in which the heat-lysis step is bypassed and thus allows the screening of mesophilic polymerases with broad application potentials ranging from diagnostics and DNA sequencing to replication of synthetic genetic polymers.
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Affiliation(s)
- Mu-En Chung
- SeSaM-Biotech GmbH, Aachen, Germany.,Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany
| | | | | | | | - Ulrich Schwaneberg
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Aachen, Germany.,DWI-Leibniz-Institute for Interactive Materials, Aachen, Germany
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35
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Thompson AS, Barrett SE, Weiden AG, Venkatesh A, Seto MKC, Gottlieb SZP, Leconte AM. Accurate and Efficient One-Pot Reverse Transcription and Amplification of 2'-Fluoro-Modified Nucleic Acids by Commercial DNA Polymerases. Biochemistry 2020; 59:2833-2841. [PMID: 32659079 DOI: 10.1021/acs.biochem.0c00494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
DNA is a foundational tool in biotechnology and synthetic biology but is limited by sensitivity to DNA-modifying enzymes. Recently, researchers have identified DNA polymerases that can enzymatically synthesize long oligonucleotides of modified DNA (M-DNA) that are resistant to DNA-modifying enzymes. Most applications require M-DNA to be reverse transcribed, typically using a RNA reverse transcriptase, back into natural DNA for sequence analysis or further manipulation. Here, we tested commercially available DNA-dependent DNA polymerases for their ability to reverse transcribe and amplify M-DNA in a one-pot reaction. Three of the six polymerases chosen (Phusion, Q5, and Deep Vent) could reverse transcribe and amplify synthetic 2'F M-DNA in a single reaction with <5 × 10-3 error per base pair. We further used Q5 DNA polymerase to reverse transcribe and amplify M-DNA synthesized by two candidate M-DNA polymerases (SFP1 and SFM4-6), allowing for quantification of the frequency, types, and locations of errors made during M-DNA synthesis. From these studies, we identify SFP1 as one of the most accurate M-DNA polymerases identified to date. Collectively, these studies establish a simple, robust method for the conversion of 2'F M-DNA to DNA in <1 h using commercially available materials, significantly improving the ease of use of M-DNA.
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Affiliation(s)
- Arianna S Thompson
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Susanna E Barrett
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aurora G Weiden
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Ananya Venkatesh
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Madison K C Seto
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Simone Z P Gottlieb
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
| | - Aaron M Leconte
- W. M. Keck Science Department of Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, California 91711, United States
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36
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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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37
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Houlihan G, Arangundy-Franklin S, Porebski BT, Subramanian N, Taylor AI, Holliger P. Discovery and evolution of RNA and XNA reverse transcriptase function and fidelity. Nat Chem 2020; 12:683-690. [PMID: 32690899 DOI: 10.1038/s41557-020-0502-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/01/2020] [Indexed: 12/11/2022]
Abstract
The ability of reverse transcriptases (RTs) to synthesize a complementary DNA from natural RNA and a range of unnatural xeno nucleic acid (XNA) template chemistries, underpins key methods in molecular and synthetic genetics. However, RTs have proven challenging to discover and engineer, in particular for the more divergent XNA chemistries. Here we describe a general strategy for the directed evolution of RT function for any template chemistry called compartmentalized bead labelling and demonstrate it by the directed evolution of efficient RTs for 2'-O-methyl RNA and hexitol nucleic acids and the discovery of RTs for the orphan XNA chemistries D-altritol nucleic acid and 2'-methoxyethyl RNA, for which previously no RTs existed. Finally, we describe the engineering of XNA RTs with active exonucleolytic proofreading as well as the directed evolution of RNA RTs with very high complementary DNA synthesis fidelities, even in the absence of proofreading.
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Affiliation(s)
- Gillian Houlihan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Benjamin T Porebski
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Nithya Subramanian
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.
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38
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Nikoomanzar A, Vallejo D, Yik EJ, Chaput JC. Programmed Allelic Mutagenesis of a DNA Polymerase with Single Amino Acid Resolution. ACS Synth Biol 2020; 9:1873-1881. [PMID: 32531152 DOI: 10.1021/acssynbio.0c00236] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Most DNA polymerase libraries sample unknown portions of mutational space and are constrained by the limitations of random mutagenesis. Here we describe a programmed allelic mutagenesis (PAM) strategy to comprehensively evaluate all possible single-point mutations in the entire catalytic domain of a replicative DNA polymerase. By applying the PAM strategy with ultrafast high-throughput screening, we show how DNA polymerases can be mapped for allelic mutations that exhibit enhanced activity for unnatural nucleic acid substrates. We suggest that comprehensive missense mutational scans may aid the discovery of specificity determining residues that are necessary for reprogramming the biological functions of natural DNA polymerases.
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Affiliation(s)
- Ali Nikoomanzar
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Derek Vallejo
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - Eric J. Yik
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697-3958, United States
- Department of Chemistry, University of California, Irvine, California 92697-3958, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3958, United States
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39
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Johnson MK, Kottur J, Nair DT. A polar filter in DNA polymerases prevents ribonucleotide incorporation. Nucleic Acids Res 2020; 47:10693-10705. [PMID: 31544946 PMCID: PMC6846668 DOI: 10.1093/nar/gkz792] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 09/02/2019] [Accepted: 09/09/2019] [Indexed: 12/17/2022] Open
Abstract
The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2’-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4–Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.
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Affiliation(s)
- Mary K Johnson
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India.,National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore 560065, India
| | - Jithesh Kottur
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
| | - Deepak T Nair
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India
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40
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Röthlisberger P, Levi-Acobas F, Leumann CJ, Hollenstein M. Enzymatic synthesis of biphenyl-DNA oligonucleotides. Bioorg Med Chem 2020; 28:115487. [PMID: 32284226 DOI: 10.1016/j.bmc.2020.115487] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 12/25/2022]
Abstract
The incorporation of nucleotides equipped with C-glycosidic aromatic nucleobases into DNA and RNA is an alluring strategy for a number of practical applications including fluorescent labelling of oligonucleotides, expansion of the genetic alphabet for the generation of aptamers and semi-synthetic organisms, or the modulation of excess electron transfer within DNA. However, the generation of C-nucleoside containing oligonucleotides relies mainly on solid-phase synthesis which is quite labor intensive and restricted to short sequences. Here, we explore the possibility of constructing biphenyl-modified DNA sequences using enzymatic synthesis. The presence of multiple biphenyl-units or biphenyl residues modified with electron donors and acceptors permits the incorporation of a single dBphMP nucleotide. Moreover, templates with multiple abasic sites enable the incorporation of up to two dBphMP nucleotides, while TdT-mediated tailing reactions produce single-stranded DNA oligonucleotides with four biphenyl residues appended at the 3'-end.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Fabienne Levi-Acobas
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Department of Genome and Genetics, Paris, France.
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41
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Shao Q, Chen T, Sheng K, Liu Z, Zhang Z, Romesberg FE. Selection of Aptamers with Large Hydrophobic 2'-Substituents. J Am Chem Soc 2020; 142:2125-2128. [PMID: 31961667 DOI: 10.1021/jacs.9b10538] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Previously, we evolved a DNA polymerase, SFM4-3, for the recognition of substrates modified at their 2' positions with a fluoro, O-methyl, or azido substituent. Here we use SFM4-3 to synthesize 2'-azido-modified DNA; we then use the azido group to attach different, large hydrophobic groups via click chemistry. We show that SFM4-3 recognizes the modified templates under standard conditions, producing natural DNA and thereby allowing amplification. To demonstrate the utility of this remarkable property, we use SFM4-3 to select aptamers with large hydrophobic 2' substituents that bind human neutrophil elastase or the blood coagulation protein factor IXa. The results indicate that SFM4-3 should facilitate the discovery of aptamers that adopt novel and perhaps more protein-like folds with hydrophobic cores that in turn allow them to access novel activities.
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Affiliation(s)
- Qian Shao
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Tingjian Chen
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Kai Sheng
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhixia Liu
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Zhuochen Zhang
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Floyd E Romesberg
- Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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42
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Aptamers: A Review of Their Chemical Properties and Modifications for Therapeutic Application. Molecules 2019; 24:molecules24234229. [PMID: 31766318 PMCID: PMC6930564 DOI: 10.3390/molecules24234229] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 11/20/2019] [Indexed: 12/29/2022] Open
Abstract
Aptamers are short, single-stranded oligonucleotides that bind to specific target molecules. The shape-forming feature of single-stranded oligonucleotides provides high affinity and excellent specificity toward targets. Hence, aptamers can be used as analogs of antibodies. In December 2004, the US Food and Drug Administration approved the first aptamer-based therapeutic, pegaptanib (Macugen), targeting vascular endothelial growth factor, for the treatment of age-related macular degeneration. Since then, however, no aptamer medication for public health has appeared. During these relatively silent years, many trials and improvements of aptamer therapeutics have been performed, opening multiple novel directions for the therapeutic application of aptamers. This review summarizes the basic characteristics of aptamers and the chemical modifications available for aptamer therapeutics.
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43
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Abstract
To increase the scope of natural biosystem, nucleic acids have been intensively modified. One direction includes the development of a synthetic alternative to the native DNA and RNA, denoted Xenobiotic nucleic acids (XNAs) that are able to store and transfer genetic information either by base-modification or backbone-modification. Another line of research aims to develop alternative third base pair additional to natural A:T and G:C. These unnatural base pairs (UBPs) can store increased information content encoded in three base pairs. This review outlines the recent progress made towards XNA and UBP applications as new components of the genomic DNA as well as biostable aptamers. New achievements in the replacement of a bacterial genome by unnatural non-canonical nucleotides are also described.
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Affiliation(s)
- Elena Eremeeva
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, 3000 Leuven, Belgium.
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44
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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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45
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Zhou H, Rauch S, Dai Q, Cui X, Zhang Z, Nachtergaele S, Sepich C, He C, Dickinson BC. Evolution of a reverse transcriptase to map N 1-methyladenosine in human messenger RNA. Nat Methods 2019; 16:1281-1288. [PMID: 31548705 PMCID: PMC6884687 DOI: 10.1038/s41592-019-0550-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 08/05/2019] [Indexed: 11/09/2022]
Abstract
Chemical modifications to messenger RNA are increasingly recognized as a critical regulatory layer in the flow of genetic information, but quantitative tools to monitor RNA modifications in a whole-transcriptome and site-specific manner are lacking. Here we describe a versatile platform for directed evolution that rapidly selects for reverse transcriptases that install mutations at sites of a given type of RNA modification during reverse transcription, allowing for site-specific identification of the modification. To develop and validate the platform, we evolved the HIV-1 reverse transcriptase against N1-methyladenosine (m1A). Iterative rounds of selection yielded reverse transcriptases with both robust read-through and high mutation rates at m1A sites. The optimal evolved reverse transcriptase enabled detection of well-characterized m1A sites and revealed hundreds of m1A sites in human mRNA. This work develops and validates the reverse transcriptase evolution platform, and provides new tools, analysis methods and datasets to study m1A biology.
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Affiliation(s)
- Huiqing Zhou
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Simone Rauch
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Xiaolong Cui
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - Zijie Zhang
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Sigrid Nachtergaele
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA
| | - Caraline Sepich
- Department of Chemistry, University of Chicago, Chicago, IL, USA.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.,University of Chicago Medical Scientist Training Program, Chicago, USA
| | - Chuan He
- Department of Chemistry, University of Chicago, Chicago, IL, USA. .,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. .,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA. .,Howard Hughes Medical Institute, University of Chicago, Chicago, IL, USA.
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46
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Oller‐Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non‐Canonical Amino Acids Using Orthogonal Ribosome‐Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Benjamí Oller‐Salvia
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
| | - Jason W. Chin
- Medical Research Council Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK
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47
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Vanmeert M, Razzokov J, Mirza MU, Weeks SD, Schepers G, Bogaerts A, Rozenski J, Froeyen M, Herdewijn P, Pinheiro VB, Lescrinier E. Rational design of an XNA ligase through docking of unbound nucleic acids to toroidal proteins. Nucleic Acids Res 2019; 47:7130-7142. [PMID: 31334814 PMCID: PMC6649754 DOI: 10.1093/nar/gkz551] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 05/24/2019] [Accepted: 06/12/2019] [Indexed: 02/06/2023] Open
Abstract
Xenobiotic nucleic acids (XNA) are nucleic acid analogues not present in nature that can be used for the storage of genetic information. In vivo XNA applications could be developed into novel biocontainment strategies, but are currently limited by the challenge of developing XNA processing enzymes such as polymerases, ligases and nucleases. Here, we present a structure-guided modelling-based strategy for the rational design of those enzymes essential for the development of XNA molecular biology. Docking of protein domains to unbound double-stranded nucleic acids is used to generate a first approximation of the extensive interaction of nucleic acid processing enzymes with their substrate. Molecular dynamics is used to optimise that prediction allowing, for the first time, the accurate prediction of how proteins that form toroidal complexes with nucleic acids interact with their substrate. Using the Chlorella virus DNA ligase as a proof of principle, we recapitulate the ligase's substrate specificity and successfully predict how to convert it into an XNA-templated XNA ligase.
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Affiliation(s)
- Michiel Vanmeert
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Jamoliddin Razzokov
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Muhammad Usman Mirza
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- Centre for Research in Molecular Medicine (CRiMM), University of Lahore, Pakistan
| | - Stephen D Weeks
- Biocrystallography, KU Leuven, Herestraat 49, box 822, 3000 Leuven, Belgium
| | - Guy Schepers
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Annemie Bogaerts
- Research group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Jef Rozenski
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Mathy Froeyen
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Piet Herdewijn
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
| | - Vitor B Pinheiro
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
- University College London, Department of Structural and Molecular Biology, Gower Street, London, WC1E 6BT, UK
| | - Eveline Lescrinier
- Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Herestraat 49, box 1041, 3000 Leuven, Belgium
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48
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Nucleic acid enzymes based on functionalized nucleosides. Curr Opin Chem Biol 2019; 52:93-101. [PMID: 31307007 DOI: 10.1016/j.cbpa.2019.06.007] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/28/2019] [Accepted: 06/06/2019] [Indexed: 12/29/2022]
Abstract
Nucleic acid-based enzymes have recently joined their proteinaceous counterparts as important biocatalysts. While RNA enzymes (ribozymes) are found in nature, deoxyribozymes or DNAzymes are man-made entities. Numerous ribozymes and DNAzymes have been identified by Darwinian selection methods to catalyze a broad array of chemical transformations. Despite these important advances, practical applications involving nucleic acid enzymes are often plagued by relatively poor pharmacokinetic properties and cellular uptake, rapid degradation by nucleases and/or by the limited chemical arsenal carried by natural DNA and RNA. In this review, the two main chemical approaches for the modification of nucleic acid-based catalysts, particularly DNAzymes, are described. These methods aim at improving the functional properties of nucleic acid enzymes by mitigating some of these shortcomings. In this context, recent developments in the post-SELEX processing of existing nucleic acid catalysts as well as efforts for the selection of DNAzymes and ribozymes with modified nucleoside triphosphates are summarized.
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49
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Oller-Salvia B, Chin JW. Efficient Phage Display with Multiple Distinct Non-Canonical Amino Acids Using Orthogonal Ribosome-Mediated Genetic Code Expansion. Angew Chem Int Ed Engl 2019; 58:10844-10848. [PMID: 31157495 PMCID: PMC6771915 DOI: 10.1002/anie.201902658] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Indexed: 11/10/2022]
Abstract
Phage display is a powerful approach for evolving proteins and peptides with new functions, but the properties of the molecules that can be evolved are limited by the chemical diversity encoded. Herein, we report a system for incorporating non-canonical amino acids (ncAAs) into proteins displayed on phage using the pyrrolysyl-tRNA synthetase/tRNA pair. We improve the efficiency of ncAA incorporation using an evolved orthogonal ribosome (riboQ1), and encode a cyclopropene-containing ncAA (CypK) at diverse sites on a displayed single-chain antibody variable fragment (ScFv), in response to amber and quadruplet codons. CypK and an alkyne-containing ncAA are incorporated at distinct sites, enabling the double labeling of ScFv with distinct probes, through mutually orthogonal reactions, in a one-pot procedure. These advances expand the number of functionalities that can be encoded on phage-displayed proteins and provide a foundation to further expand the scope of phage display applications.
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Affiliation(s)
- Benjamí Oller-Salvia
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jason W Chin
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
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50
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Taylor AI, Houlihan G, Holliger P. Beyond DNA and RNA: The Expanding Toolbox of Synthetic Genetics. Cold Spring Harb Perspect Biol 2019; 11:11/6/a032490. [PMID: 31160351 DOI: 10.1101/cshperspect.a032490] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The remarkable physicochemical properties of the natural nucleic acids, DNA and RNA, define modern biology at the molecular level and are widely believed to have been central to life's origins. However, their ability to form repositories of information as well as functional structures such as ligands (aptamers) and catalysts (ribozymes/DNAzymes) is not unique. A range of nonnatural alternatives, collectively termed xeno nucleic acids (XNAs), are also capable of supporting genetic information storage and propagation as well as evolution. This gives rise to a new field of "synthetic genetics," which seeks to expand the nucleic acid chemical toolbox for applications in both biotechnology and molecular medicine. In this review, we outline XNA polymerase and reverse transcriptase engineering as a key enabling technology and summarize the application of "synthetic genetics" to the development of aptamers, enzymes, and nanostructures.
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Affiliation(s)
- Alexander I Taylor
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Gillian Houlihan
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Philipp Holliger
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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