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Laatri S, El Khayari S, Qriouet Z. Exploring the molecular aspect and updating evolutionary approaches to the DNA polymerase enzymes for biotechnological needs: A comprehensive review. Int J Biol Macromol 2024; 276:133924. [PMID: 39033894 DOI: 10.1016/j.ijbiomac.2024.133924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 07/07/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024]
Abstract
DNA polymerases are essential enzymes that play a key role in living organisms, as they participate in the synthesis and maintenance of the DNA molecule. The intrinsic properties of these enzymes have been widely observed and studied to understand their functions, activities, and behavior, which has allowed their natural power in DNA synthesis to be exploited in modern biotechnology, to the point of making them true pillars of the field. In this context, the laboratory evolution of these enzymes, either by directed evolution or rational design, has led to the generation of a wide range of new DNA polymerases with novel properties, suitable for a variety of biotechnological needs. In this review, we examine DNA polymerases at the molecular level, their biotechnological use, and their evolutionary methods in relation to the novel properties sought, providing a chronological selection of evolved DNA polymerases cited in the literature that we consider to be of great interest. To our knowledge, this work is the first to bring together the molecular, functional and evolutionary aspects of the DNA polymerase enzyme. We believe it will be of great interest to researchers whose aim is to produce new lines of evolved DNA polymerases.
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Affiliation(s)
- Said Laatri
- Microbiology and Molecular Biology Laboratory, Faculty of Sciences, Mohammed V-Souissi University, Rabat 10100, Morocco.
| | | | - Zidane Qriouet
- Pharmacology and Toxicology Laboratory, Faculty of Medicine and Pharmacy, Mohammed V-Souissi University, Rabat 10100, Morocco
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2
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Hriňová K, Dlapová J, Kubala B, Kormanová Ľ, Levarski Z, Struhárňanská E, Turňa J, Stuchlík S. Production of Reverse Transcriptase and DNA Polymerase in Bacterial Expression Systems. Bioengineering (Basel) 2024; 11:727. [PMID: 39061809 PMCID: PMC11274053 DOI: 10.3390/bioengineering11070727] [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: 06/03/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
DNA amplification and reverse transcription enzymes have proven to be invaluable in fast and reliable diagnostics and research applications because of their processivity, specificity, and robustness. Our study focused on the production of mutant Taq DNA polymerase and mutant M-MLV reverse transcriptase in the expression hosts Vibrio natriegens and Escherichia coli under various expression conditions. We also examined nonspecific extracellular production in V. natriegens. Intracellularly, M-MLV was produced in V. natriegens at the level of 11% of the total cell proteins (TCPs) compared with 16% of TCPs in E. coli. We obtained a soluble protein that accounted for 11% of the enzyme produced in V. natriegens and 22% of the enzyme produced in E. coli. Taq pol was produced intracellularly in V. natriegens at the level of 30% of TCPs compared with 26% of TCPs in E. coli. However, Taq pol was almost non-soluble in E. coli, whereas in V. natriegens, we obtained a soluble protein that accounted for 23% of the produced enzyme. We detected substantial extracellular production of Taq pol. Thus, V. natriegens is a suitable alternative host with the potential for production of recombinant proteins.
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Affiliation(s)
- Kristína Hriňová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
| | - Johana Dlapová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
| | - Bohuš Kubala
- Laboratory for Microbial Ecology, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 84551 Bratislava, Slovakia;
| | - Ľubica Kormanová
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
| | - Zdenko Levarski
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
- Science Park, Comenius University in Bratislava, 84104 Bratislava, Slovakia
- ReKoMBe, s.r.o., 84102 Bratislava, Slovakia
| | - Eva Struhárňanská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
- ReKoMBe, s.r.o., 84102 Bratislava, Slovakia
| | - Ján Turňa
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
- Science Park, Comenius University in Bratislava, 84104 Bratislava, Slovakia
- ReKoMBe, s.r.o., 84102 Bratislava, Slovakia
| | - Stanislav Stuchlík
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University in Bratislava, 84215 Bratislava, Slovakia; (K.H.); (J.D.); (Ľ.K.); (E.S.); (J.T.); (S.S.)
- Science Park, Comenius University in Bratislava, 84104 Bratislava, Slovakia
- ReKoMBe, s.r.o., 84102 Bratislava, Slovakia
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3
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Nuryana I, Laksmi FA, Dewi KS, Akbar FR, Nurhayati, Harmoko R. Codon optimization of a gene encoding DNA polymerase from Pyrococcus furiosus and its expression in Escherichia coli. J Genet Eng Biotechnol 2023; 21:129. [PMID: 37987973 PMCID: PMC10663413 DOI: 10.1186/s43141-023-00605-7] [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: 05/03/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND DNA polymerase is an essential component in PCR assay for DNA synthesis. Improving DNA polymerase with characteristics indispensable for a powerful assay is crucial because it can be used in wide-range applications. Derived from Pyrococcus furiosus, Pfu DNA polymerase (Pfu pol) is one of the excellent polymerases due to its high fidelity. Therefore, we aimed to develop Pfu pol from a synthetic gene with codon optimization to increase its protein yield in Escherichia coli. RESULTS Recombinant Pfu pol was successfully expressed and purified with a two-step purification process using nickel affinity chromatography, followed by anion exchange chromatography. Subsequently, the purified Pfu pol was confirmed by Western blot analysis, resulting in a molecular weight of approximately 90 kDa. In the final purification process, we successfully obtained a large amount of purified enzyme (26.8 mg/L). Furthermore, the purified Pfu pol showed its functionality and efficiency when tested for DNA amplification using the standard PCR. CONCLUSIONS Overall, a high-level expression of recombinant Pfu pol was achieved by employing our approach in the present study. In the future, our findings will be useful for studies on synthesizing recombinant DNA polymerase in E. coli expression system.
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Affiliation(s)
- Isa Nuryana
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Fina Amreta Laksmi
- Research Center for Applied Microbiology, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia.
| | - Kartika Sari Dewi
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
| | - Faiz Raihan Akbar
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Nurhayati
- Department of Biology, Faculty of Sciences and Mathematics, Universitas Diponegoro, Jalan Prof Soedarto, SH, Kampus UNDIP Tembalang, Semarang, 50275, Indonesia
| | - Rikno Harmoko
- Research Center for Genetic Engineering, National Research and Innovation Agency, Jalan Raya Bogor Km 46, Cibinong, Bogor, 16911, Indonesia
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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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5
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Li X, Chen B, Chen W, Pu Z, Qi X, Yang L, Wu J, Yu H. Customized multiple sequence alignment as an effective strategy to improve performance of Taq DNA polymerase. Appl Microbiol Biotechnol 2023; 107:6507-6525. [PMID: 37658164 DOI: 10.1007/s00253-023-12744-5] [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: 04/13/2023] [Revised: 08/06/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023]
Abstract
Engineering Taq DNA polymerase (TaqPol) for improved activity, stability and sensitivity was critical for its wide applications. Multiple sequence alignment (MSA) has been widely used in engineering enzymes for improved properties. Here, we first designed TaqPol mutations based on MSA of 2756 sequences from both thermophilic and non-thermophilic organisms. Two double mutations were generated including a variant H676F/R677G showing a decrease in both activity and stability, and a variant Y686R/E687K showing an improved activity, but a decreased stability. Mutations targeted on coevolutionary residues of Arg677 and Tyr686 were then applied to rescue stability or activity loss of the double mutants, which achieved a partial success. Sequence analysis revealed that the two mutations are abundant in non-thermophilic sequences but not in thermophilic homologues. Then, a small-scale MSA containing sequences from only thermophilic organisms was applied to predict 13 single variants and two of them, E507Q and E734N showed a simultaneous increase in both stability and activity, even in sensitivity. A customized MSA was hence more effective in engineering a thermophilic enzyme and could be used in engineering other enzymes. Molecular dynamics simulations revealed the impact of mutations on the protein dynamics and interactions between TaqPol and substrates. KEY POINTS: • The pool of sequence for alignment is critical to engineering Taq DNA polymerase. • The variants with low properties can be rescued by mutations in coevolving network. • Improving binding with DNA can improve DNA polymerase stability and activity.
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Affiliation(s)
- Xinjia Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Binbin Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Wanyi Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Zhongji Pu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Xin Qi
- Building No.4, Zhongguancun Dongsheng International Science Park, No. 1 North Yongtaizhuang Road, Haidian District, Beijing, 100192, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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6
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Kormanová Ľ, Levarski Z, Minich A, Varga V, Levarská L, Struhárňanská E, Turňa J, Stuchlík S. Novel expression system based on enhanced permeability of Vibrio natriegens cells induced by D,D- carboxypeptidase overexpression. World J Microbiol Biotechnol 2023; 39:277. [PMID: 37568013 PMCID: PMC10421817 DOI: 10.1007/s11274-023-03723-z] [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: 02/02/2023] [Accepted: 08/06/2023] [Indexed: 08/13/2023]
Abstract
Vibrio natriegens is a fast-growing, non-pathogenic marine bacterium with promising features for biotechnological applications such as high-level recombinant protein production or fast DNA propagation. A remarkable short generation time (< 10 min), robust proteosynthetic activity and versatile metabolism with abilities to utilise wide range of substrates contribute to its establishment as a future industrial platform for fermentation processes operating with high productivity.D,D-carboxypeptidases are membrane-associated enzymes involved in peptidoglycan biosynthesis and cell wall formation. This study investigates the impact of overexpressed D,D-carboxypeptidases on membrane integrity and the increased leakage of intracellular proteins into the growth medium in V. natriegens. Our findings confirm that co-expression of these enzymes can enhance membrane permeability, thereby facilitating the transport of target proteins into the extracellular environment, without the need for secretion signals, tags, or additional permeabilization methods. Using only a single step IMAC chromatography, we were able to purify AfKatG, MDBP or Taq polymerase in total yields of 117.9 ± 56.0 mg/L, 36.5 ± 12.9 mg/L and 26.5 ± 6.0 mg/L directly from growth medium, respectively. These results demonstrate the feasibility of our V. natriegens based system as a broadly applicable extracellular tag-less recombinant protein producer.
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Affiliation(s)
- Ľubica Kormanová
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
| | - Zdenko Levarski
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
- Science Park, Comenius University in Bratislava, Ilkovičova 8, Bratislava, 811 04 Slovak Republic
| | - Andrej Minich
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
| | - Viktor Varga
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
| | - Lenka Levarská
- Science Park, Comenius University in Bratislava, Ilkovičova 8, Bratislava, 811 04 Slovak Republic
| | - Eva Struhárňanská
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
| | - Ján Turňa
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
| | - Stanislav Stuchlík
- Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, Bratislava, 811 04 Slovak Republic
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Lee SJ, Park SY, Lee KH, Lee MW, Yu CY, Maeng J, Kim HD, Kim SW. Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase. Int J Mol Sci 2023; 24:11405. [PMID: 37511160 PMCID: PMC10379934 DOI: 10.3390/ijms241411405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Taq DNA polymerases have played an important role in molecular biology for several years and are frequently used for polymerase chain reaction (PCR); hence, there is an increasing interest in developing a convenient method for preparing Taq DNA polymerase for routine use in laboratories. We developed a method using Escherichia coli (E. coli) that expresses thermostable Taq DNA polymerase directly in the PCR without purification. The Taq gene was transformed into E. coli and expressed. After overnight incubation and washing, E. coli-expressing Taq DNA polymerase (EcoliTaq) was used as the DNA polymerase without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. With a high-pH buffer containing 2% Tween 20 and 0.4 M trehalose, EcoliTaq facilitated direct PCR amplification from anticoagulated whole blood samples. EcoliTaq exhibited good performance in allele-specific PCR using both purified DNA and whole blood samples. Furthermore, it proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification. We developed a simple and cost-effective direct and hot-start PCR method in which EcoliTaq was used directly as a PCR enzyme, thus eliminating the laborious and time-consuming steps of polymerase purification.
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Affiliation(s)
- Sun Ju Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Sang-Yong Park
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Kwang-Ho Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, ASAN Medical Center, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Min-Woo Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Chae-Yeon Yu
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Jaeyoung Maeng
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Hyeong-Dong Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Suhng Wook Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
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8
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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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9
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Kesici MZ, Tinnefeld P, Vera AM. A simple and general approach to generate photoactivatable DNA processing enzymes. Nucleic Acids Res 2021; 50:e31. [PMID: 34904657 PMCID: PMC8989547 DOI: 10.1093/nar/gkab1212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/08/2021] [Accepted: 11/25/2021] [Indexed: 11/29/2022] Open
Abstract
DNA processing enzymes, such as DNA polymerases and endonucleases, have found many applications in biotechnology, molecular diagnostics, and synthetic biology, among others. The development of enzymes with controllable activity, such as hot-start or light-activatable versions, has boosted their applications and improved the sensitivity and specificity of the existing ones. However, current approaches to produce controllable enzymes are experimentally demanding to develop and case-specific. Here, we introduce a simple and general method to design light-start DNA processing enzymes. In order to prove its versatility, we applied our method to three DNA polymerases commonly used in biotechnology, including the Phi29 (mesophilic), Taq, and Pfu polymerases, and one restriction enzyme. Light-start enzymes showed suppressed polymerase, exonuclease, and endonuclease activity until they were re-activated by an UV pulse. Finally, we applied our enzymes to common molecular biology assays and showed comparable performance to commercial hot-start enzymes.
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Affiliation(s)
- Merve-Zeynep Kesici
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München 81377, Germany
| | - Philip Tinnefeld
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München 81377, Germany
| | - Andrés Manuel Vera
- Department of Chemistry and Center for NanoScience, Ludwig-Maximilians-Universität München, München 81377, Germany
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10
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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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11
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Barnes WM, Zhang Z, Kermekchiev MB. A Single Amino Acid Change to Taq DNA Polymerase Enables Faster PCR, Reverse Transcription and Strand-Displacement. Front Bioeng Biotechnol 2021; 8:553474. [PMID: 33520948 PMCID: PMC7841393 DOI: 10.3389/fbioe.2020.553474] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
A change of an aspartic acid to asparagine of Taq (Thermus aquaticus) DNA polymerase is a gain of function mutation that supports faster PCR: the extension times for PCR amplification can be 2-3 times shorter. Surprising results from negative controls led to the discovery of strand-displacement ability and reverse transcriptase activity of Taq D732N DNA polymerase. We demonstrate that the mutant enzyme can, by itself, catalyze RT-PCR, and RT-LAMP assays. Residue 732 is on the surface of the enzyme, not near the active site.
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Affiliation(s)
- Wayne M Barnes
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, United States.,DNA Polymerase Technology, Inc., St. Louis, MO, United States
| | - Zhian Zhang
- DNA Polymerase Technology, Inc., St. Louis, MO, United States
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12
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. The influence of quality of primers on the formation of primer dimers in PCR. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1251-1269. [PMID: 32799617 DOI: 10.1080/15257770.2020.1803354] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Polymerase chain reaction (PCR) is the most commonly used method for nucleic acids amplification. PCR performance depends on several causes, among which the quality of primers is one of the main determinants affecting specificity, sensitivity and reliability of the reaction. Here, we report on the results of the detailed study devoted to the dimerization of the primers during PCR. The course and specificity of the reaction were studied on the model DNA templates as well as genomic DNA using primers that form amplifiable heterodimeric structures with different thermodynamic stability. It was confirmed that more than two 3'-overlapping nucleotides cause a considerable accumulation of primer dimers. It turned out that the presence of any DNA promotes the formation of dimers even for primers, which do not tend to nonspecific amplification in the absence of DNA. It was shown that dimerization could not be eliminated by commonly used techniques. Even the use of hot-start DNA polymerases does not prevent PD formation if primers with stable 3'-overlapping are employed. Despite several advantages of PCR with abutting primers, their close disposition has no benefits regarding the formation of PD if low-quality primers are utilized.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Aizilya A Galimova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences, Ufa, Bashkortostan, Russia
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13
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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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14
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Spyrydonov V, Pihida D, Sereda A, Likhanov A, Yu W. Production and evaluation of egg derived hot start antibodies. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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15
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Yang Z, Le JT, Hutter D, Bradley KM, Overton BR, McLendon C, Benner SA. Eliminating primer dimers and improving SNP detection using self-avoiding molecular recognition systems. Biol Methods Protoc 2020; 5:bpaa004. [PMID: 32395633 PMCID: PMC7200914 DOI: 10.1093/biomethods/bpaa004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/25/2023] Open
Abstract
Despite its widespread value to molecular biology, the polymerase chain reaction (PCR) encounters modes that unproductively consume PCR resources and prevent clean signals, especially when high sensitivity, high SNP discrimination, and high multiplexing are sought. Here, we show how "self-avoiding molecular recognition systems" (SAMRS) manage such difficulties. SAMRS nucleobases pair with complementary nucleotides with strengths comparable to the A:T pair, but do not pair with other SAMRS nucleobases. This should allow primers holding SAMRS components to avoid primer-primer interactions, preventing primer dimers, allowing more sensitive SNP detection, and supporting higher levels of multiplex PCR. The experiments here examine the PCR performances of primers containing different numbers of SAMRS components placed strategically at different positions, and put these performances in the context of estimates of SAMRS:standard pairing strengths. The impact of these variables on primer dimer formation, the overall efficiency and sensitivity of SAMRS-based PCR, and the value of SAMRS primers when detecting single nucleotide polymorphisms (SNPs) are also evaluated. With appropriately chosen polymerases, SNP discrimination can be greater than the conventional allele-specific PCR, with the further benefit of avoiding primer dimer artifacts. General rules guiding the design of SAMRS-modified primers are offered to support medical research and clinical diagnostics products.
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Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jennifer T Le
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Daniel Hutter
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Benjamin R Overton
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Blvd, Box 7, Alachua, FL 32615, USA
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
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16
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Direct S-Poly(T) Plus assay in quantification of microRNAs without RNA extraction and its implications in colorectal cancer biomarker studies. J Transl Med 2019; 17:316. [PMID: 31547825 PMCID: PMC6757382 DOI: 10.1186/s12967-019-2061-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Advances in microRNAs (miRNAs) biomarkers have generated disease markers with potential clinical values. However, none of these published results have been applied in clinic until today. The main reason could be the lack of simple but robust miRNA measurements. METHODS We built up a simple but ultrasensitive RT-qPCR protocol, Direct S-Poly(T) Plus assay, for detecting miRNAs without RNA purification. In this study, the method was optimized and compared with other RNA purification-based miRNA assays, and the sensitivity was tested. Using Direct S-Poly(T) Plus method, seven potential miRNA biomarkers of colorectal cancer were validated. RESULTS It is possible to detect approximately 100 miRNAs with minimal plasma inputs (20 μl) and time (~ 140 min) with this approach. The sensitivity of this method was 2.7-343-fold higher than that of the stem-loop method, and comparable with S-Poly(T) plus method. 7 validated miRNA biomarkers of colorectal cancer by Direct S-Poly(T) plus assay could discriminate colorectal cancer stage I from healthy individuals, and promised satisfactory discrimination with the area under receiver operating characteristic (ROC) curve ranging from 0.79 to 0.94 (p value < 0.001). CONCLUSIONS This simple and robust protocol may have strong impact on the development of specific miRNAs as biomarkers in clinic.
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17
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Engineering Polymerases for New Functions. Trends Biotechnol 2019; 37:1091-1103. [PMID: 31003719 DOI: 10.1016/j.tibtech.2019.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/08/2019] [Accepted: 03/19/2019] [Indexed: 01/04/2023]
Abstract
DNA polymerases are critical tools in biotechnology, enabling efficient and accurate amplification of DNA templates, yet many desired functions are not readily available in natural DNA polymerases. New or improved functions can be engineered in DNA polymerases by mutagenesis or through the creation of protein chimeras. Engineering often necessitates the development of new techniques, such as selections in water-in-oil emulsions that connect genotype to phenotype and allow more flexibility in engineering than phage display. Engineering efforts have led to DNA polymerases that can withstand extreme conditions or the presence of inhibitors, as well as polymerases with the ability to copy modified DNA templates. In this review we discuss polymerases for biotechnology that have been reported along with tools to enable further development.
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18
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Modeste E, Mawby L, Miller B, Wu E, Parish CA. A Molecular Dynamics Investigation of the Thermostability of Cold-Sensitive I707L KlenTaq1 DNA Polymerase and Its Wild-Type Counterpart. J Chem Inf Model 2019; 59:2423-2431. [PMID: 30897332 DOI: 10.1021/acs.jcim.9b00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA polymerase I from Thermus aquaticus ( Taq DNA polymerase) is useful for polymerase chain reactions because of its exceptional thermostability; however, its activity at low temperatures can cause amplification of unintended products. Mutation of isoleucine 707 to leucine (I707L) slows Taq DNA polymerase at low temperatures, which decreases unwanted amplification due to mispriming. In this work, unrestrained molecular dynamics (MD) simulations were performed on I707L and wild-type (WT) Taq DNA polymerase at 341 and 298 K to determine how the mutation affects the dynamic nature of the protein. The results suggest that I707L Taq DNA polymerase remains relatively immobile at room temperature and becomes more flexible at the higher temperature, while the WT Taq DNA polymerase demonstrates less substantial differences in dynamics at high and low temperatures. These results are in agreement with previous experimental results on the I707L mutant Taq DNA polymerase that show dynamic differences at high and low temperatures. The decreased mobility of the mutant at low temperature suggests that the mutant remains longer in the blocked conformation, and this may lead to reduced activity relative to the WT at 298 K. Principal component analysis revealed that the mutation results in decoupled movements of the Q helix and fingers domain. This decoupled nature of the mutant gives way to an increasingly flexible N-terminal end of the Q helix at 341 K, a characteristic not seen for WT Taq DNA polymerase.
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Affiliation(s)
- Erica Modeste
- Department of Chemistry, Gottwald Center for the Sciences , University of Richmond , Richmond , Virginia 23713 , United States
| | - Lily Mawby
- Department of Chemistry, Gottwald Center for the Sciences , University of Richmond , Richmond , Virginia 23713 , United States
| | - Bill Miller
- Department of Chemistry , Truman State University , Kirksville , Missouri 63501 , United States
| | - Eugene Wu
- Department of Biology, Gottwald Center for the Sciences , University of Richmond , Richmond , Virginia 23713 , United States
| | - Carol A Parish
- Department of Chemistry, Gottwald Center for the Sciences , University of Richmond , Richmond , Virginia 23713 , United States
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19
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Identification of Thermus aquaticus DNA polymerase variants with increased mismatch discrimination and reverse transcriptase activity from a smart enzyme mutant library. Sci Rep 2019; 9:590. [PMID: 30679705 PMCID: PMC6345897 DOI: 10.1038/s41598-018-37233-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 12/02/2018] [Indexed: 12/13/2022] Open
Abstract
DNA polymerases the key enzymes for several biotechnological applications. Obviously, nature has not evolved these enzymes to be compatible with applications in biotechnology. Thus, engineering of a natural scaffold of DNA polymerases may lead to enzymes improved for several applications. Here, we investigated a two-step approach for the design and construction of a combinatorial library of mutants of KlenTaq DNA polymerase. First, we selected amino acid sites for saturation mutagenesis that interact with the primer/template strands or are evolutionarily conserved. From this library, we identified mutations that little interfere with DNA polymerase activity. Next, these functionally active mutants were combined randomly to construct a second library with enriched sequence diversity. We reasoned that the combination of mutants that have minuscule effect on enzyme activity and thermostability, will result in entities that have an increased mutation load but still retain activity. Besides activity and thermostability, we screened the library for entities with two distinct properties. Indeed, we identified two different KlenTaq DNA polymerase variants that either exhibit increased mismatch extension discrimination or increased reverse transcription PCR activity, respectively.
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20
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Jiang W, Yue S, He S, Chen C, Liu S, Jiang H, Tong H, Liu X, Wang J, Zhang F, Sun H, Li M, Wang C. New design of probe and central-homo primer pairs to improve TaqMan™ PCR accuracy for HBV detection. J Virol Methods 2018; 254:25-30. [PMID: 29407210 DOI: 10.1016/j.jviromet.2018.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 01/22/2018] [Accepted: 01/22/2018] [Indexed: 01/03/2023]
Abstract
Quantitative PCR (qPCR) assay using TaqMan™ probe was widely used in the detection of different nucleic acids. However, this technology has several drawbacks, including false negative results caused by primer-dimer (PD) and false positive issues due to primer-probe aggregations. Here, we designed a modified TaqMan™-Molecular Beacon probe by adding an antisense base and a new type of primer pair named central-homo primer pairs bearing 5-10 bases homologous sequence on the 3' end. Using the HBV qPCR assay as a proof of concept, the new design significantly improved the accuracy of the TaqMan™ qPCR assay for HBV detection. Application of the central-homo primer pair led to significantly delayed Ct values by 5-10 cycles compared with conventional primer design. The modified probe containing an antisense base did not produce any detectable signal in repeating primer-probe aggregation experiments. Furthermore, the use of the central-homo primer pair and the non-competitive internal control could solve the false negative problem caused by PD formation. We validated this customized duplex qPCR system using 208 clinical samples collected from patients in clinic showing accuracy was higher than that of the conventional qPCR method.
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Affiliation(s)
- Wencan Jiang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Suwen Yue
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Shang He
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chen Chen
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Shanshan Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Hong Jiang
- Beijing Tag Array Molecular Test Co., Ltd, Beijing 100085, People's Republic of China
| | - Hongli Tong
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Xiaoting Liu
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Jianan Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China; College of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Fan Zhang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Huizhen Sun
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Mianyang Li
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China
| | - Chengbin Wang
- Department of Clinical Laboratory Medicine, Chinese PLA General Hospital & Chinese PLA Medical School, Beijing 100853, People's Republic of China.
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21
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Aye SL, Fujiwara K, Ueki A, Doi N. Engineering of DNA polymerase I from Thermus thermophilus using compartmentalized self-replication. Biochem Biophys Res Commun 2018; 499:170-176. [PMID: 29550479 DOI: 10.1016/j.bbrc.2018.03.098] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 03/13/2018] [Indexed: 11/30/2022]
Abstract
Although compartmentalized self-replication (CSR) and compartmentalized partnered replication (CPR) are powerful tools for directed evolution of proteins and gene circuits, limitations remain in the emulsion PCR process with the wild-type Taq DNA polymerase used so far, including long run times, low amounts of product, and false negative results due to inhibitors. In this study, we developed a high-efficiency mutant of DNA polymerase I from Thermus thermophilus HB27 (Tth pol) suited for CSR and CPR. We modified the wild-type Tth pol by (i) deletion of the N-terminal 5' to 3' exonuclease domain, (ii) fusion with the DNA-binding protein Sso7d, (iii) introduction of four known effective point mutations from other DNA polymerase mutants, and (iv) codon optimization to reduce the GC content. Consequently, we obtained a mutant that provides higher product yields than the conventional Taq pol without decreased fidelity. Next, we performed four rounds of CSR selection with a randomly mutated library of this modified Tth pol and obtained mutants that provide higher product yields in fewer cycles of emulsion PCR than the parent Tth pol as well as the conventional Taq pol.
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Affiliation(s)
- Seaim Lwin Aye
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Kei Fujiwara
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Asuka Ueki
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan
| | - Nobuhide Doi
- Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Yokohama 223-8522, Japan.
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22
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Marciano MA, Panicker SX, Liddil GD, Lindgren D, Sweder KS. Development of a Method to Extract Opium Poppy (Papaver somniferum L.) DNA from Heroin. Sci Rep 2018; 8:2590. [PMID: 29416103 PMCID: PMC5803222 DOI: 10.1038/s41598-018-20996-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/29/2018] [Indexed: 01/03/2023] Open
Abstract
This study is the first to report the successful development of a method to extract opium poppy (Papaver somniferum L.) DNA from heroin samples. Determining of the source of an unknown heroin sample (forensic geosourcing) is vital to informing domestic and foreign policy related to counter-narcoterrorism. Current profiling methods focus on identifying process-related chemical impurities found in heroin samples. Changes to the geographically distinct processing methods may lead to difficulties in classifying and attributing heroin samples to a region/country. This study focuses on methods to optimize the DNA extraction and amplification of samples with low levels of degraded DNA and inhibiting compounds such as heroin. We compared modified commercial-off-the-shelf extraction methods such as the Qiagen Plant, Stool and the Promega Maxwell-16 RNA-LEV tissue kits for the ability to extract opium poppy DNA from latex, raw and cooked opium, white and brown powder heroin and black tar heroin. Opium poppy DNA was successfully detected in all poppy-derived samples, including heroin. The modified Qiagen stool method with post-extraction purification and a two-stage, dual DNA polymerase amplification procedure resulted in the highest DNA yield and minimized inhibition. This paper describes the initial phase in establishing a DNA-based signature method to characterize heroin.
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Affiliation(s)
- Michael A Marciano
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA.
| | - Sini X Panicker
- U.S. Drug Enforcement Administration, Special Testing and Research Laboratory, Dulles, VA, 20166, USA
| | - Garrett D Liddil
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
| | - Danielle Lindgren
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
| | - Kevin S Sweder
- Forensic & National Security Sciences Institute, Syracuse University, Syracuse, New York, 13244, USA
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23
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DNA polymerases and biotechnological applications. Curr Opin Biotechnol 2017; 48:187-195. [PMID: 28618333 DOI: 10.1016/j.copbio.2017.04.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 04/17/2017] [Indexed: 01/04/2023]
Abstract
A multitude of biotechnological techniques used in basic research as well as in clinical diagnostics on an everyday basis depend on DNA polymerases and their intrinsic capability to replicate DNA strands with astoundingly high fidelity. Applications with fundamental importance to modern molecular biology, including the polymerase chain reaction and DNA sequencing, would not be feasible without the advances made in characterizing these enzymes over the course of the last 60 years. Nonetheless, the still growing application scope of DNA polymerases necessitates the identification of novel enzymes with tailor-made properties. In the recent past, DNA polymerases optimized for diverse PCR and sequencing applications as well as enzymes that accept a variety of unnatural substrates for the synthesis and reverse transcription of modified nucleic acids have been developed.
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24
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Rosenblum SL, Weiden AG, Lewis EL, Ogonowsky AL, Chia HE, Barrett SE, Liu MD, Leconte AM. Design and Discovery of New Combinations of Mutant DNA Polymerases and Modified DNA Substrates. Chembiochem 2017; 18:816-823. [PMID: 28160372 DOI: 10.1002/cbic.201600701] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Indexed: 11/06/2022]
Abstract
Chemical modifications can enhance the properties of DNA by imparting nuclease resistance and generating more-diverse physical structures. However, native DNA polymerases generally cannot synthesize significant lengths of DNA with modified nucleotide triphosphates. Previous efforts have identified a mutant of DNA polymerase I from Thermus aquaticus DNA (SFM19) as capable of synthesizing a range of short, 2'-modified DNAs; however, it is limited in the length of the products it can synthesize. Here, we rationally designed and characterized ten mutants of SFM19. From this, we identified enzymes with substantially improved activity for the synthesis of 2'F-, 2'OH-, 2'OMe-, and 3'OMe-modified DNA as well as for reverse transcription of 2'OMe DNA. We also evaluated mutant DNA polymerases previously only tested for synthesis for 2'OMe DNA and showed that they are capable of an expanded range of modified DNA synthesis. This work significantly expands the known combinations of modified DNA and Taq DNA polymerase mutants.
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Affiliation(s)
- Sydney L Rosenblum
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aurora G Weiden
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Eliza L Lewis
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Alexie L Ogonowsky
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Hannah E Chia
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Susanna E Barrett
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Mira D Liu
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
| | - Aaron M Leconte
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA, 91711, USA
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25
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Schoenbrunner NJ, Gupta AP, Young KKY, Will SG. Covalent modification of primers improves PCR amplification specificity and yield. Biol Methods Protoc 2017; 2:bpx011. [PMID: 32161793 PMCID: PMC6994073 DOI: 10.1093/biomethods/bpx011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 05/31/2017] [Accepted: 11/09/2017] [Indexed: 01/01/2023] Open
Abstract
We report a method for covalent modification of primers that enhances the specificity of PCR and increases the yield of specific amplification products at the end of PCR. The introduction of thermally stable covalent modifications, such as alkyl groups to the exocyclic amines of deoxyadenosine or cytosine residues at the 3'-ends of primers results in enhanced specificity of reactions. This higher specificity can result in greater sensitivity of detection by reducing competition with non-productive reactions. The reduction in the amplification of unintended byproducts is most apparent when both primers are modified at their respective 3'-ends. The T Ms of such modified primers are only slightly affected by the inclusion of these modifiers. The principal mode of action is believed to be driven by the poor enzyme extension of substrates with closely juxtaposed bulky alkyl groups, such as would result from the replication of primer dimer artifact.
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Affiliation(s)
| | | | | | - Stephen G Will
- Research Department, Roche Molecular Systems, Inc., 4300 Hacienda Drive, Pleasanton, CA 94588, USA
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26
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Su SH, Krysan PJ. A double-mutant collection targeting MAP kinase related genes in Arabidopsis for studying genetic interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:867-878. [PMID: 27490954 DOI: 10.1111/tpj.13292] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 07/17/2016] [Accepted: 08/01/2016] [Indexed: 06/06/2023]
Abstract
Mitogen-activated protein kinase cascades are conserved in all eukaryotes. In Arabidopsis thaliana there are approximately 80 genes encoding MAP kinase kinase kinases (MAP3K), 10 genes encoding MAP kinase kinases (MAP2K), and 20 genes encoding MAP kinases (MAPK). Reverse genetic analysis has failed to reveal abnormal phenotypes for a majority of these genes. One strategy for uncovering gene function when single-mutant lines do not produce an informative phenotype is to perform a systematic genetic interaction screen whereby double-mutants are created from a large library of single-mutant lines. Here we describe a new collection of 275 double-mutant lines derived from a library of single-mutants targeting genes related to MAP kinase signaling. To facilitate this study, we developed a high-throughput double-mutant generating pipeline using a system for growing Arabidopsis seedlings in 96-well plates. A quantitative root growth assay was used to screen for evidence of genetic interactions in this double-mutant collection. Our screen revealed four genetic interactions, all of which caused synthetic enhancement of the root growth defects observed in a MAP kinase 4 (MPK4) single-mutant line. Seeds for this double-mutant collection are publicly available through the Arabidopsis Biological Resource Center. Scientists interested in diverse biological processes can now screen this double-mutant collection under a wide range of growth conditions in order to search for additional genetic interactions that may provide new insights into MAP kinase signaling.
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Affiliation(s)
- Shih-Heng Su
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Patrick J Krysan
- Horticulture Department and Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA
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Abstract
Cold-sensitive phenotypes have helped us understand macromolecular assembly and biological phenomena, yet few attempts have been made to understand the basis of cold sensitivity or to elicit it by design. We report a method for rational design of cold-sensitive phenotypes. The method involves generation of partial loss-of-function mutants, at either buried or functional sites, coupled with selective overexpression strategies. The only essential input is amino acid sequence, although available structural information can be used as well. The method has been used to elicit cold-sensitive mutants of a variety of proteins, both monomeric and dimeric, and in multiple organisms, namely Escherichia coli, Saccharomyces cerevisiae, and Drosophila melanogaster This simple, yet effective technique of inducing cold sensitivity eliminates the need for complex mutations and provides a plausible molecular mechanism for eliciting cold-sensitive phenotypes.
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Yamagami T, Matsukawa H, Tsunekawa S, Kawarabayasi Y, Ishino S, Ishino Y. A longer finger-subdomain of family A DNA polymerases found by metagenomic analysis strengthens DNA binding and primer extension abilities. Gene 2015; 576:690-5. [PMID: 26476294 DOI: 10.1016/j.gene.2015.10.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The family A DNA polymerases from thermophilic bacteria are useful for PCR. The DNA polymerase from Thermus aquaticus (Taq polymerase) was the original enzyme used when practical PCR was developed, and it has remained the standard enzyme for PCR to date. Knowledge gained from structure-function relationship studies of Taq polymerase is applicable to create PCR enzymes with enhanced performance. We collected the deduced amino acid sequences of the regions from motif A to motif C in the family A DNA polymerases from metagenomic sequence data, obtained by sequencing DNAs from microorganisms isolated from various hot spring areas in Japan. The corresponding regions of the polA gene for Taq polymerase were substituted with the metagenomic DNA gene fragments, and various chimeric DNA polymerases were prepared. Based on the properties of these chimeric enzymes and their sequences, we found an insertion sequence that affects the primer extension ability of the family A DNA polymerases. The insertion sequence is located in the finger subdomain, and it may enhance the affinity of the enzyme to DNA. Mutant Taq polymerases with the corresponding 9 amino acid insertion displayed enhanced PCR performance.
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Affiliation(s)
- Takeshi Yamagami
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan
| | - Hiroaki Matsukawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Sae Tsunekawa
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yutaka Kawarabayasi
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan.
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan; JST, CREST, Tokyo, Japan.
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Schultz HJ, Gochi AM, Chia HE, Ogonowsky AL, Chiang S, Filipovic N, Weiden AG, Hadley EE, Gabriel SE, Leconte AM. Taq DNA Polymerase Mutants and 2'-Modified Sugar Recognition. Biochemistry 2015; 54:5999-6008. [PMID: 26334839 DOI: 10.1021/acs.biochem.5b00689] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical modifications to DNA, such as 2' modifications, are expected to increase the biotechnological utility of DNA; however, these modified forms of DNA are limited by their inability to be effectively synthesized by DNA polymerase enzymes. Previous efforts have identified mutant Thermus aquaticus DNA polymerase I (Taq) enzymes capable of recognizing 2'-modified DNA nucleotides. While these mutant enzymes recognize these modified nucleotides, they are not capable of synthesizing full length modified DNA; thus, further engineering is required for these enzymes. Here, we describe comparative biochemical studies that identify useful, but previously uncharacterized, properties of these enzymes; one enzyme, SFM19, is able to recognize a range of 2'-modified nucleotides much wider than that previously examined, including fluoro, azido, and amino modifications. To understand the molecular origins of these differences, we also identify specific amino acids and combinations of amino acids that contribute most to the previously evolved unnatural activity. Our data suggest that a negatively charged amino acid at 614 and mutation of the steric gate residue, E615, to glycine make up the optimal combination for modified oligonucleotide synthesis. These studies yield an improved understanding of the mutational origins of 2'-modified substrate recognition as well as identify SFM19 as the best candidate for further engineering, whether via rational design or directed evolution.
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Affiliation(s)
- Hayley J Schultz
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Andrea M Gochi
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Hannah E Chia
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Alexie L Ogonowsky
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Sharon Chiang
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Nedim Filipovic
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Aurora G Weiden
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Emma E Hadley
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Sara E Gabriel
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
| | - Aaron M Leconte
- W. M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges , Claremont, California 91711, United States
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Rutschke N, Zimmermann J, Möller R, Klöck G, Winterhalter M, Leune A. Hot start reverse transcriptase: an approach for improved real-time RT-PCR performance. J Anal Sci Technol 2015; 6:20. [PMID: 32226638 PMCID: PMC7099353 DOI: 10.1186/s40543-015-0063-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 06/14/2015] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Reverse transcriptase is an indispensable enzyme for real-time reverse transcriptase (RT)-PCR, a standard method in molecular diagnostics for detection and quantification of defined RNA molecules. The prevention of non-specific products due to elongation of misprimed oligonucleotides by the enzyme at temperatures beneath the specific annealing temperature is one of the biggest challenges in real-time RT-PCR.In the present study, an aptamer directed against the reverse transcriptase was analyzed for its potential to attain a temperature-dependent reverse transcriptase ("hot start" RT). FINDINGS The hot start effect was investigated in a one-step real-time RT-PCR assay for the detection of Middle East respiratory syndrome coronavirus (MERS-CoV). Results with aptamer revealed a reduced RT activity at low temperatures while achieving full activity at the specific annealing temperature of 55 °C. Sensitivity (limit of detection (LoD) 95 %) of the MERS-CoV assay was increased by about two times in the presence of aptamer. CONCLUSIONS The study demonstrates the potential of aptamer-dependent hot start RT for the improvement of diagnostic real-time RT-PCR assays.
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Affiliation(s)
- Nils Rutschke
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Jan Zimmermann
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
| | - Ronny Möller
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Gerd Klöck
- Institute of Environmental Biology and Biotechnology, University of Applied Sciences Bremen, Am Neustadtswall 30, 28199 Bremen, Germany
| | - Mathias Winterhalter
- School of Engineering and Science, Jacobs University, Campus Ring 1, 28759 Bremen, Germany
| | - Annika Leune
- altona Diagnostics GmbH, Moerkenstr. 12, 22767 Hamburg, Germany
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Wu EY, Walsh AR, Materne EC, Hiltner EP, Zielinski B, Miller BR, Mawby L, Modeste E, Parish CA, Barnes WM, Kermekchiev MB. A conservative isoleucine to leucine mutation causes major rearrangements and cold sensitivity in KlenTaq1 DNA polymerase. Biochemistry 2015; 54:881-9. [PMID: 25537790 PMCID: PMC4310628 DOI: 10.1021/bi501198f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Assembly of polymerase chain reactions at room temperature can sometimes lead to low yields or unintentional products due to mispriming. Mutation of isoleucine 707 to leucine in DNA polymerase I from Thermus aquaticus substantially decreases its activity at room temperature without compromising its ability to amplify DNA. To understand why a conservative change to the enzyme over 20 Å from the active site can have a large impact on its activity at low temperature, we solved the X-ray crystal structure of the large (5'-to-3' exonuclease-deleted) fragment of Taq DNA polymerase containing the cold-sensitive mutation in the ternary (E-DNA-ddNTP) and binary (E-DNA) complexes. The I707L KlenTaq1 ternary complex was identical to the wild-type in the closed conformation except for the mutation and a rotamer change in nearby phenylalanine 749, suggesting that the enzyme should remain active. However, soaking out of the nucleotide substrate at low temperature results in an altered binary complex made possible by the rotamer change at F749 near the tip of the polymerase O-helix. Surprisingly, two adenosines in the 5'-template overhang fill the vacated active site by stacking with the primer strand, thereby blocking the active site at low temperature. Replacement of the two overhanging adenosines with pyrimidines substantially increased activity at room temperature by keeping the template overhang out of the active site, confirming the importance of base stacking. These results explain the cold-sensitive phenotype of the I707L mutation in KlenTaq1 and serve as an example of a large conformational change affected by a conservative mutation.
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Affiliation(s)
- Eugene Y Wu
- Department of Biology and ‡Department of Chemistry, University of Richmond , Richmond, Virginia 23173, United States
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32
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Yamagami T, Ishino S, Kawarabayasi Y, Ishino Y. Mutant Taq DNA polymerases with improved elongation ability as a useful reagent for genetic engineering. Front Microbiol 2014; 5:461. [PMID: 25232352 PMCID: PMC4153296 DOI: 10.3389/fmicb.2014.00461] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/14/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, DNA labeling, mutagenesis, and other experiments. Thermostable DNA polymerases are especially useful and became quite valuable after the development of PCR technology. A DNA polymerase from Thermus aquaticus (Taq polymerase) is the most famous DNA polymerase as a PCR enzyme, and has been widely used all over the world. In this study, the gene fragments of the family A DNA polymerases were amplified by PCR from the DNAs from microorganisms within environmental soil samples, using a primer set for the two conserved regions. The corresponding region of the pol gene for Taq polymerase was substituted with the amplified gene fragments, and various chimeric DNA polymerases were prepared. Based on the properties of these chimeric enzymes and their sequences, two residues, E742 and A743, in Taq polymerase were found to be critical for its elongation ability. Taq polymerases with mutations at 742 and 743 actually showed higher DNA affinity and faster primer extension ability. These factors also affected the PCR performance of the DNA polymerase, and improved PCR results were observed with the mutant Taq polymerase.
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Affiliation(s)
- Takeshi Yamagami
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Sonoko Ishino
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Yutaka Kawarabayasi
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan ; Health Research Institute, National Institute of Advanced Industrial Science and Technology Amagasaki, Japan
| | - Yoshizumi Ishino
- Protein Chemistry and Engineering, Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
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Ishino S, Ishino Y. DNA polymerases as useful reagents for biotechnology - the history of developmental research in the field. Front Microbiol 2014; 5:465. [PMID: 25221550 PMCID: PMC4148896 DOI: 10.3389/fmicb.2014.00465] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 08/15/2014] [Indexed: 11/13/2022] Open
Abstract
DNA polymerase is a ubiquitous enzyme that synthesizes complementary DNA strands according to the template DNA in living cells. Multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. In addition to their fundamental role in maintaining genome integrity during replication and repair, DNA polymerases are widely used for DNA manipulation in vitro, including DNA cloning, sequencing, labeling, mutagenesis, and other purposes. The fundamental ability of DNA polymerases to synthesize a deoxyribonucleotide chain is conserved. However, the more specific properties, including processivity, fidelity (synthesis accuracy), and substrate nucleotide selectivity, differ among the enzymes. The distinctive properties of each DNA polymerase may lead to the potential development of unique reagents, and therefore searching for novel DNA polymerase has been one of the major focuses in this research field. In addition, protein engineering techniques to create mutant or artificial DNA polymerases have been successfully developing powerful DNA polymerases, suitable for specific purposes among the many kinds of DNA manipulations. Thermostable DNA polymerases are especially important for PCR-related techniques in molecular biology. In this review, we summarize the history of the research on developing thermostable DNA polymerases as reagents for genetic manipulation and discuss the future of this research field.
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Affiliation(s)
- Sonoko Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University Fukuoka, Japan
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34
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Arezi B, McKinney N, Hansen C, Cayouette M, Fox J, Chen K, Lapira J, Hamilton S, Hogrefe H. Compartmentalized self-replication under fast PCR cycling conditions yields Taq DNA polymerase mutants with increased DNA-binding affinity and blood resistance. Front Microbiol 2014; 5:408. [PMID: 25177317 PMCID: PMC4132270 DOI: 10.3389/fmicb.2014.00408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2014] [Accepted: 07/18/2014] [Indexed: 11/13/2022] Open
Abstract
Faster-cycling PCR formulations, protocols, and instruments have been developed to address the need for increased throughput and shorter turn-around times for PCR-based assays. Although run times can be cut by up to 50%, shorter cycle times have been correlated with lower detection sensitivity and increased variability. To address these concerns, we applied Compartmentalized Self Replication (CSR) to evolve faster-cycling mutants of Taq DNA polymerase. After five rounds of selection using progressively shorter PCR extension times, individual mutations identified in the fastest-cycling clones were randomly combined using ligation-based multi-site mutagenesis. The best-performing combinatorial mutants exhibit 35- to 90-fold higher affinity (lower Kd ) for primed template and a moderate (2-fold) increase in extension rate compared to wild-type Taq. Further characterization revealed that CSR-selected mutations provide increased resistance to inhibitors, and most notably, enable direct amplification from up to 65% whole blood. We discuss the contribution of individual mutations to fast-cycling and blood-resistant phenotypes.
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35
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Greenough L, Menin JF, Desai NS, Kelman Z, Gardner AF. Characterization of family D DNA polymerase from Thermococcus sp. 9°N. Extremophiles 2014; 18:653-64. [PMID: 24794034 PMCID: PMC4065339 DOI: 10.1007/s00792-014-0646-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/13/2014] [Indexed: 11/28/2022]
Abstract
Accurate DNA replication is essential for maintenance of every genome. All archaeal genomes except Crenarchaea, encode for a member of Family B (polB) and Family D (polD) DNA polymerases. Gene deletion studies in Thermococcus kodakaraensis and Methanococcus maripaludis show that polD is the only essential DNA polymerase in these organisms. Thus, polD may be the primary replicative DNA polymerase for both leading and lagging strand synthesis. To understand this unique archaeal enzyme, we report the biochemical characterization of a heterodimeric polD from Thermococcus. PolD contains both DNA polymerase and proofreading 3′–5′ exonuclease activities to ensure efficient and accurate genome duplication. The polD incorporation fidelity was determined for the first time. Despite containing 3′–5′ exonuclease proofreading activity, polD has a relatively high error rate (95 × 10−5) compared to polB (19 × 10−5) and at least 10-fold higher than the polB DNA polymerases from yeast (polε and polδ) or Escherichia coli DNA polIII holoenzyme. The implications of polD fidelity and biochemical properties in leading and lagging strand synthesis are discussed.
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Affiliation(s)
- Lucia Greenough
- New England Biolabs, Inc., 240 County Road, Ipswich, MA, 01938, USA
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36
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Satterfield BC. Cooperative primers: 2.5 million-fold improvement in the reduction of nonspecific amplification. J Mol Diagn 2013; 16:163-73. [PMID: 24370857 DOI: 10.1016/j.jmoldx.2013.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 10/26/2013] [Accepted: 10/30/2013] [Indexed: 10/25/2022] Open
Abstract
The increasing need to multiplex nucleic acid reactions presses test designers to the limits of amplification specificity in PCR. Although more than a dozen hot starts have been developed for PCR to reduce primer-dimer formation, none can stop the propagation of primer-dimers once formed. Even a small number of primer-dimers can result in false-negatives and/or false-positives. Herein, we demonstrate a new class of primer technology that greatly reduces primer-dimer propagation, showing successful amplification of 60 template copies with no signal dampening in a background of 150,000,000 primer-dimers. In contrast, normal primers, with or without a hot start, experienced signal dampening with as few as 60 primer-dimers and false-negatives with only 600 primer-dimers. This represents more than a 2.5 million-fold improvement in reduction of nonspecific amplification. We also show how a probe can be incorporated into the cooperative primer, with 2.5 times more signal than conventional fluorescent probes.
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37
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Terpe K. Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 2013; 97:10243-54. [DOI: 10.1007/s00253-013-5290-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/20/2013] [Accepted: 09/22/2013] [Indexed: 11/29/2022]
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Bush SM, Krysan PJ. iTILLING: personalized mutation screening. Methods Mol Biol 2013; 1062:175-91. [PMID: 24057366 DOI: 10.1007/978-1-62703-580-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
One powerful approach to studying gene function is to analyze the phenotype of an organism carrying a mutant allele of a gene of interest. In order to use this experimental approach, one must have the ability to easily isolate individual organisms carrying desired mutations. A widely used method for accomplishing this task in plants and other organisms is a procedure called TILLING. A traditional TILLING project has at its foundation an ordered mutant population produced by treating seeds with a chemical mutagen. From this mutagenized seed, thousands of individual mutant lines are produced, and corresponding DNA samples are collected. For several plant species, publicly accessible screening facilities have been established that perform mutant screens on a gene-by-gene basis in response to customer requests using PCR and heteroduplex detection methods. The iTILLING method described in this chapter represents an individualized version of the TILLING process. Performing a traditional TILLING experiment requires a large investment in time and resources to establish the well-ordered mutant population. By contrast, iTILLING is a low-investment alternative that provides the individual research lab with a practical solution to mutation screening. The main difference between the two approaches is that iTILLING is not based on the establishment of a durable, organized mutant population. Instead, a system for growing Arabidopsis seedlings in 96-well plates is used to produce an ephemeral mutant population for screening. Because the intention is not to develop a long-term resource, a considerable savings in time and money is realized when using iTILLING as compared to traditional TILLING. iTILLING is not intended to serve as a replacement to traditional TILLING. Rather, iTILLING provides a strategy by which custom mutagenesis screens can be performed by individual labs using unique genetic backgrounds that are of specific interest to that research group.
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Affiliation(s)
- Susan M Bush
- Department of Plant Biology, University of California-Davis, Davis, CA, USA
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Liu XP, Liu JH. Characterization of family IV UDG from Aeropyrum pernix and its application in hot-start PCR by family B DNA polymerase. PLoS One 2011; 6:e27248. [PMID: 22087273 PMCID: PMC3210769 DOI: 10.1371/journal.pone.0027248] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2011] [Accepted: 10/12/2011] [Indexed: 11/19/2022] Open
Abstract
Recombinant uracil-DNA glycosylase (UDG) from Aeropyrum pernix (A. pernix) was expressed in E. coli. The biochemical characteristics of A. pernix UDG (ApeUDG) were studied using oligonucleotides carrying a deoxyuracil (dU) base. The optimal temperature range and pH value for dU removal by ApeUDG were 55-65°C and pH 9.0, respectively. The removal of dU was inhibited by the divalent ions of Zn, Cu, Co, Ni, and Mn, as well as a high concentration of NaCl. The opposite base in the complementary strand affected the dU removal by ApeUDG as follows: U/C≈U/G>U/T≈U/AP≈U/->U/U≈U/I>U/A. The phosphorothioate around dU strongly inhibited dU removal by ApeUDG. Based on the above biochemical characteristics and the conservation of amino acid residues, ApeUDG was determined to belong to the IV UDG family. ApeUDG increased the yield of PCR by Pfu DNA polymerase via the removal of dU in amplified DNA. Using the dU-carrying oligonucleotide as an inhibitor and ApeUDG as an activator of Pfu DNA polymerase, the yield of undesired DNA fragments, such as primer-dimer, was significantly decreased, and the yield of the PCR target fragment was increased. This strategy, which aims to amplify the target gene with high specificity and yield, can be applied to all family B DNA polymerases.
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Affiliation(s)
- Xi-Peng Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Jian-Hua Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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40
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Affiliation(s)
- Ramon Kranaster
- Fachbereich Chemie, Universität Konstanz, 78457 Konstanz, Germany
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41
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Nandagopal B, Sankar S, Lingesan K, Appu KC, Padmini B, Sridharan G, Gopinath AK. Prevalence of Salmonella typhi among patients with febrile illness in rural and peri-urban populations of Vellore district, as determined by nested PCR targeting the flagellin gene. Mol Diagn Ther 2010; 14:107-12. [PMID: 20359254 DOI: 10.1007/bf03256360] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND AND OBJECTIVE Fever is one of the most common illnesses in all age groups in India. Typhoid fever is a continuing problem in developing countries such as India, which has poor sanitation facilities. The diagnosis of typhoid fever is still made by conventional culture-based isolation and identification. Serologic diagnostic tests, though widely used, have many deficiencies. Our objective was to investigate a molecular nested polymerase chain reaction (nPCR) technique to detect Salmonella typhi among patients with febrile illness in rural and peri-urban communities in Vellore district (Tamil Nadu, India). METHODS nPCR targeting the flagellin gene (fliC) was carried out using HotStar Taq DNA polymerase on DNA extracted from the buffy coat fraction of blood samples. Blood culture was done in a completely automated blood culture system, BacT/Alert(R), on prospectively collected blood samples. Relevant clinicopathologic data were obtained. RESULTS nPCR was found to have a lower limit of detection of 0.01 colony-forming units per milliliter. The prevalence of typhoid fever as estimated by nPCR was 4.7% in pyrexia of unknown origin (PUO) in the rural/peri-urban communities of Vellore district. The prevalence of S. typhi as estimated by blood culture was 2.0%, which was lower than the nPCR estimation. nPCR had sensitivity and specificity of 100% and 97.3%, respectively. The observed agreement between blood culture and nPCR was 0.973 and the Kappa coefficient was 0.59 (p < 0.0001). The frequency of typhoid fever as detected by nPCR was 4.35% among rural patients and 5.32% among peri-urban individuals. CONCLUSION nPCR on DNA extracts of buffy-coat samples using HotStar Taq was found to be a valuable and specific technique for diagnosis of typhoid fever.
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Affiliation(s)
- Balaji Nandagopal
- Sri Narayani Hospital & Research Centre, Vellore, Tamil Nadu, India.
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Bush SM, Krysan PJ. iTILLING: a personalized approach to the identification of induced mutations in Arabidopsis. PLANT PHYSIOLOGY 2010; 154:25-35. [PMID: 20668060 PMCID: PMC2938168 DOI: 10.1104/pp.110.159897] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
TILLING (for Targeting Induced Local Lesions IN Genomes) is a well-established method for identifying plants carrying point mutations in genes of interest. A traditional TILLING project requires a significant investment of time and resources to establish the mutant population and screening infrastructure. Here, we describe a modified TILLING procedure that substantially reduces the investment needed to perform mutation screening. Our motivation for developing iTILLING was to make it practical for individual laboratories to rapidly perform mutation screens using specialized genetic backgrounds. With iTILLING, M2 seeds are collected in bulk from the mutagenized population of plants, greatly reducing the labor needed to manage the mutant lines. Growth of the M2 seedlings for mutation screening, tissue collection, and DNA extraction are all performed in 96-well format. Mutations are then identified using high-resolution melt-curve analysis of gene-specific polymerase chain reaction products. Individual plants carrying mutations of interest are transferred from the 96-well growth plates to soil. One scientist can complete an iTILLING screen in less than 4 months. As a proof-of-principle test, we applied iTILLING to Arabidopsis (Arabidopsis thaliana) plants that were homozygous for the mekk1-1 (for MAPK/ERK kinase kinase 1) mutation and also carried a MEKK1 rescue construct. The goal of our screen was to identify mutations in the closely linked MEKK2 and MEKK3 loci. We obtained five mutations in MEKK2 and seven mutations in MEKK3, all located within 20 kb of the mekk1-1 T-DNA insertion. Using repeated iterations of the iTILLING process, mutations in three or more tandemly duplicated genes could be generated.
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Cherkasov D, Biet T, Bäuml E, Traut W, Lohoff M. New nucleotide analogues with enhanced signal properties. Bioconjug Chem 2010; 21:122-9. [PMID: 20047309 DOI: 10.1021/bc900364f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We describe synthesis and testing of a novel type of dye-modified nucleotides which we call macromolecular nucleotides (m-Nucs). Macromolecular nucleotides comprise a nucleotide moiety, a macromolecular linear linker, and a large macromolecular ligand carrying multiple fluorescent dyes. With incorporation of the nucleotide moiety into the growing nucleic acid strand during enzymatic synthesis, the macromolecular ligand together with the coupled dyes is bound to the nucleic acid. By the use of this new class of modified nucleotides, signals from multiple dye molecules can be obtained after a single enzymatic incorporation event. The modified nucleotides are considered especially useful in the fields of nanobiotechnology, where signal stability and intensity is a limiting factor.
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Affiliation(s)
- Dmitry Cherkasov
- Institute for Medical Microbiology, Philipps University of Marburg, Hans-Meerweinstrasse 2, 35043 Marburg, Germany.
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Abstract
Hot Start activation approaches are increasingly being used to improve the performance of PCR. Since the inception of Hot Start as a means of blocking DNA polymerase extension at lower temperatures, a number of approaches have been developed that target the essential reaction components such as magnesium ion, DNA polymerase, oligonucleotide primers, and dNTPs. Herein, five different Hot Start activation protocols are presented. The first method presents the use of barriers as a means of segregating key reaction components until a Hot Start activation step. The second and third protocols demonstrate Hot Start approaches to block DNA polymerase activity through the use of anti-DNA polymerase antibodies and accessory proteins, respectively. The fourth and fifth protocols utilize thermolabile chemical modifications to the oligonucleotide primers and dNTPs. The results presented demonstrate that all protocols significantly improve the specificity of traditional thermal cycling protocols.
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Affiliation(s)
- Natasha Paul
- Department of Research and Development, TriLink BioTechnologies, Inc., San Diego, CA, USA.
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Mi L, Wen Y, Pan D, Wang Y, Fan C, Hu J. Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2009; 5:2597-600. [PMID: 19722185 DOI: 10.1002/smll.200901147] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A new gold-nanoparticle (AuNP)-based strategy to dynamically modulate the activity of DNA polymerases and realize a hot-start (HS)-like effect in the polymerase chain reaction (PCR) is reported, which effectively prevents unwanted nonspecific amplification and improves the performance of PCRs. A high-fidelity Pfu DNA polymerase is employed as the model system. Interestingly, AuNPs inactivate the polymerase activity of Pfu at low temperature, thus resembling an antibody-based HS PCR. This inhibition effect of AuNPs is demonstrated for the preamplification polymerization activity of the PCR, which largely suppresses nonspecific amplification at temperatures between 30 and 60 degrees C and leads to highly specific and sensitive PCR amplification with Pfu. Significantly, the fidelity of Pfu is not sacrificed in the presence of AuNPs. Therefore, this AuNP-based HS strategy provides a straightforward and potentially versatile approach to realize high-performance PCR amplification.
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Affiliation(s)
- Lijuan Mi
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, P.R. China
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Lebedev A. Heat-activatable primers for hot-start PCR: oligonucleotide synthesis and basic PCR setup. ACTA ACUST UNITED AC 2009; Chapter 4:Unit 4.35 1-17. [PMID: 19746355 DOI: 10.1002/0471142700.nc0435s38] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
2'-Deoxyribonucleoside-3'-O-(4-oxotetradec-1-yl) phosphoramidites (OXT phosphoramidites) are used to prepare modified oligodeoxyribonucleotide primers containing heat cleavable OXT phosphotriester protecting groups at 3'-ultimate and penultimate internucleotide linkages. The OXT-modified primers significantly improve performance of the polymerase chain reaction (PCR) compared to standard DNA primers by substantially reducing or eliminating the accumulation of PCR artifacts such as dimerized primers and misprimed amplicons. Basic protocols for synthesis of OXT-modified oligonucleotide primers and for performing hot-start PCR are described.
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Giese H, Lam R, Selden R, Tan E. Fast multiplexed polymerase chain reaction for conventional and microfluidic short tandem repeat analysis. J Forensic Sci 2009; 54:1287-96. [PMID: 19840207 DOI: 10.1111/j.1556-4029.2009.01200.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The time required for short tandem repeat (STR) amplification is determined by the temperature ramp rates of the thermal cycler, the components of the reaction mix, and the properties of the reaction vessel. Multiplex amplifications in microfluidic biochip-based and conventional tube-based thermal cyclers have been demonstrated in 17.3 and 19 min, respectively. Optimized 28-cycle amplification protocols generated alleles with signal strengths above calling thresholds, heterozygous peak height ratios of greater than 0.65, and incomplete nontemplate nucleotide addition and stutter of less than 15%. Full CODIS-compatible profiles were generated using the Profiler Plus ID, COfiler and Identifiler primer sets. PCR performance over a wide range of DNA template levels from 0.006 to 4 ng was characterized by separation and detection on a microfluidic electrophoresis system, Genebench-FX. The fast multiplex PCR approach has the potential to reduce process time and cost for STR analysis and enables development of a fully integrated microfluidic forensic DNA analysis system.
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Eilert KD, Foran DR. Polymerase Resistance to Polymerase Chain Reaction Inhibitors in Bone. J Forensic Sci 2009; 54:1001-7. [DOI: 10.1111/j.1556-4029.2009.01116.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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