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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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2
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Medžiūnė J, Kapustina Ž, Žeimytė S, Jakubovska J, Sindikevičienė R, Čikotienė I, Lubys A. Advanced preparation of fragment libraries enabled by oligonucleotide-modified 2',3'-dideoxynucleotides. Commun Chem 2022; 5:34. [PMID: 36697673 PMCID: PMC9814608 DOI: 10.1038/s42004-022-00649-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 02/07/2022] [Indexed: 02/01/2023] Open
Abstract
The ever-growing demand for inexpensive, rapid, and accurate exploration of genomes calls for refinement of existing sequencing techniques. The development of next-generation sequencing (NGS) was a revolutionary milestone in genome analysis. While modified nucleotides already were inherent tools in sequencing and imaging, further modification of nucleotides enabled the expansion into even more diverse applications. Herein we describe the design and synthesis of oligonucleotide-tethered 2',3'-dideoxynucleotide (ddONNTP) terminators bearing universal priming sites attached to the nucleobase, as well as their enzymatic incorporation and performance in read-through assays. In the context of NGS library preparation, the incorporation of ddONNTP fulfills two requirements at once: the fragmentation step is integrated into the workflow and the obtained fragments are readily labeled by platform-specific adapters. DNA polymerases can incorporate ddONNTP nucleotides, as shown by primer extension assays. More importantly, reading through the unnatural linkage during DNA synthesis was demonstrated, with 25-30% efficiency in single-cycle extension.
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Affiliation(s)
- Justina Medžiūnė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, LT-03225 Lithuania
| | - Žana Kapustina
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, LT-10257 Lithuania
| | - Simona Žeimytė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Jevgenija Jakubovska
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Rūta Sindikevičienė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
| | - Inga Čikotienė
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania ,grid.6441.70000 0001 2243 2806Faculty of Chemistry and Geosciences, Vilnius University, Vilnius, LT-03225 Lithuania
| | - Arvydas Lubys
- grid.420349.8Department of Research and Development, Thermo Fisher Scientific Baltics, Vilnius, LT-02241 Lithuania
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3
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Ge J, Hu Y, Deng R, Li Z, Zhang K, Shi M, Yang D, Cai R, Tan W. Highly Sensitive MicroRNA Detection by Coupling Nicking-Enhanced Rolling Circle Amplification with MoS2 Quantum Dots. Anal Chem 2020; 92:13588-13594. [DOI: 10.1021/acs.analchem.0c03405] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jia Ge
- College of Chemistry, Green Catalysis Center, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Yun Hu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Zhaohui Li
- College of Chemistry, Green Catalysis Center, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Kaixiang Zhang
- College of Chemistry, Green Catalysis Center, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Muling Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, College of Material Science and Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Dan Yang
- Centre of Translational Atomaterials, Faculty of Science, Engineering and Technology, Swinburne University of Technology, P.O. Box 218, Hawthorn 3122, Australia
| | - Ren Cai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, College of Material Science and Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, College of Material Science and Engineering, and Collaborative Research Center of Molecular Engineering for Theranostics, Hunan University, Changsha 410082, China
- Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Foundation for Applied Molecular Evolution, 13709 Progress Boulevard, Alachua, Florida 32615, United States
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4
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Combining the Sensitivity of LAMP and Simplicity of Primer Extension via a DNA-Modified Nucleotide. CHEMISTRY 2020. [DOI: 10.3390/chemistry2020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
LAMP is an approach for isothermal nucleic acids diagnostics with increasing importance but suffers from the need of tedious systems design and optimization for every new target. Here, we describe an approach for its simplification based on a single nucleoside-5′-O-triphosphate (dNTP) that is covalently modified with a DNA strand. We found that the DNA-modified dNTP is a substrate for DNA polymerases in versatile primer extension reactions despite its size and that the incorporated DNA indeed serves as a target for selective LAMP analysis.
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5
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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Synthesis and Enzymatic Characterization of Sugar-Modified Nucleoside Triphosphate Analogs. Methods Mol Biol 2019; 1973:1-13. [PMID: 31016692 DOI: 10.1007/978-1-4939-9216-4_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Chemical modification of nucleic acids can be achieved by the enzymatic polymerization of modified nucleoside triphosphates (dN*TPs). This approach obviates some of the requirements and drawbacks imposed by the more traditional solid-phase synthesis of oligonucleotides. Here, we describe the protocol that is necessary to synthesize dN*TPs and evaluate their substrate acceptance by polymerases for their subsequent use in various applications including selection experiments to identify aptamers. The protocol is exemplified for a sugar-constrained nucleoside analog, 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, Institut Pasteur, Paris, France.
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6
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Jakubovska J, Tauraite D, Birštonas L, Meškys R. N4-acyl-2'-deoxycytidine-5'-triphosphates for the enzymatic synthesis of modified DNA. Nucleic Acids Res 2019; 46:5911-5923. [PMID: 29846697 PMCID: PMC6158702 DOI: 10.1093/nar/gky435] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023] Open
Abstract
A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N4-acylated 2′-deoxycytidine nucleotides (dCAcyl). We find that a variety of family A and B DNA polymerases efficiently use dCAcylTPs as substrates. In addition to the formation of complementary CAcyl•G pair, a strong base-pairing between N4-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo–), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dCAcylTPs but is prone to form CAcyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N4-acylated-deoxycytidine nucleotides. These data reveal novel N4-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.
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Affiliation(s)
- Jevgenija Jakubovska
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Daiva Tauraite
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Lukas Birštonas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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7
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Batule BS, Lee CY, Park KS, Park HG. Polymerization-sensitive switch-on monomer for terminal transferase activity assay. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2019; 47:256-259. [PMID: 30688096 DOI: 10.1080/21691401.2018.1552593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We herein describe a simple but efficient method for the determination of terminal transferase (TdT) activity, which relies on our finding that Fe(III)-quenched boron-dipyrromethene (BODIPY)-ATP is utilized as a switch-on monomer for polymerization and enables the facile synthesis of fluorescence oligonucleotides without additional, post-processing steps. As TdT carries out the synthesis of DNA by adding the monomers into growing chains, Fe(III) is displaced from BODIPY with the release of pyrophosphate group, which consequently leads to the generation of highly fluorescent long oligonucleotides. With this strategy, we selectively detected the TdT activity with high sensitivity. In addition, its practical applicability was successfully demonstrated by determining TdT activities in human serum.
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Affiliation(s)
- Bhagwan S Batule
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Chang Yeol Lee
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
| | - Ki Soo Park
- b Department of Biological Engineering, College of Engineering , Konkuk University , Seoul , Republic of Korea
| | - Hyun Gyu Park
- a Department of Chemical and Biomolecular Engineering (BK21+ Program) , KAIST , Daejeon , Republic of Korea
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8
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Balintová J, Welter M, Marx A. Antibody-nucleotide conjugate as a substrate for DNA polymerases. Chem Sci 2018; 9:7122-7125. [PMID: 30310633 PMCID: PMC6137436 DOI: 10.1039/c8sc01839a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/18/2018] [Indexed: 01/04/2023] Open
Abstract
Here we report on the development of an antibody-modified nucleotide and its sequence-selective incorporation into nascent DNA catalysed by DNA polymerases. Although the modification of the nucleotide is several orders of magnitude larger than the natural dNTP substrate and even exceeds the size of the DNA polymerase, it is well accepted by the enzyme. Moreover, the recognition of the antibody is not abolished by the conjugation but can be recognized by a secondary antibody that is conjugated to a signal-generating enzyme (i.e., horse radish peroxidase). This product can thus be exploited for a colorimetric read-out of nucleotide incorporation by the naked eye that allows detection of DNA as low as 10 amol. In future, assays like the one described herein might allow nucleic acid diagnostics at single nucleotide resolution without any laboratory equipment.
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Affiliation(s)
- J Balintová
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
| | - M Welter
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
| | - A Marx
- Department of Chemistry , University of Konstanz , Universitätsstrasse 10 , 78457 Konstanz , Germany .
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9
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Röthlisberger P, Hollenstein M. Aptamer chemistry. Adv Drug Deliv Rev 2018; 134:3-21. [PMID: 29626546 DOI: 10.1016/j.addr.2018.04.007] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/28/2018] [Accepted: 04/03/2018] [Indexed: 12/12/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules capable of tightly binding to specific targets. These functional nucleic acids are obtained by an in vitro Darwinian evolution method coined SELEX (Systematic Evolution of Ligands by EXponential enrichment). Compared to their proteinaceous counterparts, aptamers offer a number of advantages including a low immunogenicity, a relative ease of large-scale synthesis at affordable costs with little or no batch-to-batch variation, physical stability, and facile chemical modification. These alluring properties have propelled aptamers into the forefront of numerous practical applications such as the development of therapeutic and diagnostic agents as well as the construction of biosensing platforms. However, commercial success of aptamers still proceeds at a weak pace. The main factors responsible for this delay are the susceptibility of aptamers to degradation by nucleases, their rapid renal filtration, suboptimal thermal stability, and the lack of functional group diversity. Here, we describe the different chemical methods available to mitigate these shortcomings. Particularly, we describe the chemical post-SELEX processing of aptamers to include functional groups as well as the inclusion of modified nucleoside triphosphates into the SELEX protocol. These methods will be illustrated with successful examples of chemically modified aptamers used as drug delivery systems, in therapeutic applications, and as biosensing devices.
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10
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Röthlisberger P, Levi-Acobas F, Sarac I, Marlière P, Herdewijn P, Hollenstein M. On the enzymatic incorporation of an imidazole nucleotide into DNA. Org Biomol Chem 2018; 15:4449-4455. [PMID: 28485736 DOI: 10.1039/c7ob00858a] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The expansion of the genetic alphabet with an additional, artificial base pair is of high relevance for numerous applications in synthetic biology. The enzymatic construction of metal base pairs is an alluring strategy that would ensure orthogonality to canonical nucleic acids. So far, very little is known on the enzymatic fabrication of metal base pairs. Here, we report on the synthesis and the enzymatic incorporation of an imidazole nucleotide into DNA. The imidazole nucleotide dIm is known to form highly stable dIm-Ag+-dIm artificial base pairs that cause minimal structural perturbation of DNA duplexes and was considered to be an ideal candidate for the enzymatic construction of metal base pairs. We demonstrate that dImTP is incorporated with high efficiency and selectivity opposite a templating dIm nucleotide by the Kf exo-. The presence of Mn2+, and to a smaller extent Ag+, enhances the efficiency of this polymerization reaction, however, without being strictly required. In addition, multiple incorporation events could be observed, albeit with modest efficiency. We demonstrate that the dIm-Mn+-dIm cannot be constructed by DNA polymerases and suggest that parameters other than stability of a metal base pair and its impact on the structure of DNA duplexes govern the enzymatic formation of artificial metal base pairs.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.
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11
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Crystal structures of ternary complexes of archaeal B-family DNA polymerases. PLoS One 2017; 12:e0188005. [PMID: 29211756 PMCID: PMC5718519 DOI: 10.1371/journal.pone.0188005] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/30/2017] [Indexed: 01/04/2023] Open
Abstract
Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.
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12
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Balintová J, Simonova A, Białek-Pietras M, Olejniczak A, Lesnikowski ZJ, Hocek M. Carborane-linked 2'-deoxyuridine 5'-O-triphosphate as building block for polymerase synthesis of carborane-modified DNA. Bioorg Med Chem Lett 2017; 27:4786-4788. [PMID: 29017785 DOI: 10.1016/j.bmcl.2017.09.064] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Revised: 09/13/2017] [Accepted: 09/30/2017] [Indexed: 11/16/2022]
Abstract
5-[(p-Carborane-2-yl)ethynyl]-2'-deoxyuridine 5'-O-triphosphate was synthesized and used as a good substrate in enzymatic construction of carborane-modified DNA or oligonucleotides containing up to 21 carborane moieties in primer extension reactions by DNA polymerases.
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Affiliation(s)
- Jana Balintová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic
| | - Magdalena Białek-Pietras
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland
| | - Agnieszka Olejniczak
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland
| | - Zbigniew J Lesnikowski
- Institute of Medical Biology, Polish Academy of Sciences, Laboratory of Molecular Virology and Biological Chemistry, 106 Lodowa St., Lodz 93-232, Poland.
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague 6, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic.
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13
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Zou M, Wang S. An Aptamer-based Self-Catalytic Colorimetric Assay for Carcinoembryonic Antigen. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11236] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mingjing Zou
- Central Laboratory; Heze Medical College; Heze 274030 China
| | - Shuyu Wang
- Clinical Laboratory; Heze City Hospital; Heze 274000 China
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14
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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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15
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Diafa S, Evéquoz D, Leumann CJ, Hollenstein M. Enzymatic Synthesis of 7',5'-Bicyclo-DNA Oligonucleotides. Chem Asian J 2017; 12:1347-1352. [PMID: 28371464 DOI: 10.1002/asia.201700374] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/30/2017] [Indexed: 01/06/2023]
Abstract
The selection of artificial genetic polymers with tailor-made properties for their application in synthetic biology requires the exploration of new nucleosidic scaffolds that can be used in selection experiments. Herein, we describe the synthesis of a bicyclo-DNA triphosphate (i.e., 7',5'-bc-TTP) and show its potential to serve for the generation of new xenonucleic acids (XNAs) based on this scaffold. 7',5'-bc-TTP is a good substrate for Therminator DNA polymerase, and up to seven modified units can be incorporated into a growing DNA chain. In addition, this scaffold sustains XNA-dependent DNA synthesis and potentially also XNA-dependent XNA synthesis. However, DNA-dependent XNA synthesis on longer templates is hampered by competitive misincorporation of deoxyadenosine triphosphate (dATP) caused by the slow rate of incorporation of 7',5'-bc-TTP.
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Affiliation(s)
- Stella Diafa
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Damien Evéquoz
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Christian J Leumann
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
| | - Marcel Hollenstein
- Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3523, 28, rue du Docteur Roux, 75724, Paris Cedex 15, France
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16
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Hottin A, Betz K, Diederichs K, Marx A. Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides. Chemistry 2017; 23:2109-2118. [PMID: 27901305 DOI: 10.1002/chem.201604515] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Indexed: 01/12/2023]
Abstract
Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.
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Affiliation(s)
- Audrey Hottin
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Kay Diederichs
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Department of Biology, University of Konstanz, Universitätsstrasse 10, 78457, Konstanz, Germany
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17
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Hollenstein M, Damha MJ. Rolling Circle Amplification with Chemically Modified Nucleoside Triphosphates. ACTA ACUST UNITED AC 2016; 67:7.26.1-7.26.15. [PMID: 27911492 DOI: 10.1002/cpnc.17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Modified nucleoside triphosphates (dN*TPs) represent facile and versatile precursors for the introduction of chemical diversity into nucleic acids. While dN*TPs have been utilized in a plethora of practical applications, very little attention has been devoted to the assessment of their compatibility with isothermal amplification strategies. In this context, rolling circle amplification (RCA) is a wide-spread enzymatic replication method in which small single-stranded DNA (ssDNA) circles serve as templates in primer extension reactions yielding very long, ssDNA products. RCA is a pivotal tool for the generation of biosensor and diagnostic devices and is currently evaluated for its usefulness to create novel drug delivery systems. This unit describes the experimental procedures for the synthesis of modified RCA products using dN*TPs bearing chemical alterations at any possible location of the nucleosidic scaffold. Two ligation methods are presented for the generation of the DNA nanocircles that serve as templates for RCA, followed by a description of the RCA method itself and an assessment of the nuclease resistance of the ensuing products. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Marcel Hollenstein
- Department of Structural Biology and Chemistry, Pasteur Institute, Paris, France
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
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18
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Welter M, Verga D, Marx A. Sequence-Specific Incorporation of Enzyme-Nucleotide Chimera by DNA Polymerases. Angew Chem Int Ed Engl 2016; 55:10131-5. [PMID: 27392211 DOI: 10.1002/anie.201604641] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Indexed: 02/06/2023]
Abstract
DNA polymerases select the right nucleotide for the growing polynucleotide chain based on the shape and geometry of the nascent nucleotide pairs and thereby ensure high DNA replication selectivity. High-fidelity DNA polymerases are believed to possess tight active sites that allow little deviation from the canonical structures. However, DNA polymerases are known to use nucleotides with small modifications as substrates, which is key for numerous core biotechnology applications. We show that even high-fidelity DNA polymerases are capable of efficiently using nucleotide chimera modified with a large protein like horseradish peroxidase as substrates for template-dependent DNA synthesis, despite this "cargo" being more than 100-fold larger than the natural substrates. We exploited this capability for the development of systems that enable naked-eye detection of DNA and RNA at single nucleotide resolution.
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Affiliation(s)
- Moritz Welter
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Daniela Verga
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457, Konstanz, Germany.
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19
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Kong D, Yeung W, Hili R. Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates. ACS COMBINATORIAL SCIENCE 2016; 18:355-70. [PMID: 27275512 DOI: 10.1021/acscombsci.6b00059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.
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Affiliation(s)
- Dehui Kong
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Wayland Yeung
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
| | - Ryan Hili
- Department of Chemistry, University of Georgia, 140 Cedar
Street, Athens, Georgia 30602, United States
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20
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Welter M, Verga D, Marx A. Sequenz-spezifischer Einbau von Enzym-Nukleotid-Chimären durch DNA-Polymerasen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604641] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Moritz Welter
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Daniela Verga
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
| | - Andreas Marx
- Fachbereich Chemie, Graduiertenschule Chemische Biologie Konstanz; Universität Konstanz; Universitätsstraße 10 78457 Konstanz Deutschland
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21
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Hottin A, Marx A. Structural Insights into the Processing of Nucleobase-Modified Nucleotides by DNA Polymerases. Acc Chem Res 2016; 49:418-27. [PMID: 26947566 DOI: 10.1021/acs.accounts.5b00544] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The DNA polymerase-catalyzed incorporation of modified nucleotides is employed in many biological technologies of prime importance, such as next-generation sequencing, nucleic acid-based diagnostics, transcription analysis, and aptamer selection by systematic enrichment of ligands by exponential amplification (SELEX). Recent studies have shown that 2'-deoxynucleoside triphosphates (dNTPs) that are functionalized with modifications at the nucleobase such as dyes, affinity tags, spin and redox labels, or even oligonucleotides are substrates for DNA polymerases, even if modifications of high steric demand are used. The position at which the modification is introduced in the nucleotide has been identified as crucial for retaining substrate activity for DNA polymerases. Modifications are usually attached at the C5 position of pyrimidines and the C7 position of 7-deazapurines. Furthermore, it has been shown that the nature of the modification may impact the efficiency of incorporation of a modified nucleotide into the nascent DNA strand by a DNA polymerase. This Account places functional data obtained in studies of the incorporation of modified nucleotides by DNA polymerases in the context of recently obtained structural data. Crystal structure analysis of a Thermus aquaticus (Taq) DNA polymerase variant (namely, KlenTaq DNA polymerase) in ternary complex with primer-template DNA and several modified nucleotides provided the first structural insights into how nucleobase-modified triphosphates are tolerated. We found that bulky modifications are processed by KlenTaq DNA polymerase as a result of cavities in the protein that enable the modification to extend outside the active site. In addition, we found that the enzyme is able to adapt to different modifications in a flexible manner and adopts different amino acid side-chain conformations at the active site depending on the nature of the nucleotide modification. Different "strategies" (i.e., hydrogen bonding, cation-π interactions) enable the protein to stabilize the respective protein-substrate complex without significantly changing the overall structure of the complex. Interestingly, it was also discovered that a modified nucleotide may be more efficiently processed by KlenTaq DNA polymerase when the 3'-primer terminus is also a modified nucleotide instead of a nonmodified natural one. Indeed, the modifications of two modified nucleotides at adjacent positions can interact with each other (i.e., by π-π interactions) and thereby stabilize the enzyme-substrate complex, resulting in more efficient transformation. Several studies have indicated that archeal DNA polymerases belonging to sequence family B are better suited for the incorporation of nucleobase-modified nucleotides than enzymes from family A. However, significantly less structural data are available for family B DNA polymerases. In order to gain insights into the preference for modified substrates by members of family B, we succeeded in obtaining binary structures of 9°N and KOD DNA polymerases bound to primer-template DNA. We found that the major groove of the archeal family B DNA polymerases is better accessible than in family A DNA polymerases. This might explain the observed superiority of family B DNA polymerases in polymerizing nucleotides that bear bulky modifications located in the major groove, such as modification at C5 of pyrimidines and C7 of 7-deazapurines. Overall, this Account summarizes our recent findings providing structural insight into the mechanism by which modified nucleotides are processed by DNA polymerases. It provides guidelines for the design of modified nucleotides, thus supporting future efforts based on the acceptance of modified nucleotides by DNA polymerases.
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Affiliation(s)
- Audrey Hottin
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department
of Chemistry and
Konstanz Research School Chemical Biology University of Konstanz Universitätsstrasse 10, 78457 Konstanz, Germany
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22
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Wu H, Liu Y, Wang H, Wu J, Zhu F, Zou P. Label-free and enzyme-free colorimetric detection of microRNA by catalyzed hairpin assembly coupled with hybridization chain reaction. Biosens Bioelectron 2016; 81:303-308. [PMID: 26985582 DOI: 10.1016/j.bios.2016.03.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/01/2016] [Accepted: 03/08/2016] [Indexed: 11/25/2022]
Abstract
In this study, a simple, label-free, and enzyme-free colorimetric biosensor has been developed for amplified detection of let-7a microRNA (miRNA) on the basis of dual signal amplification strategy. The sensing system mainly consists of four unlabeled hairpin probes termed H1, H2, H3, and H4. Upon sensing of the target miRNA, hairpin H1 is opened. Then hairpin H2 hybridizes with H1 forming H1-H2 duplex and frees the target miRNA that can be recycled to trigger another reaction cycle. In addition, the newly formed H1-H2 duplex hybridizes with hairpin H3, and this triggers the autonomous cross-opening of the two hairpins H3 and H4 through hybridization chain reaction. During this process, numerous split G-quadruplex structures are generated and further associate with cofactor hemin to form massive peroxidase-mimicking DNAzymes. The resulting DNAzymes catalyze the H2O2-mediated oxidation of colorless 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS(2-)) to the green-colored ABTS(•-), inducing a remarkably amplified colorimetric signal. This newly developed sensing system exhibits high sensitivity toward miRNA with a detection limit of 7.4fM and a large dynamic range of 6 orders of magnitude from 10fM to 10nM. Furthermore, it exhibits a good performance to discriminate single-base difference among the miRNA family members and holds a great potential for early diagnosis in gene-related diseases.
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Affiliation(s)
- Hao Wu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China.
| | - Yaling Liu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Hongyong Wang
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Jun Wu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Feifan Zhu
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China
| | - Pei Zou
- Key Laboratory of Nuclear Medicine, Ministry of Health, Jiangsu Key Laboratory of Molecular Nuclear Medicine, Jiangsu Institute of Nuclear Medicine, Wuxi, Jiangsu 214063, China.
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23
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Dadová J, Cahová H, Hocek M. Polymerase Synthesis of Base-Modified DNA. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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24
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Verga D, Welter M, Marx A. Sequence selective naked-eye detection of DNA harnessing extension of oligonucleotide-modified nucleotides. Bioorg Med Chem Lett 2015; 26:841-844. [PMID: 26774580 DOI: 10.1016/j.bmcl.2015.12.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 11/18/2022]
Abstract
DNA polymerases can efficiently and sequence selectively incorporate oligonucleotide (ODN)-modified nucleotides and the incorporated oligonucleotide strand can be employed as primer in rolling circle amplification (RCA). The effective amplification of the DNA primer by Φ29 DNA polymerase allows the sequence-selective hybridisation of the amplified strand with a G-quadruplex DNA sequence that has horse radish peroxidase-like activity. Based on these findings we develop a system that allows DNA detection with single-base resolution by naked eye.
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Affiliation(s)
- Daniela Verga
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Moritz Welter
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany.
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25
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Hollenstein M. DNA Catalysis: The Chemical Repertoire of DNAzymes. Molecules 2015; 20:20777-804. [PMID: 26610449 PMCID: PMC6332124 DOI: 10.3390/molecules201119730] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 12/24/2022] Open
Abstract
Deoxyribozymes or DNAzymes are single-stranded catalytic DNA molecules that are obtained by combinatorial in vitro selection methods. Initially conceived to function as gene silencing agents, the scope of DNAzymes has rapidly expanded into diverse fields, including biosensing, diagnostics, logic gate operations, and the development of novel synthetic and biological tools. In this review, an overview of all the different chemical reactions catalyzed by DNAzymes is given with an emphasis on RNA cleavage and the use of non-nucleosidic substrates. The use of modified nucleoside triphosphates (dN*TPs) to expand the chemical space to be explored in selection experiments and ultimately to generate DNAzymes with an expanded chemical repertoire is also highlighted.
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Affiliation(s)
- Marcel Hollenstein
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.
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26
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Mačková M, Boháčová S, Perlíková P, Poštová Slavětínská L, Hocek M. Polymerase Synthesis and Restriction Enzyme Cleavage of DNA Containing 7-Substituted 7-Deazaguanine Nucleobases. Chembiochem 2015; 16:2225-36. [PMID: 26382079 DOI: 10.1002/cbic.201500315] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Indexed: 01/06/2023]
Abstract
Previous studies of polymerase synthesis of base-modified DNAs and their cleavage by restriction enzymes have mostly related only to 5-substituted pyrimidine and 7-substituted 7-deazaadenine nucleotides. Here we report the synthesis of a series of 7-substituted 7-deazaguanine 2'-deoxyribonucleoside 5'-O-triphosphates (dG(R) TPs), their use as substrates for polymerase synthesis of modified DNA and the influence of the modification on their cleavage by type II restriction endonucleases (REs). The dG(R) TPs were generally good substrates for polymerases but the PCR products could not be visualised on agarose gels by intercalator staining, due to fluorescence quenching. The presence of 7-substituted 7-deazaguanine residues in recognition sequences of REs in most cases completely blocked the cleavage.
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Affiliation(s)
- Michaela Mačková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Soňa Boháčová
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Pavla Perlíková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center, Flemingovo nám. 2, 16610, Prague 6, Czech Republic. .,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12843, Prague 2, Czech Republic.
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27
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Zhu J, Zhang L, Dong S, Wang E. How to split a G-quadruplex for DNA detection: new insight into the formation of DNA split G-quadruplex. Chem Sci 2015; 6:4822-4827. [PMID: 29142717 PMCID: PMC5667574 DOI: 10.1039/c5sc01287b] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 05/31/2015] [Indexed: 01/30/2023] Open
Abstract
Here, we get a new insight into the formation of a split G-quadruplex from the viewpoints of the split mode and guanine base number. An unusual result is that the split mode 4 : 8 performed best in six split modes, including the frequently used mode 1 : 3 and 2 : 2 in the split G-quadruplex enhanced fluorescence assay. Circular dichroism spectra verified the conclusion. The application of the split G-quadruplex based assay in DNA detection was performed on the point mutations of the JAK2 V617F and HBB genes. A multi-target analysis method based on a pool of G-segments split from T30695 (GGGTGGGTGGGTGGGT) by the magic "law of 4 : 8" was established.
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Affiliation(s)
- Jinbo Zhu
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
- University of Chinese Academy of Sciences , Beijing , 100049 , P. R. China
| | - Libing Zhang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
| | - Erkang Wang
- State Key Laboratory of Electroanalytical Chemistry , Changchun Institute of Applied Chemistry , Chinese Academy of Sciences , Changchun 130022 , P. R. China .
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28
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Ma L, Diao A. Design of enzyme-interfaced DNA logic operations (AND, OR and INHIBIT) with an assaying application for single-base mismatch. Chem Commun (Camb) 2015; 51:10233-5. [DOI: 10.1039/c5cc02835c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We devised AND, OR and INHIBIT logic gates.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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