1
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Liu Z, Yan B, Liu H, Liu X, Xiao X, Ming Z. Enhancing APE1 detection through apurinic/apyrimidinic site inhibition of DNA polymerase: an innovative, highly sensitive approach. Chem Commun (Camb) 2024; 60:4695-4698. [PMID: 38592754 DOI: 10.1039/d4cc00304g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
This study presents an innovative method for the highly sensitive detection of apurinic/apyrimidinic endonuclease 1 (APE1), a crucial biomarker and target for cancer diagnosis and treatment. The method is predicated on our discovery that the apurinic or apyrimidinic site (AP site) can inhibit the activity of Taq DNA polymerase. Subsequent experiments further led to the development of a new amplification method based on the digestion activity of Lambda exonuclease. This approach showed potential to detect trace amounts of APE1 in biological samples with high sensitivity.
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Affiliation(s)
- Zhijun Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Bei Yan
- Institute of Medical Sciences, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, 750004, China
| | - Huan Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xiao Liu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Xianjin Xiao
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Zhihao Ming
- Department of Urology, The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410006, China.
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2
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Wang Y, Shi Y, Hellinga HW, Beese LS. Thermally controlled intein splicing of engineered DNA polymerases provides a robust and generalizable solution for accurate and sensitive molecular diagnostics. Nucleic Acids Res 2023; 51:5883-5894. [PMID: 37166959 PMCID: PMC10287962 DOI: 10.1093/nar/gkad368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/18/2023] [Accepted: 05/09/2023] [Indexed: 05/12/2023] Open
Abstract
DNA polymerases are essential for nucleic acid synthesis, cloning, sequencing and molecular diagnostics technologies. Conditional intein splicing is a powerful tool for controlling enzyme reactions. We have engineered a thermal switch into thermostable DNA polymerases from two structurally distinct polymerase families by inserting a thermally activated intein domain into a surface loop that is integral to the polymerase active site, thereby blocking DNA or RNA template access. The fusion proteins are inactive, but retain their structures, such that the intein excises during a heat pulse delivered at 70-80°C to generate spliced, active polymerases. This straightforward thermal activation step provides a highly effective, one-component 'hot-start' control of PCR reactions that enables accurate target amplification by minimizing unwanted by-products generated by off-target reactions. In one engineered enzyme, derived from Thermus aquaticus DNA polymerase, both DNA polymerase and reverse transcriptase activities are controlled by the intein, enabling single-reagent amplification of DNA and RNA under hot-start conditions. This engineered polymerase provides high-sensitivity detection for molecular diagnostics applications, amplifying 5-6 copies of the tested DNA and RNA targets with >95% certainty. The design principles used to engineer the inteins can be readily applied to construct other conditionally activated nucleic acid processing enzymes.
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Affiliation(s)
- You Wang
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Yuqian Shi
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Homme W Hellinga
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
| | - Lorena S Beese
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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3
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Bulygin AA, Kuznetsova AA, Fedorva OS, Kuznetsov NA. [Comparative Analysis of Family A DNA-Polymerases as a Searching Tool for Enzymes with New Properties]. Mol Biol (Mosk) 2023; 57:185-196. [PMID: 37000648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/07/2022] [Indexed: 06/19/2023]
Abstract
DNA polymerases catalyze DNA synthesis during DNA replication, repair, and recombination. A number of DNA polymerases, such as the Taq enzyme from Thermus aquaticus, are used in various applications of molecular biology and biotechnology, in particular as DNA amplification tools. However, the efficiency of these enzymes depends on factors such as DNA origin, primer composition, template length, GC-content, and the ability to form stable secondary structures. These limitations in the use of currently known DNA polymerases lead to the search for new enzymes with improved properties. This review summarizes the main structural and molecular-kinetic features of the functioning of DNA-polymerases belonging to structural family A, including Taq polymerase. A phylogenetic analysis of these enzymes was carried out, which made it possible to establish a highly conserved consensus sequence containing 62 amino acid residues distributed over the structure of the enzyme. A comparative analysis of these amino acid residues among poorly studied DNA-polymerases revealed 7 enzymes that potentially have the properties necessary for use in DNA amplification.
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Affiliation(s)
- A A Bulygin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
| | - A A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - O S Fedorva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
| | - N A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, 630090 Russia
- Novosibirsk National Research State University, Novosibirsk, 630090 Russia
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Turvey MW, Gabriel KN, Lee W, Taulbee JJ, Kim JK, Chen S, Lau CJ, Kattan RE, Pham JT, Majumdar S, Garcia D, Weiss GA, Collins PG. Single-molecule Taq DNA polymerase dynamics. Sci Adv 2022; 8:eabl3522. [PMID: 35275726 PMCID: PMC8916733 DOI: 10.1126/sciadv.abl3522] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/21/2022] [Indexed: 06/14/2023]
Abstract
Taq DNA polymerase functions at elevated temperatures with fast conformational dynamics-regimes previously inaccessible to mechanistic, single-molecule studies. Here, single-walled carbon nanotube transistors recorded the motions of Taq molecules processing matched or mismatched template-deoxynucleotide triphosphate pairs from 22° to 85°C. By using four enzyme orientations, the whole-enzyme closures of nucleotide incorporations were distinguished from more rapid, 20-μs closures of Taq's fingers domain testing complementarity and orientation. On average, one transient closure was observed for every nucleotide binding event; even complementary substrate pairs averaged five transient closures between each catalytic incorporation at 72°C. The rate and duration of the transient closures and the catalytic events had almost no temperature dependence, leaving all of Taq's temperature sensitivity to its rate-determining open state.
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Affiliation(s)
- Mackenzie W. Turvey
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Kristin N. Gabriel
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Wonbae Lee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Jeffrey J. Taulbee
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Joshua K. Kim
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Silu Chen
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Calvin J. Lau
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
| | - Rebecca E. Kattan
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
| | - Jenifer T. Pham
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | - Sudipta Majumdar
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
| | | | - Gregory A. Weiss
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA 92697-3900, USA
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92697-3958, USA
| | - Philip G. Collins
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA 92697-4575, USA
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Abstract
Evolution is essential to the generation of complexity and ultimately life. It relies on the propagation of the properties, traits, and characteristics that allow an organism to survive in a challenging environment. It is evolution that shaped our world over about four billion years by slow and iterative adaptation. While natural evolution based on selection is slow and gradual, directed evolution allows the fast and streamlined optimization of a phenotype under selective conditions. The potential of directed evolution for the discovery and optimization of enzymes is mostly limited by the throughput of the tools and methods available for screening. Over the past twenty years, versatile tools based on droplet microfluidics have been developed to address the need for higher throughput. In this Review, we provide a chronological overview of the intertwined development of microfluidics droplet-based compartmentalization methods and in vivo directed evolution of enzymes.
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Affiliation(s)
- Ariane Stucki
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Jaicy Vallapurackal
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Thomas R. Ward
- Department of ChemistryUniversity of BaselMattenstrasse 24aCH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
| | - Petra S. Dittrich
- Department of Biosystems Science and EngineeringETH ZurichMattenstrasse 26CH-4058BaselSwitzerland
- National Competence Center in Research (NCCR)Molecular Systems EngineeringBaselSwitzerland
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Desai N, Shah V, Datta B. Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay. Molecules 2021; 26:molecules26051400. [PMID: 33807659 PMCID: PMC7961521 DOI: 10.3390/molecules26051400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 01/31/2021] [Accepted: 02/24/2021] [Indexed: 12/05/2022] Open
Abstract
G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.
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Affiliation(s)
- Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology, Gandhinagar 382355, India; (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology, Gandhinagar, Gandhinagar 382355, India
- Correspondence: ; Tel.: +91-79-2395-2427; Fax: +91-79-2397-2622
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7
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Baek HE, Bandivadekar RR, Pandit P, Mah M, Sehgal RNM, Tell LA. TaqMan quantitative real-time PCR for detecting Avipoxvirus DNA in various sample types from hummingbirds. PLoS One 2020; 15:e0230701. [PMID: 32526768 PMCID: PMC7289624 DOI: 10.1371/journal.pone.0230701] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/25/2020] [Indexed: 11/19/2022] Open
Abstract
Background Avian pox is a viral disease documented in a wide range of bird species. Disease-related detrimental effects can cause dyspnea and dysphagia, and birds with high metabolic requirements, such as hummingbirds, are thus especially vulnerable to the pathogen. Hummingbirds have a strong presence in California, especially in urban environments. However, little is understood regarding the impact of pox virus on hummingbird populations. Currently, diagnosing a pox infection relies on obtaining a tissue biopsy, which poses significant risks to birds and challenges in the field. Understanding the ecology of hummingbird pox viral infections could be advanced by a minimally invasive ante-mortem diagnostic method. Our aim was to address whether pox infections can be diagnosed using integumentary system samples besides tissue biopsies. To meet this goal, we tested multiple integumentary sample types using a quantitative real-time PCR assay. A secondary study goal was to determine which sample types (ranging from minimally to highly invasive sampling) were optimal for identifying infected birds. Methodology and principal findings Pox-like lesion tissue, pectoral muscle, feathers, toenail clippings, blood, and swabs (both pox-like lesion tissue and non pox-like lesion tissue) were taken from live birds and carcasses of two species of hummingbirds found in California. To maximize successful diagnosis, especially for samples with low viral load, a real-time quantitative PCR assay was developed for detecting the hummingbird-specific Avipoxvirus 4b core protein gene. Avipoxvirus DNA was successfully amplified from all sample types obtained from 27 individuals. These results were compared to those of conventional PCR and comparisons were also made among sample types, utilizing lesion tissue samples as the gold standard. Conclusions and significance Hummingbird avian pox can be diagnosed without relying on tissue biopsies. We identify that feather samples, of which contour feathers yielded the best results, can be used for diagnosing infected birds, thus reducing sampling risk. In sum, the real-time PCR assay detected viral DNA in various integumentary system sample types and will be useful in future studies of hummingbird disease ecology.
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Affiliation(s)
- Hanna E Baek
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Ruta R Bandivadekar
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Pranav Pandit
- EpiCenter for Disease Dynamics, One Health Institute, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Michelle Mah
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Ravinder N M Sehgal
- Department of Biology, San Francisco State University, San Francisco, CA, United States of America
| | - Lisa A Tell
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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Lopata A, Jójárt B, Surányi ÉV, Takács E, Bezúr L, Leveles I, Bendes ÁÁ, Viskolcz B, Vértessy BG, Tóth J. Beyond Chelation: EDTA Tightly Binds Taq DNA Polymerase, MutT and dUTPase and Directly Inhibits dNTPase Activity. Biomolecules 2019; 9:biom9100621. [PMID: 31627475 PMCID: PMC6843921 DOI: 10.3390/biom9100621] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 11/25/2022] Open
Abstract
EDTA is commonly used as an efficient chelator of metal ion enzyme cofactors. It is highly soluble, optically inactive and does not interfere with most chemicals used in standard buffers making EDTA a common choice to generate metal-free conditions for biochemical and biophysical investigations. However, the controversy in the literature on metal-free enzyme activities achieved using EDTA or by other means called our attention to a putative effect of EDTA beyond chelation. Here, we show that EDTA competes for the nucleotide binding site of the nucleotide hydrolase dUTPase by developing an interaction network within the active site similar to that of the substrate. To achieve these findings, we applied kinetics and molecular docking techniques using two different dUTPases. Furthermore, we directly measured the binding of EDTA to dUTPases and to two other dNTPases, the Taq polymerase and MutT using isothermal titration calorimetry. EDTA binding proved to be exothermic and mainly enthalpy driven with a submicromolar dissociation constant considerably lower than that of the enzyme:substrate or the Mg:EDTA complexes. Control proteins, including an ATPase, did not interact with EDTA. Our findings indicate that EDTA may act as a selective inhibitor against dNTP hydrolyzing enzymes and urge the rethinking of the utilization of EDTA in enzymatic experiments.
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Affiliation(s)
- Anna Lopata
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
- Institute of Biophysical Chemistry, Goethe University, Frankfurt am Main, 60438 Frankfurt, Germany.
| | - Balázs Jójárt
- Institute of Food Engineering, Faculty of Engineering, University of Szeged, 6724 Szeged, Hungary.
| | - Éva V Surányi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Enikő Takács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
| | - László Bezúr
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Ibolya Leveles
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Ábris Á Bendes
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, 90220 Oulu, Finland.
| | - Béla Viskolcz
- Institute of Chemistry, University of Miskolc, 3515 Miskolc, Hungary.
| | - Beáta G Vértessy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
- Department of Applied Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary.
| | - Judit Tóth
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, 1113 Budapest, Hungary.
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9
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Abstract
Branchpoints in RNA templates are highly mutagenic, but it is not known yet whether this also applies to branchpoints in DNA templates. Here, we report how nucleic acid polymerases replicate a 2',5'-branched DNA (bDNA) molecule. We constructed long-chained bDNA templates containing a branch guanosine and T7 promoters at both arms by splinted ligation. Quantitative real-time PCR analysis was used to investigate whether a branchpoint blocks DNA synthesis from the two arms in the same manner. We find that the blocking effect of a branchpoint is arm-specific. DNA synthesis from the 2'-arm is more than 20,000-fold decreased, whereas from the 3'-arm only 15-fold. Our sequence analysis of full-length nucleic acid generated by Taq DNA polymerase, Moloney murine leukemia virus reverse transcriptase, and T7 RNA polymerase from the 2'-arm of bDNA shows that the branched guanine has a dual coding potential and can base-pair with cytosine and guanine. We find that branchpoint templating is influenced by the type of the surrounding nucleic acid and is probably modulated by polymerase and RNase H active sites. We show that the branchpoint bypass by the polymerases from the 3'-arm of bDNA is predominantly error-free, indicating that bDNA is not as highly mutagenic as 2',5'-branched RNA.
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Affiliation(s)
- Jessica Döring
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
| | - Thomas Hurek
- Department of Microbe-Plant Interactions, CBIB (Center for Biomolecular Interactions Bremen), University of Bremen, D-28334 Bremen, Germany
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Zasedateleva OA, Vasiliskov VA, Surzhikov SA, Kuznetsova VE, Shershov VE, Guseinov TO, Smirnov IP, Yurasov RA, Spitsyn MA, Chudinov AV. dUTPs conjugated with zwitterionic Cy3 or Cy5 fluorophore analogues are effective substrates for DNA amplification and labelling by Taq polymerase. Nucleic Acids Res 2018; 46:e73. [PMID: 29648660 PMCID: PMC6158613 DOI: 10.1093/nar/gky247] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 03/13/2018] [Accepted: 03/24/2018] [Indexed: 02/05/2023] Open
Abstract
To develop structural modifications of dNTPs that are compatible with Taq DNA polymerase activity, we synthesized eight dUTP derivatives conjugated with Cy3 or Cy5 dye analogues that differed in charge and charge distribution throughout the fluorophore. These dUTP derivatives and commercial Cy3- and Cy5-dUTP were studied in Taq polymerase-dependent polymerase chain reactions (PCRs) and in primer extension reactions using model templates containing one, two and three adjacent adenine nucleotides. The relative amounts of amplified DNA and the kinetic parameters Km and Vmax characterizing the incorporation of labelled dUMPs have been estimated using fluorescence measurements and analysed. The dUTPs labelled with electroneutral zwitterionic analogues of Cy3 or Cy5 fluorophores were used by Taq polymerase approximately one order of magnitude more effectively than the dUTPs labelled with negatively charged analogues of Cy3 or Cy5. The nucleotidyl transferase activity of Taq polymerase was also observed and resulted in the addition of dUMPs labelled with electroneutral or positively charged fluorophores to the 3' ends of DNA. The introduction of mutually compensating charges into fluorophores or other functional groups conjugated to dNTPs can be considered a basis for the creation of PCR-compatible modified nucleoside triphosphates.
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Affiliation(s)
- Olga A Zasedateleva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Vadim A Vasiliskov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Sergey A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Viktoriya E Kuznetsova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Valeriy E Shershov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Timur O Guseinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Igor P Smirnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Roman A Yurasov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Maksim A Spitsyn
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
| | - Alexander V Chudinov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilov Street, 119991 Moscow, Russia
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11
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Meroni A, Mentegari E, Crespan E, Muzi-Falconi M, Lazzaro F, Podestà A. The Incorporation of Ribonucleotides Induces Structural and Conformational Changes in DNA. Biophys J 2017; 113:1373-1382. [PMID: 28978432 PMCID: PMC5627062 DOI: 10.1016/j.bpj.2017.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 07/20/2017] [Accepted: 07/25/2017] [Indexed: 02/04/2023] Open
Abstract
Ribonucleotide incorporation is the most common error occurring during DNA replication. Cells have hence developed mechanisms to remove ribonucleotides from the genome and restore its integrity. Indeed, the persistence of ribonucleotides into DNA leads to severe consequences, such as genome instability and replication stress. Thus, it becomes important to understand the effects of ribonucleotides incorporation, starting from their impact on DNA structure and conformation. Here we present a systematic study of the effects of ribonucleotide incorporation into DNA molecules. We have developed, to our knowledge, a new method to efficiently synthesize long DNA molecules (hundreds of basepairs) containing ribonucleotides, which is based on a modified protocol for the polymerase chain reaction. By means of atomic force microscopy, we could therefore investigate the changes, upon ribonucleotide incorporation, of the structural and conformational properties of numerous DNA populations at the single-molecule level. Specifically, we characterized the scaling of the contour length with the number of basepairs and the scaling of the end-to-end distance with the curvilinear distance, the bending angle distribution, and the persistence length. Our results revealed that ribonucleotides affect DNA structure and conformation on scales that go well beyond the typical dimension of the single ribonucleotide. In particular, the presence of ribonucleotides induces a systematic shortening of the molecules, together with a decrease of the persistence length. Such structural changes are also likely to occur in vivo, where they could directly affect the downstream DNA transactions, as well as interfere with protein binding and recognition.
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Affiliation(s)
- Alice Meroni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Elisa Mentegari
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Emmanuele Crespan
- DNA Enzymology and Molecular Virology, Institute of Molecular Genetics IGM-CNR, Pavia, Italy
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy.
| | - Federico Lazzaro
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy
| | - Alessandro Podestà
- Dipartimento di Fisica and C.I.Ma.I.Na, Università degli Studi di Milano, Milano, Italy.
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Kaltenbrunner M, Hochegger R, Cichna-Markl M. Development and validation of a fallow deer (Dama dama)-specific TaqMan real-time PCR assay for the detection of food adulteration. Food Chem 2017; 243:82-90. [PMID: 29146373 DOI: 10.1016/j.foodchem.2017.09.087] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 07/25/2017] [Accepted: 09/17/2017] [Indexed: 11/18/2022]
Abstract
The aim of the present study was to develop a real-time PCR assay for the identification and quantification of fallow deer (Dama dama) in food to detect food adulteration. Despite high sequence homology among different deer species, a fallow deer-specific primer/probe system targeting a fragment of the nuclear MC1-R gene was designed. This primer/probe system did not amplify DNA from 19 other animals and 50 edible plant species. Moderate cross-reactivity was observed for sika deer, red deer, roe deer, reindeer and wild boar. The LOD and LOQ of the real-time PCR assay were 0.1% and 0.4%, respectively. To validate the assay, DNA mixtures, meat extract mixtures, meat mixtures and model game sausages were analyzed. Satisfactory quantitative results were obtained when the calibration mixture was similar to the analyzed sample in both the composition and concentration of the animal species of interest.
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Affiliation(s)
- Maria Kaltenbrunner
- Austrian Agency for Health and Food Safety, Institute for Food Safety, Department of Molecular Biology and Microbiology, Spargelfeldstraße 191, 1220 Vienna, Austria; Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria.
| | - Rupert Hochegger
- Austrian Agency for Health and Food Safety, Institute for Food Safety, Department of Molecular Biology and Microbiology, Spargelfeldstraße 191, 1220 Vienna, Austria.
| | - Margit Cichna-Markl
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 38, 1090 Vienna, Austria.
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13
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Abstract
Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNAHisGUG has been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNAHisGUG containing G-1, U-1, A-1, or C-1 or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNAHisGUG containing U-1 as well as the one containing G-1 Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNAHisGUG variants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNAHisGUG halves containing G-1, U-1, or G1 as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNAHisGUG molecules and provide insights into tRNAHisGUG maturation and the regulation of tRNA half production.
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Affiliation(s)
- Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA
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14
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Wyss LA, Nilforoushan A, Williams DM, Marx A, Sturla SJ. The use of an artificial nucleotide for polymerase-based recognition of carcinogenic O6-alkylguanine DNA adducts. Nucleic Acids Res 2016; 44:6564-73. [PMID: 27378785 PMCID: PMC5001614 DOI: 10.1093/nar/gkw589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/15/2022] Open
Abstract
Enzymatic approaches for locating alkylation adducts at single-base resolution in DNA could enable new technologies for understanding carcinogenesis and supporting personalized chemotherapy. Artificial nucleotides that specifically pair with alkylated bases offer a possible strategy for recognition and amplification of adducted DNA, and adduct-templated incorporation of an artificial nucleotide has been demonstrated for a model DNA adduct O(6)-benzylguanine by a DNA polymerase. In this study, DNA adducts of biological relevance, O(6)-methylguanine (O(6)-MeG) and O(6)-carboxymethylguanine (O(6)-CMG), were characterized to be effective templates for the incorporation of benzimidazole-derived 2'-deoxynucleoside-5'-O-triphosphates ( BENZI: TP and BIM: TP) by an engineered KlenTaq DNA polymerase. The enzyme catalyzed specific incorporation of the artificial nucleotide BENZI: opposite adducts, with up to 150-fold higher catalytic efficiency for O(6)-MeG over guanine in the template. Furthermore, addition of artificial nucleotide BENZI: was required for full-length DNA synthesis during bypass of O(6)-CMG. Selective incorporation of the artificial nucleotide opposite an O(6)-alkylguanine DNA adduct was verified using a novel 2',3'-dideoxy derivative of BENZI: TP. The strategy was used to recognize adducts in the presence of excess unmodified DNA. The specific processing of BENZI: TP opposite biologically relevant O(6)-alkylguanine adducts is characterized herein as a basis for potential future DNA adduct sequencing technologies.
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Affiliation(s)
- Laura A Wyss
- Department of Health Sciences and Technology, ETH Zu¨rich, 8092 Zürich, Switzerland
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zu¨rich, 8092 Zürich, Switzerland
| | - David M Williams
- Center for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield, Sheffield S3 7HF, UK
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, 78457 Konstanz, Germany
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zu¨rich, 8092 Zürich, Switzerland
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15
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Nagy A, Černíková L, Vitásková E, Křivda V, Dán Á, Dirbáková Z, Jiřincová H, Procházka B, Sedlák K, Havlíčková M. MeltMan: Optimization, Evaluation, and Universal Application of a qPCR System Integrating the TaqMan qPCR and Melting Analysis into a Single Assay. PLoS One 2016; 11:e0151204. [PMID: 27031831 PMCID: PMC4816343 DOI: 10.1371/journal.pone.0151204] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/23/2016] [Indexed: 12/05/2022] Open
Abstract
In the present work, we optimised and evaluated a qPCR system integrating 6-FAM (6-carboxyfluorescein)-labelled TaqMan probes and melting analysis using the SYTO 82 (S82) DNA binding dye in a single reaction. We investigated the influence of the S82 on various TaqMan and melting analysis parameters and defined its optimal concentration. In the next step, the method was evaluated in 36 different TaqMan assays with a total of 729 paired reactions using various DNA and RNA templates, including field specimens. In addition, the melting profiles of interest were correlated with the electrophoretic patterns. We proved that the S82 is fully compatible with the FAM-TaqMan system. Further, the advantages of this approach in routine diagnostic TaqMan qPCR were illustrated with practical examples. These included solving problems with flat or other atypical amplification curves or even false negativity as a result of probe binding failure. Our data clearly show that the integration of the TaqMan qPCR and melting analysis into a single assay provides an additional control option as well as the opportunity to perform more complex analyses, get more data from the reactions, and obtain analysis results with higher confidence.
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Affiliation(s)
- Alexander Nagy
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
| | - Lenka Černíková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Eliška Vitásková
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
| | - Vlastimil Křivda
- Laboratory of Molecular Methods, State Veterinary Institute Prague, Prague, Czech Republic
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Ádám Dán
- National Food Chain Safety Office, Veterinary Diagnostic Directorate, Molecular Biology Laboratory, Budapest, Hungary
| | - Zuzana Dirbáková
- Department of Virology, State Veterinary Institute Zvolen, Zvolen, Slovak Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
| | - Bohumír Procházka
- Department of Informatics and Biostatistics, National Institute of Public Health, Prague, Czech Republic
| | - Kamil Sedlák
- Department of Virology and Serology, State Veterinary Institute Prague, Prague, Czech Republic
| | - Martina Havlíčková
- National Reference Laboratory for Influenza, National Institute of Public Health, Prague, Czech Republic
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Kimura Y, Soma T, Kasahara N, Delobel D, Hanami T, Tanaka Y, de Hoon MJL, Hayashizaki Y, Usui K, Harbers M. Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays. PLoS One 2016; 11:e0146950. [PMID: 26863543 PMCID: PMC4749234 DOI: 10.1371/journal.pone.0146950] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/22/2015] [Indexed: 01/13/2023] Open
Abstract
Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.
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Affiliation(s)
- Yasumasa Kimura
- K.K. DNAFORM, 75–1, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0046, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takahiro Soma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Naoko Kasahara
- RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Diane Delobel
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takeshi Hanami
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Michiel J. L. de Hoon
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Kengo Usui
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Matthias Harbers
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
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Hestand MS, Van Houdt J, Cristofoli F, Vermeesch JR. Polymerase specific error rates and profiles identified by single molecule sequencing. Mutat Res 2016; 784-785:39-45. [PMID: 26829216 DOI: 10.1016/j.mrfmmm.2016.01.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Revised: 12/16/2015] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
DNA polymerases have an innate error rate which is polymerase and DNA context specific. Historically the mutational rate and profiles have been measured using a variety of methods, each with their own technical limitations. Here we used the unique properties of single molecule sequencing to evaluate the mutational rate and profiles of six DNA polymerases at the sequence level. In addition to accurately determining mutations in double strands, single molecule sequencing also captures direction specific transversions and transitions through the analysis of heteroduplexes. Not only did the error rates vary, but also the direction specific transitions differed among polymerases.
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Affiliation(s)
- Matthew S Hestand
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Jeroen Van Houdt
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Francesca Cristofoli
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium
| | - Joris R Vermeesch
- Department of Human Genetics, KU Leuven, O&N I Herestraat 49-box 602, 3000 Leuven, Belgium.
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Abstract
Phytoestrogens are popular alternatives to estrogen therapy however their effects on hemostasis in postmenopausal women are unknown. This chapter describes a protocol to determine the effect of the phytoestrogens genistein, daidzein and equol, on the expression of key genes from the hemostatic system in human hepatocyte cell models and to determine the role of estrogen receptors in mediating any response seen using in vitro culture systems and Taqman(®) gene expression analysis.
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Affiliation(s)
- Lynne A Kelly
- Department of Paediatrics, The Coombe Women and Infants University Hospital & Trinity College, Dublin 8, Ireland.
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19
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Maltby S, Plank M, Ptaschinski C, Mattes J, Foster PS. MicroRNA function in mast cell biology: protocols to characterize and modulate microRNA expression. Methods Mol Biol 2015; 1220:287-304. [PMID: 25388258 DOI: 10.1007/978-1-4939-1568-2_18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNA molecules that can modulate mRNA levels through RNA-induced silencing complex (RISC)-mediated degradation. Recognition of target mRNAs occurs through imperfect base pairing between an miRNA and its target, meaning that each miRNA can target a number of different mRNAs to modulate gene expression. miRNAs have been proposed as novel therapeutic targets and many studies are aimed at characterizing miRNA expression patterns and functions within a range of cell types. To date, limited research has focused on the function of miRNAs specifically in mast cells; however, this is an emerging field. In this chapter, we will briefly overview miRNA synthesis and function and the current understanding of miRNAs in hematopoietic development and immune function, emphasizing studies related to mast cell biology. The chapter will conclude with fundamental techniques used in miRNA studies, including RNA isolation, real-time PCR and microarray approaches for quantification of miRNA expression levels, and antagomir design to interfere with miRNA function.
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Affiliation(s)
- Steven Maltby
- Priority Research Centre for Asthma and Respiratory Diseases, School of Biomedical Sciences and Pharmacy, Faculty of Health, University of Newcastle, Lot 1 Kookaburra Circuit, New Lambton Heights, NSW, 2305, Australia,
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Abstract
Prostate cancer (PCa) is one of the most common cancer worldwide and accounts for 14.4 % of all new cancer cases. The clinical outcome and management of PCa can be significantly improved by use of biomarker assays for early detection, prognosis and also for prediction and monitoring of treatment response. MiRNAs are short, endogenous, single-stranded RNA molecules that play important role in regulation of gene expression and can modulate a number of cellular processes. Discovery of miRNAs in circulation has not only facilitated understanding their role in various diseases but also paved new avenues for biomarker discovery due to their ease of access and stability. The fact that a minimally invasive test based on miRNAs profiles can distinguish the presence or absence of disease illustrates immense potential of these molecules as predictive biomarkers.In this chapter, we have summarized the presumed mechanisms of miRNA release into the circulation and systematically summarized the studies of circulatory miRNAs in PCa. Also, we have mainly focused on the methodology of identification of circulatory miRNAs from biofluids.
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Affiliation(s)
- Anvesha Srivastava
- Department of Biology, Chemistry and Physics, Cancer Research Laboratory, University of the District of Columbia, Washington DC, 20008, USA
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Tanigawa N, Fujita T, Fujii H. Oligoribonucleotide (ORN) interference-PCR (ORNi-PCR): a simple method for suppressing PCR amplification of specific DNA sequences using ORNs. PLoS One 2014; 9:e113345. [PMID: 25405983 PMCID: PMC4236179 DOI: 10.1371/journal.pone.0113345] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Accepted: 10/22/2014] [Indexed: 11/18/2022] Open
Abstract
Polymerase chain reaction (PCR) amplification of multiple templates using common primers is used in a wide variety of molecular biological techniques. However, abundant templates sometimes obscure the amplification of minor species containing the same primer sequences. To overcome this challenge, we used oligoribonucleotides (ORNs) to inhibit amplification of undesired template sequences without affecting amplification of control sequences lacking complementarity to the ORNs. ORNs were effective at very low concentrations, with IC50 values for ORN-mediated suppression on the order of 10 nM. DNA polymerases that retain 3'-5' exonuclease activity, such as KOD and Pfu polymerases, but not those that retain 5'-3' exonuclease activity, such as Taq polymerase, could be used for ORN-mediated suppression. ORN interference-PCR (ORNi-PCR) technology should be a useful tool for both molecular biology research and clinical diagnosis.
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Affiliation(s)
- Naoki Tanigawa
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Toshitsugu Fujita
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Hodaka Fujii
- Chromatin Biochemistry Research Group, Combined Program on Microbiology and Immunology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- * E-mail:
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22
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Kubota H, Sakai T, Gawad A, Makino H, Akiyama T, Ishikawa E, Oishi K. Development of TaqMan-based quantitative PCR for sensitive and selective detection of toxigenic Clostridium difficile in human stools. PLoS One 2014; 9:e111684. [PMID: 25360662 PMCID: PMC4216139 DOI: 10.1371/journal.pone.0111684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 10/07/2014] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile is the main cause of nosocomial diarrhea, but is also found in asymptomatic subjects that are potentially involved in transmission of C. difficile infection. A sensitive and accurate detection method of C. difficile, especially toxigenic strains is indispensable for the epidemiological investigation. Methods TaqMan-based quantitative-PCR (qPCR) method for targeting 16S rRNA, tcdB, and tcdA genes of C. difficile was developed. The detection limit and accuracy of qPCR were evaluated by analyzing stool samples spiked with known amounts of C. difficile. A total of 235 stool specimens collected from 82 elderly nursing home residents were examined by qPCR, and the validity was evaluated by comparing the detection result with that by C. difficile selective culture (CDSC). Results The analysis of C. difficile-spiked stools confirmed that qPCR quantified whole C. difficile (TcdA+TcdB+, TcdA−TcdB+, and TcdA−TcdB− types), TcdB-producing strains (TcdA+TcdB+ and TcdA−TcdB+ types), and TcdA-producing strains (TcdA+TcdB+ type), respectively, with a lower detection limit of 103 cells/g of stool. Of the 235 specimens examined, 12 specimens (5.1%) were C. difficile-positive by qPCR: TcdA+TcdB+ strain in six specimens and TcdA−TcdB− strain in the other six. CDSC detected C. difficile in 9 of the 12 specimens, and toxigenic types of the isolates from the 9 specimens were consistent with those identified by qPCR, supporting the validity of our qPCR method. Moreover, the qPCR examination revealed that the carriage rate of whole C. difficile and that of toxigenic strains in the 82 subjects over a 6-month period ranged from 2.4 to 6.8% and 1.2 to 3.8%, respectively. An average qPCR count of C. difficile detected was 104.5 cells/g of stool, suggesting that C. difficile constituted a very small fraction of intestinal microbiota. Conclusion Our qPCR method should be an effective tool for both clinical diagnosis and epidemiological investigation of C. difficile.
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Affiliation(s)
- Hiroyuki Kubota
- Yakult Honsha European Research Center for Microbiology ESV, Gent-Zwijnaarde, Belgium
- Yakult Central Institute, Tokyo, Japan
- * E-mail:
| | | | - Agata Gawad
- Yakult Honsha European Research Center for Microbiology ESV, Gent-Zwijnaarde, Belgium
| | | | - Takuya Akiyama
- Yakult Honsha European Research Center for Microbiology ESV, Gent-Zwijnaarde, Belgium
- Yakult Central Institute, Tokyo, Japan
| | | | - Kenji Oishi
- Yakult Honsha European Research Center for Microbiology ESV, Gent-Zwijnaarde, Belgium
- Yakult Central Institute, Tokyo, Japan
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Lim G, Hwang HJ, Kim JH. Effect of surface hydrophobicity on activity of immobilized Taq DNA polymerase, its reusability and storage. J Nanosci Nanotechnol 2014; 14:6452-6457. [PMID: 25936135 DOI: 10.1166/jnn.2014.8844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Method of oriented and activity-preserved immobilization of biologically active proteins based on concepts of active-site masking and kinetic control was previously reported. We extended our study and found that the surface hydrophobicity had a noticeable effect on the activity of active-site protected immobilized (PIM) Taq DNA polymerase on mixed self-assembled monolayer (SAM) manufactured on Au surface. Hydrophobic SAM was created by using 12-mercaptododecanoic acid and 1-heptanethiol. The resulting Taq DNA polymerase activity was measured by performing PCR amplification and compared with previously reported values acquired with hydrophilic SAM. The maximum activity of immobilized Taq DNA polymerase was achieved at 17.5% of 12-mercaptododecanoic acid and within 90 min of reaction time which are higher than those acquired with hydrophilic SAM; maximum activity at 5% of 12-mercaptododecanoic acid and at 10 min. In order to be applicable to commercial level, immobilized enzyme need to be stable, reusable and storable. PIM Taq DNA polymerase was stably attached to the surface and could be used for as many as 10 PCR runs which were comparable to solution-phase enzyme. Even after 56 days of storage at 4 °C, immobilized enzyme pertained 70% of the initial PIM enzyme activity. These data suggest that PIM Taq DNA polymerase can be used for various commercial applications.
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Yeh ML, Huang CF, Huang CI, Liu SF, Yang HL, Hsieh MY, Huang JF, Dai CY, Chuang WL, Yu ML. Abbott RealTime HBV assay is more sensitive in detection of low viral load and little impacted by drug resistant mutation in chronic hepatitis B patients under nucleot(s)ide analogues therapy. PLoS One 2014; 9:e101790. [PMID: 25000502 PMCID: PMC4085076 DOI: 10.1371/journal.pone.0101790] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 06/10/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Selection of drug-resistant strains may lead to failure of HBV antiviral therapy. There is little information whether there is detection difference in drug resistant mutations between different viral load assays of HBV. OBJECTIVES This study is aimed to investigate whether there is drug-resistant strains related detection difference between Abbott RealTime HBV (RealTime) and CobasAmpliPrep/CobasTaqMan HBV assays 2.0 (TaqMan). STUDY DESIGN One hundred and thirty-four CHB patients who received HBV anti-viral therapy were enrolled. HBV virological markers were tested 3 months apart regularly. Serum HBV DNA levels were determined using the TaqMan and RealTime. YMDD (rt180M and rt204V) mutation was checked in patients who experienced virologic breakthrough (VBT). RESULTS The correlation of HBV DNA observed between the RealTime and TaqMan was good for all 571 samples (R2 = 0.797; P<0.001). However, the correlation in the 434 samples with HBV DNA level <3 log10 IU/ml was not as good as in all samples (R2 = 0.457). Overall, 21.5% of samples had a detection difference of ≥ 1 log10 IU/ml with 91.9% of these having HBV DNA level <3 log10 IU/ml. Twenty-four patients experienced VBT. Three of these patients had acquired the YMDD mutation and exhibited discordant viral load results between the two methods tested. In each case, persistent HBV DNA was detected by RealTime and undetectable with TaqMan. Of the patients who experienced a VBT and had acquired YMDD mutation, 4.7% had undetectable HBV DNA by TaqMan while all were detectable with RealTime. CONCLUSIONS RealTime assay is more sensitive and is little impacted by the development of drug resistant mutation.
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Affiliation(s)
- Ming-Lun Yeh
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Feng Huang
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Occupational Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ching-I Huang
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shu-Fen Liu
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Hua-Ling Yang
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Yen Hsieh
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jee-Fu Huang
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Internal Medicine, Kaohsiung Municipal Hsiao-Kang Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chia-Yen Dai
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wan-Long Chuang
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Lung Yu
- Division of Hepatobiliary, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Faculty of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Hepatitis Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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Kitabayashi M, Nishiya Y, Esaka M. A Simple and Efficient Method for High Fidelity PCR Cloning Using Antibody-neutralizing Technology. Biosci Biotechnol Biochem 2014; 67:2034-7. [PMID: 14519999 DOI: 10.1271/bbb.67.2034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We introduce the TA cloning antibody method for the high-fidelity PCR product amplified by family B DNA polymerase without purification. This method uses antibodies and Thermus aquaticus (Taq) DNA polymerase. The antibodies can inhibit only the activity of family B DNA polymerase, and Taq can co-work for A-tailing. This method has nearly cloning efficiency to that of the PCR product of Taq.
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Affiliation(s)
- Masao Kitabayashi
- Graduate School of Biosphere Sciences, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Japan
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Drum M, Kranaster R, Ewald C, Blasczyk R, Marx A. Variants of a Thermus aquaticus DNA polymerase with increased selectivity for applications in allele- and methylation-specific amplification. PLoS One 2014; 9:e96640. [PMID: 24800860 PMCID: PMC4011760 DOI: 10.1371/journal.pone.0096640] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 04/09/2014] [Indexed: 01/25/2023] Open
Abstract
The selectivity of DNA polymerases is crucial for many applications. For example, high discrimination between the extension of matched versus mismatched primer termini is desired for the detection of a single nucleotide variation at a particular locus within the genome. Here we describe the generation of thermostable mutants of the large fragment of Thermus aquaticus DNA polymerase (KlenTaq) with increased mismatch extension selectivity. In contrast to previously reported much less active KlenTaq mutants with mismatch discrimination abilities, many of the herein discovered mutants show conserved wild-type-like high activities. We demonstrate for one mutant containing the single amino acid exchange R660V the suitability for application in allele-specific amplifications directly from whole blood without prior sample purification. Also the suitability of the mutant for methylation specific amplification in the diagnostics of 5-methyl cytosines is demonstrated. Furthermore, the identified mutant supersedes other commercially available enzymes in human leukocyte antigen (HLA) analysis by sequence-specific primed polymerase chain reactions (PCRs).
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Affiliation(s)
- Matthias Drum
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Ramon Kranaster
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- myPOLS Biotec, University of Konstanz, Konstanz, Germany
| | - Christina Ewald
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
| | - Rainer Blasczyk
- Institute for Transfusion Medicine, Hannover Medical School, Hannover, Germany
| | - Andreas Marx
- Department of Chemistry, Konstanz Research School Chemical Biology, University of Konstanz, Konstanz, Germany
- * E-mail:
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Chen Y, Bogema DR, Barchia IM, Herron GA. Quantification of the pirimicarb resistance allele frequency in pooled cotton aphid (Aphis gossypii Glover) samples by TaqMan SNP genotyping assay. PLoS One 2014; 9:e91104. [PMID: 24614533 PMCID: PMC3948748 DOI: 10.1371/journal.pone.0091104] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Accepted: 02/07/2014] [Indexed: 11/25/2022] Open
Abstract
Background Pesticide resistance monitoring is a crucial part to achieving sustainable integrated pest management (IPM) in agricultural production systems. Monitoring of resistance in arthropod populations is initially performed by bioassay, a method that detects a phenotypic response to pesticides. Molecular diagnostic assays, offering speed and cost improvements, can be developed when the causative mutation for resistance has been identified. However, improvements to throughput are limited as genotyping methods cannot be accurately applied to pooled DNA. Quantifying an allele frequency from pooled DNA would allow faster and cheaper monitoring of pesticide resistance. Methodology/Principal Findings We demonstrate a new method to quantify a resistance allele frequency (RAF) from pooled insects via TaqMan assay by using raw fluorescence data to calculate the transformed fluorescence ratio k’ at the inflexion point based on a four parameter sigmoid curve. Our results show that k’ is reproducible and highly correlated with RAF (r >0.99). We also demonstrate that k’ has a non-linear relationship with RAF and that five standard points are sufficient to build a prediction model. Additionally, we identified a non-linear relationship between runs for k’, allowing the combination of samples across multiple runs in a single analysis. Conclusions/Significance The transformed fluorescence ratio (k') method can be used to monitor pesticide resistance in IPM and to accurately quantify allele frequency from pooled samples. We have determined that five standards (0.0, 0.2, 0.5, 0.8, and 1.0) are sufficient for accurate prediction and are statistically-equivalent to the 13 standard points used experimentally
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Affiliation(s)
- Yizhou Chen
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Idris M Barchia
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
| | - Grant A Herron
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, New South Wales, Australia
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Fan J, Luo Y, Michailides TJ, Guo L. Simultaneous quantification of alleles E198A and H6Y in the β-tubulin gene conferring benzimidazole resistance in Monilinia fructicola using a duplex real-time (TaqMan) PCR. Pest Manag Sci 2014; 70:245-251. [PMID: 23775824 DOI: 10.1002/ps.3549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 02/28/2013] [Accepted: 04/05/2013] [Indexed: 06/02/2023]
Abstract
BACKGROUND The benzimidazole fungicide thiophanate-methyl is commonly used for the control of brown rot of stone fruits. Low and high levels of resistance to this fungicide have been found in field isolates of the causal pathogen Monilinia fructicola. RESULTS The minor groove binding (MGB) TaqMan probes specific for alleles E198A and H6Y conferring the high and low levels of resistance in the β-tubulin gene of M. fructicola were designed. A duplex real-time PCR assay based on these probes was developed for simultaneous quantification of both mutations in a pathogen population. The specificity tests for the primers and probes were conducted using different fungal species of stone and pome fruit pathogens. Similar results were obtained between the duplex real-time (TaqMan) PCR assay and the conventional method to quantify the frequencies of alleles E198A and H6Y of eight samples from different peach orchards. CONCLUSION The MGB TaqMan probe based duplex real-time PCR provides a useful tool for simultaneous quantification of both alleles, E198A and H6Y, conferring high and low resistance, and has a potential in monitoring the benzimidazole-resistance in M. fructicola populations in stone and pome fruit orchards.
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Affiliation(s)
- Jinyan Fan
- Department of Plant Pathology, China Agricultural University, Beijing, 100193, P.R. China
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Williams MD, Wong W, Rixon A, Satoor SN, Hardikar AA, Joglekar MV. Pdx1 (GFP/w) mice for isolation, characterization, and differentiation of pancreatic progenitor cells. Methods Mol Biol 2014; 1194:271-288. [PMID: 25064109 DOI: 10.1007/978-1-4939-1215-5_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It is well known that human cells are diverse with respect to their epigenome, transcriptome, and proteome. In the context of regenerative medicine, it is important for the transplanted cells or tissues to faithfully recapitulate their intended tissue type in each of these respects. Whether the cells chosen for such an application are embryonic, postnatal, or induced pluripotent stem cells, the transplanted product must behave in a predictable and reliable manner to be a safe and effective treatment option. Irrespective of the choice of cells used in such an application, the characterization and understanding of the developmental cues responsible for establishing and maintaining the desired cell phenotype are essential.Animal models are extremely important in understanding the development of a specific tissue, which can then be subsequently extrapolated to human studies. Generation of transgenic animal models with whole-body gene knockout, conditional knockout, constitutive fluorescent gene reporters, and Cre-Lox-based conditional and lineage reporters has revolutionized the field of developmental biology. An intrinsically complex network of the actions and interactions of the multitude of different signalling cascades is required for development. A thorough understanding of such networks, gained through studies on transgenic animal models, is essential for the development of the techniques necessary to reliably differentiate a given stem or progenitor cell population into a specific cell type, such as an islet-like, insulin-producing cell aggregate.In this chapter, we describe the use of GFP (green fluorescent protein)-based reporter mice for isolation of cells of choice, analyzing gene expression in those cells as well as their use for screening signalling molecules to understand their effect on differentiation.
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Affiliation(s)
- Michael D Williams
- NHMRC Clinical Trials Centre, The University of Sydney, Medical Foundation Building, Camperdown, NSW, 2050, Australia
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Abstract
MicroRNAs (miRNAs) are important regulators of diverse biologic processes. In the hematopoietic system, miRNAs have been shown to regulate lineage fate decisions, mature immune effector cell function, apoptosis, and cell cycling, and a more limited number of miRNAs has been shown to regulate hematopoietic stem cell (HSC) self-renewal. Many of these miRNAs were initially identified as candidate regulators of HSC function by comparing miRNA expression in hematopoietic stem and progenitors cells (HSPCs) to their mature progeny. While the measurement of miRNA expression in rare cell populations such as HSCs poses practical challenges due to the low amount of RNA present, a number of techniques have been developed to measure miRNAs in small numbers of cells. Here, we describe our protocol for measuring miRNAs in purified mouse HSCs using a highly sensitive real-time quantitative PCR strategy that utilizes microfluidic array cards containing pre-spotted TaqMan probes that allows the detection of mature miRNAs in small reaction volumes. We also describe a simple data analysis method to evaluate miRNA expression profiling data using an open-source software package (HTqPCR) using mouse HSC miRNA profiling data generated in our lab.
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Affiliation(s)
- Wenhuo Hu
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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31
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Luo BZ, Mo QH, Li RS, Bo QR, Xu HN, Sha CH, Liao XY. [Rapid detection of novel avian influenza virus subtype H7N9 by multiplex real-time RT-PCR]. Bing Du Xue Bao 2014; 30:1-5. [PMID: 24772890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In order to develop a rapid detection kit for novel avian influenza virus (AIV) subtype H7N9, two sets of specific primers and probes were designed based on the nucleotide sequences of hemagglutinin antigen (HA) and neuraminidase antigen (NA) of novel H7N9 virus (2013) available in GenBank to establish the method of TaqMan probe-based multiplex real-time RT-PCR for rapid detection of AIV subtype H7N9. The primer and probe of HA were for all H7 subtype AIVs, while the primer and probe of NA were only for novel N9 subtype AIVs. The results showed that this method had high sensitivity and specificity. This method was applicable to the testing of positive standard sample with a minimum concentration of 10 copies/microL; it not only distinguished H7 subtype from H1, H3, H5, H6, and H9 subtypes, but also distinguished novel N9 subtype from traditional N9 subtype. A total of 2700 samples from Zhuhai, China were tested by this method, and the results were as expected. For the advantages of sensitivity and specificity, the method holds promise for wide application.
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Betz K, Malyshev DA, Lavergne T, Welte W, Diederichs K, Romesberg FE, Marx A. Structural insights into DNA replication without hydrogen bonds. J Am Chem Soc 2013; 135:18637-43. [PMID: 24283923 PMCID: PMC3982147 DOI: 10.1021/ja409609j] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The genetic alphabet is composed of two base pairs, and the development of a third, unnatural base pair would increase the genetic and chemical potential of DNA. d5SICS-dNaM is one of the most efficiently replicated unnatural base pairs identified to date, but its pairing is mediated by only hydrophobic and packing forces, and in free duplex DNA it forms a cross-strand intercalated structure that makes its efficient replication difficult to understand. Recent studies of the KlenTaq DNA polymerase revealed that the insertion of d5SICSTP opposite dNaM proceeds via a mutually induced-fit mechanism, where the presence of the triphosphate induces the polymerase to form the catalytically competent closed structure, which in turn induces the pairing nucleotides of the developing unnatural base pair to adopt a planar Watson-Crick-like structure. To understand the remaining steps of replication, we now report the characterization of the prechemistry complexes corresponding to the insertion of dNaMTP opposite d5SICS, as well as multiple postchemistry complexes in which the already formed unnatural base pair is positioned at the postinsertion site. Unlike with the insertion of d5SICSTP opposite dNaM, addition of dNaMTP does not fully induce the formation of the catalytically competent closed state. The data also reveal that once synthesized and translocated to the postinsertion position, the unnatural nucleobases again intercalate. Two modes of intercalation are observed, depending on the nature of the flanking nucleotides, and are each stabilized by different interactions with the polymerase, and each appear to reduce the affinity with which the next correct triphosphate binds. Thus, continued primer extension is limited by deintercalation and rearrangements with the polymerase active site that are required to populate the catalytically active, triphosphate bound conformation.
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Affiliation(s)
- Karin Betz
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Denis A. Malyshev
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Thomas Lavergne
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Wolfram Welte
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Kay Diederichs
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, California, 92037
| | - Andreas Marx
- Departments of Chemistry and Biology, Konstanz Research School Chemical Biology, Universität Konstanz, Universitätsstrasse 10, D-78464 Konstanz, Germany
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Abstract
The detection and sorting of aqueous drops is central to microfluidic workflows for high-throughput biology applications, including directed evolution, digital PCR, and antibody screening. However, high-throughput detection and sorting of drops require optical systems and microfluidic components that are complex, difficult to build, and often yield inadequate sensitivity and throughput. Here, we demonstrate a general method to harness flow cytometry, with its unmatched speed and sensitivity, for droplet-based microfluidic sorting.
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Affiliation(s)
- Shaun W Lim
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California, San Francisco, San Francisco, California, USA
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Ouyang P, Arif M, Fletcher J, Melcher U, Ochoa Corona FM. Enhanced reliability and accuracy for field deployable bioforensic detection and discrimination of Xylella fastidiosa subsp. pauca, causal agent of citrus variegated chlorosis using razor ex technology and TaqMan quantitative PCR. PLoS One 2013; 8:e81647. [PMID: 24312333 PMCID: PMC3843690 DOI: 10.1371/journal.pone.0081647] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/15/2013] [Indexed: 11/18/2022] Open
Abstract
A reliable, accurate and rapid multigene-based assay combining real time quantitative PCR (qPCR) and a Razor Ex BioDetection System (Razor Ex) was validated for detection of Xylella fastidiosa subsp. pauca (Xfp, a xylem-limited bacterium that causes citrus variegated chlorosis [CVC]). CVC, which is exotic to the United States, has spread through South and Central America and could significantly impact U.S. citrus if it arrives. A method for early, accurate and sensitive detection of Xfp in plant tissues is needed by plant health officials for inspection of products from quarantined locations, and by extension specialists for detection, identification and management of disease outbreaks and reservoir hosts. Two sets of specific PCR primers and probes, targeting Xfp genes for fimbrillin and the periplasmic iron-binding protein were designed. A third pair of primers targeting the conserved cobalamin synthesis protein gene was designed to detect all possible X. fastidiosa (Xf) strains. All three primer sets detected as little as 1 fg of plasmid DNA carrying X. fastidiosa target sequences and genomic DNA of Xfp at as little as 1 - 10 fg. The use of Razor Ex facilitates a rapid (about 30 min) in-field assay capability for detection of all Xf strains, and for specific detection of Xfp. Combined use of three primer sets targeting different genes increased the assay accuracy and broadened the range of detection. To our knowledge, this is the first report of a field-deployable rapid and reliable bioforensic detection and discrimination method for a bacterial phytopathogen based on multigene targets.
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Affiliation(s)
- Ping Ouyang
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Mohammad Arif
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Jacqueline Fletcher
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * (JF); (MOC)
| | - Ulrich Melcher
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Francisco Manuel Ochoa Corona
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity, Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, Oklahoma, United States of America
- * (JF); (MOC)
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Wilcox TM, McKelvey KS, Young MK, Jane SF, Lowe WH, Whiteley AR, Schwartz MK. Robust detection of rare species using environmental DNA: the importance of primer specificity. PLoS One 2013; 8:e59520. [PMID: 23555689 PMCID: PMC3608683 DOI: 10.1371/journal.pone.0059520] [Citation(s) in RCA: 215] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/15/2013] [Indexed: 11/18/2022] Open
Abstract
Environmental DNA (eDNA) is being rapidly adopted as a tool to detect rare animals. Quantitative PCR (qPCR) using probe-based chemistries may represent a particularly powerful tool because of the method’s sensitivity, specificity, and potential to quantify target DNA. However, there has been little work understanding the performance of these assays in the presence of closely related, sympatric taxa. If related species cause any cross-amplification or interference, false positives and negatives may be generated. These errors can be disastrous if false positives lead to overestimate the abundance of an endangered species or if false negatives prevent detection of an invasive species. In this study we test factors that influence the specificity and sensitivity of TaqMan MGB assays using co-occurring, closely related brook trout (Salvelinus fontinalis) and bull trout (S. confluentus) as a case study. We found qPCR to be substantially more sensitive than traditional PCR, with a high probability of detection at concentrations as low as 0.5 target copies/µl. We also found that number and placement of base pair mismatches between the Taqman MGB assay and non-target templates was important to target specificity, and that specificity was most influenced by base pair mismatches in the primers, rather than in the probe. We found that insufficient specificity can result in both false positive and false negative results, particularly in the presence of abundant related species. Our results highlight the utility of qPCR as a highly sensitive eDNA tool, and underscore the importance of careful assay design.
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Affiliation(s)
- Taylor M Wilcox
- United States Department of Agriculture Forest Service, Rocky Mountain Research Station, Missoula, Montana, United States of America.
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Kho SL, Chua KH, George E, Tan JAMA. High throughput molecular confirmation of β-thalassemia mutations using novel TaqMan probes. Sensors (Basel) 2013; 13:2506-14. [PMID: 23429513 PMCID: PMC3649372 DOI: 10.3390/s130202506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 01/25/2013] [Accepted: 02/06/2013] [Indexed: 11/29/2022]
Abstract
β-Thalassemia is a public health problem where 4.5% of Malaysians are β-thalassemia carriers. The genetic disorder is caused by defects in the β-globin gene complex which lead to reduced or complete absence of β-globin chain synthesis. Five TaqMan genotyping assays were designed and developed to detect the common β-thalassemia mutations in Malaysian Malays. The assays were evaluated with 219 “blinded” DNA samples and the results showed 100% sensitivity and specificity. The in-house designed TaqMan genotyping assays were found to be cost- and time-effective for characterization of β-thalassemia mutations in the Malaysian population.
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Affiliation(s)
- Siew Leng Kho
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (S.L.K.); (K.H.C.)
| | - Kek Heng Chua
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (S.L.K.); (K.H.C.)
| | - Elizabeth George
- Department of Pathology-Hematology, Faculty of Medicine and Health Sciences, University Putra Malaysia, Serdang, Selangor 43400, Malaysia; E-Mail:
| | - Jin Ai Mary Anne Tan
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; E-Mails: (S.L.K.); (K.H.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +603-7967-4903; Fax: +603-7967-6600
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Meng QL, Qiu F, Shen LP, Bi SL. [Establishment and application of TaqMan real-time RT-PCR for the detection of hepatitis E virus]. Zhonghua Shi Yan He Lin Chuang Bing Du Xue Za Zhi 2012; 26:486-488. [PMID: 23627038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To establish a specific TaqMan-based Real-time PCR assay for the detection of hepatitis E virus (HEV). METHODS According to the references, primers-probe sets which were located in ORF2, the conservative part of HEV genome were designed and therefore we established a HEV TaqMan real-time RT-PCR assay with great performance of specificity, sensitivity and reproducibility. And then it was used in the detection of HEV RNA in clinical samples. RESULTS The HEV Real-time RT-PCR assay established in this study were able to detect HEV RNA with a detection limit of 10 copies/reaction. When the detection of a same sample was repeated for several times, coefficients of variation (CV) was all less than 1.53%. Our data also suggested that there were 1.87 x 10(6)-8.12 x 10(9) RNA copies in 1 ml of the clinical samples. CONCLUSION The TaqMan-based Real-time PCR assay established in this study was specific and precise for the rapid detection of HEV RNA. It was applied successfully in the pathogen detection of clinical samples.
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Affiliation(s)
- Qing-Ling Meng
- Institute for Viral Disease Control and Prevention, China CDC, Beijing 102206, China
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Zhang AM, Lu HD, Xue JP, Tao XK, Xue T, Sheng W, Zhu YF. [Study on optimization of SRAP-PCR reaction system for Pinellia ternata in Suzhou]. Zhongguo Zhong Yao Za Zhi 2012; 37:3815-3818. [PMID: 23627186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
OBJECTIVE To investigate the optimization system of SRAP-PCR molecular marker technology in the analysis on Pinellia ternata. METHOD SRAP-PCR reaction system for P. ternata was optimized by L16 (5(4)) orthogonal design with five elements (dNTPs, Mg2+, the template DNA, primers, Taq enzyme) and four standards. RESULT The most suitable forward primer for SRAP for Pinellia ternata was 5'-TGAGTCCAAACCGGAAG-3', while the reverse primer was 5'-GACTGCGTACGAATTACG-3'. The optimized reaction system contained 70 ng DNA template, 0.9 micromol x L(-1) primer, 0.20 mmol x L(-1) dNTP s, 1.5 - 2.0 mmol x L(-1) Mg2+, and 2 U Taq enzyme. CONCLUSION SRAP-PCR system for P. ternata is established to lay a foundation for future construction of SRAP genetic map of P. ternata.
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Affiliation(s)
- Ai-Min Zhang
- Anhui Key Laboratory of Plant Resources and Biology, School of Life Science, Huaibei Normal University, Huaibei 235000, China
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Pungitore CR, García C, Sotero Martín V, Tonn CE. Inhibition of Taq DNA polymerase by iridoid aglycone derivates. Cell Mol Biol (Noisy-le-grand) 2012; 58 Suppl:OL1786-OL1790. [PMID: 23137851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 11/02/2012] [Indexed: 06/01/2023]
Abstract
Faithful replication of DNA molecules by DNA polymerases is essential for genome integrity and correct transmission of genetic information in all living organisms. DNA polymerases have recently emerged as important cellular targets for chemical intervention in the development of anti--cancer agents. Herein we report additional synthesis of simplified bicyclic aglycones of iridoids and their biological activity against Taq DNA polymerase with the object to find out some of the likely molecular targets implicated in the biological activity showed for this kind of compounds. The compounds 14, 33 and 34 showed inhibitory activity against Taq DNA polymerase with IC(50) values of 13.47, 17.65 and 18.31 μM, respectively. These results would allow proposing to DNA polymerases as the molecular targets implicated in this bioactivity and enhance the iridoid aglycones as leader molecule to develop new drugs for cancer therapy.
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Affiliation(s)
- C R Pungitore
- Area de Química Orgánica, Facultad de Química, Bioquímica y Farmacia- Universidad Nacional de San Luis, San Luis, Argentine.
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Lim G, Kim J, Kim JH. Optimization of the masking molecule for active-site-protected immobilization of Taq DNA polymerase and its application. Anal Biochem 2012; 432:139-41. [PMID: 23036837 DOI: 10.1016/j.ab.2012.09.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2012] [Revised: 09/19/2012] [Accepted: 09/24/2012] [Indexed: 11/17/2022]
Abstract
The method of oriented and activity-preserved immobilization of biologically active proteins based on concepts of active-site masking and kinetic control was further developed in this study. Minimal requirements for the masking DNA molecule were found to be a 5'overhang of 5-7 nucleotides and a double-stranded region of 11-13 bp to retain approximately 70% of the enzyme activity. The amplification range of protected immobilized (PIM) Taq DNA polymerase was over 1.2 kb. These data suggest that PIM Taq DNA polymerase can be used for various commercial applications.
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Affiliation(s)
- Gumjung Lim
- Department of Chemistry, Kyung Hee University, Seoul 130-701, Republic of Korea
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Danilevich VN, Vasilenko EA, Pechnikova EV, Grishin EV. [New morphotypes of condensed DNA microparticles formed in PCR with KlenTaq- and Taq-polymerases and with plasmid DNAs as templates]. Mikrobiologiia 2012; 81:126-137. [PMID: 22629690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
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42
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Zwielehner J, Lassl C, Hippe B, Pointner A, Switzeny OJ, Remely M, Kitzweger E, Ruckser R, Haslberger AG. Changes in human fecal microbiota due to chemotherapy analyzed by TaqMan-PCR, 454 sequencing and PCR-DGGE fingerprinting. PLoS One 2011; 6:e28654. [PMID: 22194876 PMCID: PMC3237468 DOI: 10.1371/journal.pone.0028654] [Citation(s) in RCA: 148] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Accepted: 11/11/2011] [Indexed: 12/14/2022] Open
Abstract
Background We investigated whether chemotherapy with the presence or absence of antibiotics against different kinds of cancer changed the gastrointestinal microbiota. Methodology/Principal Findings Feces of 17 ambulant patients receiving chemotherapy with or without concomitant antibiotics were analyzed before and after the chemotherapy cycle at four time points in comparison to 17 gender-, age- and lifestyle-matched healthy controls. We targeted 16S rRNA genes of all bacteria, Bacteroides, bifidobacteria, Clostridium cluster IV and XIVa as well as C. difficile with TaqMan qPCR, denaturing gradient gel electrophoresis (DGGE) fingerprinting and high-throughput sequencing. After a significant drop in the abundance of microbiota (p = 0.037) following a single treatment the microbiota recovered within a few days. The chemotherapeutical treatment marginally affected the Bacteroides while the Clostridium cluster IV and XIVa were significantly more sensitive to chemotherapy and antibiotic treatment. DGGE fingerprinting showed decreased diversity of Clostridium cluster IV and XIVa in response to chemotherapy with cluster IV diversity being particularly affected by antibiotics. The occurrence of C. difficile in three out of seventeen subjects was accompanied by a decrease in the genera Bifidobacterium, Lactobacillus, Veillonella and Faecalibacterium prausnitzii. Enterococcus faecium increased following chemotherapy. Conclusions/Significance Despite high individual variations, these results suggest that the observed changes in the human gut microbiota may favor colonization with C.difficile and Enterococcus faecium. Perturbed microbiota may be a target for specific mitigation with safe pre- and probiotics.
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Affiliation(s)
| | | | - Berit Hippe
- Department of Nutritional Sciences, Vienna, Austria
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Rodríguez S, Eriksson M. Low and high expressing alleles of the LMNA gene: implications for laminopathy disease development. PLoS One 2011; 6:e25472. [PMID: 21980471 PMCID: PMC3183053 DOI: 10.1371/journal.pone.0025472] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Accepted: 09/05/2011] [Indexed: 11/18/2022] Open
Abstract
Today, there are at least a dozen different genetic disorders caused by mutations within the LMNA gene, and collectively, they are named laminopathies. Interestingly, the same mutation can cause phenotypes with different severities or even different disorders and might, in some cases, be asymptomatic. We hypothesized that one possible contributing mechanism for this phenotypic variability could be the existence of high and low expressing alleles in the LMNA locus. To investigate this hypothesis, we developed an allele-specific absolute quantification method for lamin A and lamin C transcripts using the polymorphic rs4641(C/T)LMNA coding SNP. The contribution of each allele to the total transcript level was investigated in nine informative human primary dermal fibroblast cultures from Hutchinson-Gilford progeria syndrome (HGPS) and unaffected controls. Our results show differential expression of the two alleles. The C allele is more frequently expressed and accounts for ∼70% of the lamin A and lamin C transcripts. Analysis of samples from six patients with Hutchinson-Gilford progeria syndrome showed that the c.1824C>T, p.G608G mutation is located in both the C and the T allele, which might account for the variability in phenotype seen among HGPS patients. Our method should be useful for further studies of human samples with mutations in the LMNA gene and to increase the understanding of the link between genotype and phenotype in laminopathies.
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Affiliation(s)
- Sofía Rodríguez
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, Huddinge, Sweden
| | - Maria Eriksson
- Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institutet, Huddinge, Sweden
- * E-mail:
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Zhong Q, Bhattacharya S, Kotsopoulos S, Olson J, Taly V, Griffiths AD, Link DR, Larson JW. Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR. Lab Chip 2011; 11:2167-74. [PMID: 21584334 DOI: 10.1039/c1lc20126c] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented.
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Affiliation(s)
- Qun Zhong
- RainDance Technologies, Inc., 44 Hartwell Ave., Lexington, MA 02150, USA.
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Chang SS, Hsu HL, Cheng JC, Tseng CP. An efficient strategy for broad-range detection of low abundance bacteria without DNA decontamination of PCR reagents. PLoS One 2011; 6:e20303. [PMID: 21637859 PMCID: PMC3102696 DOI: 10.1371/journal.pone.0020303] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2010] [Accepted: 04/29/2011] [Indexed: 02/04/2023] Open
Abstract
Background Bacterial DNA contamination in PCR reagents has been a long standing problem that hampers the adoption of broad-range PCR in clinical and applied microbiology, particularly in detection of low abundance bacteria. Although several DNA decontamination protocols have been reported, they all suffer from compromised PCR efficiency or detection limits. To date, no satisfactory solution has been found. Methodology/Principal Findings We herein describe a method that solves this long standing problem by employing a broad-range primer extension-PCR (PE-PCR) strategy that obviates the need for DNA decontamination. In this method, we first devise a fusion probe having a 3′-end complementary to the template bacterial sequence and a 5′-end non-bacterial tag sequence. We then hybridize the probes to template DNA, carry out primer extension and remove the excess probes using an optimized enzyme mix of Klenow DNA polymerase and exonuclease I. This strategy allows the templates to be distinguished from the PCR reagent contaminants and selectively amplified by PCR. To prove the concept, we spiked the PCR reagents with Staphylococcus aureus genomic DNA and applied PE-PCR to amplify template bacterial DNA. The spiking DNA neither interfered with template DNA amplification nor caused false positive of the reaction. Broad-range PE-PCR amplification of the 16S rRNA gene was also validated and minute quantities of template DNA (10–100 fg) were detectable without false positives. When adapting to real-time and high-resolution melting (HRM) analytical platforms, the unique melting profiles for the PE-PCR product can be used as the molecular fingerprints to further identify individual bacterial species. Conclusions/Significance Broad-range PE-PCR is simple, efficient, and completely obviates the need to decontaminate PCR reagents. When coupling with real-time and HRM analyses, it offers a new avenue for bacterial species identification with a limited source of bacterial DNA, making it suitable for use in clinical and applied microbiology laboratories.
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Affiliation(s)
- Shy-Shin Chang
- Graduate Institute of Clinical Medical Sciences, Department of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Department of Medicine, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Department of Family Medicine and Emergency Medicine, Chang Gung Memorial Hospital, Tao-Yuan, Taiwan, Republic of China
| | - Hsung-Ling Hsu
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
| | - Ju-Chien Cheng
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Republic of China
| | - Ching-Ping Tseng
- Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- Molecular Medicine Research Center, Chang Gung University, Tao-Yuan, Taiwan, Republic of China
- * E-mail:
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46
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Danilevich VN, Vasilenko EA, Pechnikova EV, Sokolova OS, Grishin EV. [Micro- And Nanoparticles Of Condensed DNA Produced During PCR With Taq-polymerase In Presence Of Plasmid Matrices]. Mikrobiologiia 2011; 80:411-423. [PMID: 21861380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
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47
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Huang Q, Liu Z, Liao Y, Chen X, Zhang Y, Li Q. Multiplex fluorescence melting curve analysis for mutation detection with dual-labeled, self-quenched probes. PLoS One 2011; 6:e19206. [PMID: 21552536 PMCID: PMC3084284 DOI: 10.1371/journal.pone.0019206] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 03/22/2011] [Indexed: 12/31/2022] Open
Abstract
Probe-based fluorescence melting curve analysis (FMCA) is a powerful tool for mutation detection based on melting temperature generated by thermal denaturation of the probe-target hybrid. Nevertheless, the color multiplexing, probe design, and cross-platform compatibility remain to be limited by using existing probe chemistries. We hereby explored two dual-labeled, self-quenched probes, TaqMan and shared-stem molecular beacons, in their ability to conduct FMCA. Both probes could be directly used for FMCA and readily integrated with closed-tube amplicon hybridization under asymmetric PCR conditions. Improved flexibility of FMCA by using these probes was illustrated in three representative applications of FMCA: mutation scanning, mutation identification and mutation genotyping, all of which achieved improved color-multiplexing with easy probe design and versatile probe combination and all were validated with a large number of real clinical samples. The universal cross-platform compatibility of these probes-based FMCA was also demonstrated by a 4-color mutation genotyping assay performed on five different real-time PCR instruments. The dual-labeled, self-quenched probes offered unprecedented combined advantage of enhanced multiplexing, improved flexibility in probe design, and expanded cross-platform compatibility, which would substantially improve FMCA in mutation detection of various applications.
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Affiliation(s)
- Qiuying Huang
- Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
| | - Zanzan Liu
- Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
| | - Yiqun Liao
- Institute for Biomedical Research, Xiamen University, Xiamen, Fujian, China
| | - Xiaoyun Chen
- Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
| | - Yi Zhang
- Institute for Biomedical Research, Xiamen University, Xiamen, Fujian, China
| | - Qingge Li
- Engineering Research Center of Molecular Diagnostics, Ministry of Education, Department of Biomedical Sciences, School of Life Sciences, and the Key Laboratory of the Ministry of Education for Cell Biology and Tumor Cell Engineering, Xiamen University, Xiamen, Fujian, China
- * E-mail:
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Abstract
Three methods for assembling multiple, overlapping DNA molecules are described. Each method shares the same basic approach: (i) an exonuclease removes nucleotides from the ends of double-stranded (ds) DNA molecules, exposing complementary single-stranded (ss) DNA overhangs that are specifically annealed; (ii) the ssDNA gaps of the joined molecules are filled in by DNA polymerase, and the nicks are covalently sealed by DNA ligase. The first method employs the 3'-exonuclease activity of T4 DNA polymerase (T4 pol), Taq DNA polymerase (Taq pol), and Taq DNA ligase (Taq lig) in a two-step thermocycled reaction. The second method uses 3'-exonuclease III (ExoIII), antibody-bound Taq pol, and Taq lig in a one-step thermocycled reaction. The third method employs 5'-T5 exonuclease, Phusion® DNA polymerase, and Taq lig in a one-step isothermal reaction and can be used to assemble both ssDNA and dsDNA. These assembly methods can be used to seamlessly construct synthetic and natural genes, genetic pathways, and entire genomes and could be very useful for molecular engineering tools.
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Affiliation(s)
- Daniel G Gibson
- J. Craig Venter Institute Inc., Synthetic Biology Group, La Jolla, California, USA
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49
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Abstract
Three methods for assembling multiple, overlapping DNA molecules are described. Each method shares the same basic approach: (i) an exonuclease removes nucleotides from the ends of double-stranded (ds) DNA molecules, exposing complementary single-stranded (ss) DNA overhangs that are specifically annealed; (ii) the ssDNA gaps of the joined molecules are filled in by DNA polymerase, and the nicks are covalently sealed by DNA ligase. The first method employs the 3'-exonuclease activity of T4 DNA polymerase (T4 pol), Taq DNA polymerase (Taq pol), and Taq DNA ligase (Taq lig) in a two-step thermocycled reaction. The second method uses 3'-exonuclease III (ExoIII), antibody-bound Taq pol, and Taq lig in a one-step thermocycled reaction. The third method employs 5'-T5 exonuclease, Phusion® DNA polymerase, and Taq lig in a one-step isothermal reaction and can be used to assemble both ssDNA and dsDNA. These assembly methods can be used to seamlessly construct synthetic and natural genes, genetic pathways, and entire genomes and could be very useful for molecular engineering tools.
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Affiliation(s)
- Daniel G Gibson
- J. Craig Venter Institute Inc., Synthetic Biology Group, La Jolla, California, USA
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50
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Zhao G, Guan Y. Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions. Acta Biochim Biophys Sin (Shanghai) 2010; 42:722-8. [PMID: 20829187 DOI: 10.1093/abbs/gmq082] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
DNA polymerases amplify DNA fragments through primer extension reactions. However, polymerization behavior of short primers in the primer extension process has not been systematically explored. In this study, we examined the minimal primer length required for primer extension, and the effect of primer length, mismatches and other conditions on DNA polymerization using a non-radioactive method. Under the condition we conducted, the shortest primers polymerized by Klenow fragment (KF) and Taq DNA polymerase in our experiments were respectively heptamer and octamer. The extension efficiency was also affected by the up-stream overhanging structure of the primer-template complex. We hypothesized a simple model to interpret these observations based on the polymerase structures. Furthermore, it was found that the longer the primer, the more efficient is the primer extension. These polymerization behavior of short primers lay foundation about DNA polymerization mechanism and development of novel nucleic acid detection assays.
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Affiliation(s)
- Guojie Zhao
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
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