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Machnik G, Skudrzyk E, Bułdak Ł, Ruczyński J, Kozłowska A, Mucha P, Rekowski P, Szkróbka W, Basiak M, Bołdys A, Sławska H, Okopień B. Monitoring the Transcriptional Activity of Human Endogenous Retroviral HERV-W Family Using PNA Strand Invasion into Double-Stranded DNA. Mol Biotechnol 2018; 60:124-133. [PMID: 29313202 PMCID: PMC5799313 DOI: 10.1007/s12033-017-0057-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In the presented assay, we elaborated a method for distinguishing sequences that are genetically closely related to each other. This is particularly important in a situation where a fine balance of the allele abundance is a point of research interest. We developed a peptide nucleic acid (PNA) strand invasion technique for the differentiation between multiple sclerosis-associated retrovirus (MSRV) and ERVWE1 sequences, both molecularly similar, belonging to the human endogenous retrovirus HERV-W family. We have found that this method may support the PCR technique in screening for minor alleles which, in certain conditions, may be undetected by the standard PCR technique. We performed the analysis of different ERVWE1 and MSRV template mixtures ranging from 0 to 100% of ERVWE1 in the studied samples, finding the linear correlation between template composition and signal intensity of final reaction products. Using the PNA strand invasion assay, we were able to estimate the relative ERVWE1 expression level in human specimens such as U-87 MG, normal human astrocytes cell lines and placental tissue. The results remained in concordance with those obtained by semi-quantitative or quantitative PCR.
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Affiliation(s)
- Grzegorz Machnik
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland.
| | - Estera Skudrzyk
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Łukasz Bułdak
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Jarosław Ruczyński
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Agnieszka Kozłowska
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Piotr Mucha
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Piotr Rekowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland
| | - Witold Szkróbka
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Marcin Basiak
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Aleksandra Bołdys
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
| | - Helena Sławska
- Department of Gynaecology, Obstetrics and Oncological Gynaecology, Medical University of Silesia, Batorego 15, 41-902, Bytom, Poland
| | - Bogusław Okopień
- Department of Internal Medicine and Clinical Pharmacology, School of Medicine in Katowice, Medical University of Silesia, Medyków 18, 40-752, Katowice, Poland
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2
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Stefanska A, Gaffke L, Kaczorowska AK, Plotka M, Dabrowski S, Kaczorowski T. Highly thermostable RadA protein from the archaeon Pyrococcus woesei enhances specificity of simplex and multiplex PCR assays. J Appl Genet 2015; 57:239-49. [PMID: 26337425 DOI: 10.1007/s13353-015-0314-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 08/13/2015] [Accepted: 08/18/2015] [Indexed: 10/23/2022]
Abstract
The radA gene of the hyperthermophilic archaeon Pyrococcus woesei (Thermococcales) was cloned and overexpressed in Escherichia coli. The 1050-bp gene codes for a 349-amino-acid polypeptide with an M r of 38,397 which shows 100 % positional amino acid identity to Pyrococcus furiosus RadA and 27.1 % to the E. coli RecA protein. Recombinant RadA was overproduced in Escherichia coli as a His-tagged fusion protein and purified to electrophoretic homogeneity using a simple procedure consisting of ammonium sulfate precipitation and metal-affinity chromatography. In solution RadA exists as an undecamer (11-mer). The protein binds both to ssDNA and dsDNA. RadA has been found to be highly thermostable, it remains almost unaffected by a 4-h incubation at 94 °C. The addition of the RadA protein to either simplex or multiplex PCR assays, significantly improves the specificity of DNA amplification by eliminating non-specific products. Among applications tested the RadA protein proved to be useful in allelic discrimination assay of HADHA gene associated with long-chain 3-hydroxylacyl-CoA dehydrogenase deficiency that in infancy may lead to hypotonia, serious heart and liver problems and even sudden death.
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Affiliation(s)
- Aleksandra Stefanska
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Lidia Gaffke
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | - Magdalena Plotka
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland
| | | | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
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3
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Stefanska A, Kaczorowska AK, Plotka M, Fridjonsson OH, Hreggvidsson GO, Hjorleifsdottir S, Kristjansson JK, Dabrowski S, Kaczorowski T. Discovery and characterization of RecA protein of thermophilic bacterium Thermus thermophilus MAT72 phage Tt72 that increases specificity of a PCR-based DNA amplification. J Biotechnol 2014; 182-183:1-10. [PMID: 24786823 DOI: 10.1016/j.jbiotec.2014.04.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 03/21/2014] [Accepted: 04/15/2014] [Indexed: 10/25/2022]
Abstract
The recA gene of newly discovered Thermus thermophilus MAT72 phage Tt72 (Myoviridae) was cloned and overexpressed in Escherichia coli. The 1020-bp gene codes for a 339-amino-acid polypeptide with an Mr of 38,155 which shows 38.7% positional identity to the E. coli RecA protein. When expressed in E. coli, the Tt72 recA gene did not confer the ability to complement the ultraviolet light (254nm) sensitivity of an E. coli recA mutant. Tt72 RecA protein has been purified with good yield to catalytic and electrophoretic homogeneity using a three-step chromatography procedure. Biochemical characterization indicated that the protein can pair and promote ATP-dependent strand exchange reaction resulting in formation of a heteroduplex DNA at 60°C under conditions otherwise optimal for E. coli RecA. When the Tt72 RecA protein was included in a standard PCR-based DNA amplification reaction, the specificity of the PCR assays was significantly improved by eliminating non-specific products.
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Affiliation(s)
- Aleksandra Stefanska
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | - Magdalena Plotka
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
| | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland; Faculty of Life and Environmental Sciences, University of Iceland, Sæmundargötu 2, Reykjavik 101, Iceland.
| | | | | | | | - Tadeusz Kaczorowski
- Department of Microbiology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland.
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Bazzicalupi C, Bencini A, Bonaccini C, Giorgi C, Gratteri P, Moro S, Palumbo M, Simionato A, Sgrignani J, Sissi C, Valtancoli B. Tuning the Activity of Zn(II) Complexes in DNA Cleavage: Clues for Design of New Efficient Metallo-Hydrolases. Inorg Chem 2008; 47:5473-84. [DOI: 10.1021/ic800085n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Carla Bazzicalupi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Andrea Bencini
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Bonaccini
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Giorgi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Paola Gratteri
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Stefano Moro
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Manlio Palumbo
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Alessandro Simionato
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Jacopo Sgrignani
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Claudia Sissi
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
| | - Barbara Valtancoli
- Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Firenze, Italy, Laboratorio di Molecular Modeling, Cheminformatics and QSAR, Dipartimento di Scienze Farmaceutiche, Laboratorio di Progettazione, Sintesi e Studio di Eterocicli Biologicamente Attivi, Polo Scientifico, Università degli Studi di Firenze, Via Ugo Schiff, 6, 50019 Sesto Fiorentino (FI), Italy, and Dipartimento di Scienze Farmaceutiche, Università degli Studi di Padova, Via Marzolo 5,
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