1
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Coll De Peña A, Gutterman-Johns E, Gautam GP, Rutberg J, Frej MB, Mehta DR, Shah S, Tripathi A. Assessment of pDNA isoforms using microfluidic electrophoresis. Electrophoresis 2024. [PMID: 38571381 DOI: 10.1002/elps.202300293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/05/2024]
Abstract
The recent rise in nucleic acid-based vaccines and therapies has resulted in an increased demand for plasmid DNA (pDNA). As a result, there is added pressure to streamline the manufacturing of these vectors, particularly their design and construction, which is currently considered a bottleneck. A significant challenge in optimizing pDNA production is the lack of high-throughput and rapid analytical methods to support the numerous samples produced during the iterative plasmid construction step and for batch-to-batch purity monitoring. pDNA is generally present as one of three isoforms: supercoiled, linear, or open circular. Depending on the ultimate use, the desired isoform may be supercoiled in the initial stages for cell transfection or linear in the case of mRNA synthesis. Here, we present a high-throughput microfluidic electrophoresis method capable of detecting the three pDNA isoforms and determining the size and concentration of the predominant supercoiled and linear isoforms from 2 to 7 kb. The limit of detection of the method is 0.1 ng/µL for the supercoiled and linear isoforms and 0.5 ng/µL for the open circular isoform, with a maximum loading capacity of 10-15 ng/µL. The turnaround time is 1 min/sample, and the volume requirement is 10 µL, making the method suitable for process optimization and batch-to-batch analysis. The results presented in this study will enhance the understanding of electrophoretic transport in microscale systems dependent on molecular conformations and potentially aid technological advances in diverse areas relevant to microfluidic devices.
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Affiliation(s)
- Adriana Coll De Peña
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Everett Gutterman-Johns
- Department of Molecular Biology, Cell Biology, and Biochemistry, Division of Biology and Medicine, Brown University, Providence, Rhode Island, USA
| | | | - Jenna Rutberg
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
| | - Menel Ben Frej
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Dipti R Mehta
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Shreyas Shah
- Applied Genomics, Revvity, Hopkinton, Massachusetts, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, Rhode Island, USA
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2
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Prokhorova DV, Vokhtantsev IP, Tolstova PO, Zhuravlev ES, Kulishova LM, Zharkov DO, Stepanov GA. Natural Nucleoside Modifications in Guide RNAs Can Modulate the Activity of the CRISPR-Cas9 System In Vitro. CRISPR J 2022; 5:799-812. [PMID: 36350691 DOI: 10.1089/crispr.2022.0069] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
At the present time, the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9) system has been widely adopted as an efficient genomic editing tool. However, there are some actual problems such as the off-target effects, cytotoxicity, and immunogenicity. The incorporation of modifications into guide RNAs permits enhancing both the efficiency and the specificity of the CRISPR-Cas9 system. In this study, we demonstrate that the inclusion of N6-methyladenosine, 5-methylcytidine, and pseudouridine in trans-activating RNA (tracrRNA) or in single guide RNA (sgRNA) enables efficient gene editing in vitro. We found that the complexes of modified guide RNAs with Cas9 protein promoted cleavage of the target short/long duplexes and plasmid substrates. In addition, the modified monomers in guide RNAs allow increasing the specificity of CRISPR-Cas9 system in vitro and promote diminishing both the immunostimulating and the cytotoxic effects of sgRNAs.
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Affiliation(s)
- Daria V Prokhorova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Ivan P Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Polina O Tolstova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Evgenii S Zhuravlev
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Lilia M Kulishova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Dmitry O Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.,Department of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia
| | - Grigory A Stepanov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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3
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Sakovina L, Vokhtantsev I, Vorobyeva M, Vorobyev P, Novopashina D. Improving Stability and Specificity of CRISPR/Cas9 System by Selective Modification of Guide RNAs with 2'-fluoro and Locked Nucleic Acid Nucleotides. Int J Mol Sci 2022; 23:13460. [PMID: 36362256 PMCID: PMC9655745 DOI: 10.3390/ijms232113460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 09/01/2023] Open
Abstract
The genome editing approach using the components of the CRISPR/Cas system has found wide application in molecular biology, fundamental medicine and genetic engineering. A promising method is to increase the efficacy and specificity of CRISPR/Cas-based genome editing systems by modifying their components. Here, we designed and chemically synthesized guide RNAs (crRNA, tracrRNA and sgRNA) containing modified nucleotides (2'-O-methyl, 2'-fluoro, LNA-locked nucleic acid) or deoxyribonucleotides in certain positions. We compared their resistance to nuclease digestion and examined the DNA cleavage efficacy of the CRISPR/Cas9 system guided by these modified guide RNAs. The replacement of ribonucleotides with 2'-fluoro modified or LNA nucleotides increased the lifetime of the crRNAs, while other types of modification did not change their nuclease resistance. Modification of crRNA or tracrRNA preserved the efficacy of the CRISPR/Cas9 system. Otherwise, the CRISPR/Cas9 systems with modified sgRNA showed a remarkable loss of DNA cleavage efficacy. The kinetic constant of DNA cleavage was higher for the system with 2'-fluoro modified crRNA. The 2'-modification of crRNA also decreased the off-target effect upon in vitro dsDNA cleavage.
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Affiliation(s)
- Lubov Sakovina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ivan Vokhtantsev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
- Faculty of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Mariya Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Pavel Vorobyev
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
| | - Darya Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, 630090 Novosibirsk, Russia
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4
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Photoactivatable nanoCRISPR/Cas9 System Based on crRNA Reversibly Immobilized on Carbon Nanoparticles. Int J Mol Sci 2021; 22:ijms222010919. [PMID: 34681578 PMCID: PMC8539621 DOI: 10.3390/ijms222010919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/04/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022] Open
Abstract
Here, we proposed a new approach to engineering a photoactivatable CRISPR/Cas9 gene-editing system. The novel nanoCRISPR/Cas9 system is based on the use of auxiliary photocleavable oligodeoxyribonucleotides (PC-DNAs) complementary to crRNA. PC-DNAs contained up to three UV-sensitive linkers made of 1-(2-nitrophenyl)-1,2-ethanediol inside the oligonucleotide chain. Immobilizing PC-DNAs on the surface of carbon nanoparticles through 3′-terminal pyrene residue provided sufficient blocking of crRNA (and corresponding Cas9 activity) before UV irradiation and allows for crRNA release after UV irradiation at 365 nm, which restores Cas9 activity. We optimized the length of blocking photocleavable oligonucleotide, number of linkers, time of irradiation, and the type of carbon nanoparticles. Based on the results, we consider the nanoCRISPR/Cas9 system involving carbon-encapsulated iron nanoparticles the most promising. It provides the greatest difference of functional activity before/after irradiation and can be used in prospective for magnetic field-controlled delivery of CRISPR system into the target cells or tissues and spatiotemporal gene editing induced by UV irradiation.
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5
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Meenongwa A, Brissos RF, Soikum C, Chaveerach P, Trongpanich Y, Chaveerach U. Enhancement of biological activities of copper(II) complexes containing guanidine derivatives by enrofloxacin. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130645] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Wang Y, Cacchillo EM, Niedzwiedzki DM, Taylor JS. Ability of the Putative Decomposition Products of 2,3-dioxetanes of Indoles to Photosensitize Cyclobutane Pyrimidine Dimer (CPD) Formation and its Implications for the "Dark" (Chemisensitized) Pathway to CPDs in Melanocytes †. Photochem Photobiol 2021; 98:442-454. [PMID: 34558720 DOI: 10.1111/php.13529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 09/20/2021] [Indexed: 11/28/2022]
Abstract
The formation of cyclobutane pyrimidine dimers (CPDs) by a "dark" pathway in melanocytes has been attributed to chemisensitization by dioxetanes produced from peroxynitrite oxidation of melanin or melanin precursors. These dioxetanes are proposed to decompose to triplet state compounds which sensitize CPD formation by triplet-triplet energy transfer. To determine whether such compounds are capable of sensitizing CPD formation, the putative decomposition products of 2,3-dioxetanes of variously substituted indoles were synthesized and their triplet state energies determined at 77 K. Their ability to photosensitize CPD formation was determined by an enzyme-coupled gel electrophoresis assay in comparison with norfloxacin (NFX) which has the lowest triplet energy known to sensitize CPD formation. The decomposition products of 2,3-dioxetanes of 5-hydroxy and 5,6-dimethoxy indoles used as models for melanin precursors had lower triplet energies and were incapable of photosensitizing CPD formation. Theoretical calculations suggest that the decomposition products of the 2,3-dioxetanes of melanin precursors DHI and DHICA will have similarly low triplet energies. Decomposition products of the 2,3-dioxetanes of indoles lacking oxygen substituents had higher triplet energies than NFX and were capable of photosensitizing CPD formation, suggesting that peroxynitrite oxidation of tryptophan could play a hitherto unrecognized role in the dark pathway to CPDs.
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Affiliation(s)
- Yanjing Wang
- Department of Chemistry, Washington University, St. Louis, MO
| | | | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University, St. Louis, MO.,Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO
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7
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Akhmetova EA, Golyshev VM, Vokhtantcev IP, Meschaninova MI, Venyaminova AG, Novopashina DS. Photoactivatable CRISPR/Cas9 System. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1068162021020023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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8
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Abramenkovs A, Stenerlöw B. Removal of heat-sensitive clustered damaged DNA sites is independent of double-strand break repair. PLoS One 2018; 13:e0209594. [PMID: 30592737 PMCID: PMC6310273 DOI: 10.1371/journal.pone.0209594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/07/2018] [Indexed: 11/21/2022] Open
Abstract
DNA double-strand breaks (DSBs) are the most deleterious lesions that can arise in cells after ionizing radiation or radiometric drug treatment. In addition to prompt DSBs, DSBs may also be produced during repair, evolving from a clustered DNA damaged site, which is composed of two or more distinct lesions that are located within two helical turns. A specific type of cluster damage is the heat-sensitive clustered site (HSCS), which transforms into DSBs upon treatment at elevated temperatures. The actual lesions or mechanisms that mediate the HSCS transformation into DSBs are unknown. However, there are two possibilities; either these lesions are transformed into DSBs due to DNA lesion instability, e.g., transfer of HSCS into single-strand breaks (SSBs), or they are formed due to local DNA structure instability, e.g., DNA melting, where two SSBs on opposite strands meet and transform into a DSB. The importance of these processes in living cells is not understood, but they significantly affect estimates of DSB repair capacity. In this study, we show that HSCS removal in human cells is not affected by defects in DSB repair or inhibition of DSB repair. Under conditions where rejoining of prompt DSBs was almost completely inhibited, heat-sensitive DSBs were successfully rejoined, without resulting in increased DSB levels, indicating that HSCS do not transfer into DSB in cells under physiological conditions. Furthermore, analysis by atomic force microscopy suggests that prolonged heating of chromosomal DNA can induce structural changes that facilitate transformation of HSCS into DSB. In conclusion, the HSCS do not generate additional DSBs at physiological temperatures in human cells, and the repair of HSCS is independent of DSB repair.
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Affiliation(s)
- Andris Abramenkovs
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Bo Stenerlöw
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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9
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Sabithakala T, Chittireddy VRR. DNA binding and in vitro
anticancer activity of 2-((1H
-benzimidazol-2-yl)methylamino)acetic acid and its copper(II) mixed-polypyridyl complexes: Synthesis and crystal structure. Appl Organomet Chem 2018. [DOI: 10.1002/aoc.4550] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Thatituri Sabithakala
- Department of Chemistry; Jawaharlal Nehru Technological University Hyderabad; Hyderabad 500085 India
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10
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Efficient copper-based DNA cleavers from carboxylate benzimidazole ligands. J Biol Inorg Chem 2018; 23:1165-1183. [PMID: 30076466 DOI: 10.1007/s00775-018-1598-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 12/13/2022]
Abstract
Four copper(II) coordination compounds from 2-benzimidazole propionic acid (Hbzpr) and 4-(benzimidazol-2-yl)-3-thiobutanoic acid (Hbztb) were synthesized and fully characterized by elemental analyses, electronic spectroscopy, FT-IR and mass spectrometry. The molecular structure for the four complexes was confirmed by single-crystal X-ray crystallography. The DNA-interacting properties of the two trinuclear and two mononuclear compounds were investigated using different spectroscopic techniques including absorption titration experiments, fluorescence spectroscopy and circular dichroism spectroscopy. Trinuclear [Cu3(bzpr)4(H2O)2](NO3)2·3H2O·CH3OH (2) and [Cu3(bzpr)4Cl2]·3H2O (3) bind to DNA through non-intercalative interactions, while for mononuclear [Cu(bzpr)2(H2O)]·2H2O (1) and [Cu(bztb)2]·2H2O (4), at minor concentrations in relation to the DNA, a groove binding interaction is favored, while at higher concentrations an intercalative mode is preferred. The nuclease properties of all complexes were studied by gel electrophoresis, which showed that they were able to cleave supercoiled plasmid DNA (form I) to the nicked form (form II). Compound 4 is even capable of generating linear form III (resulting from double-strand cleavage). The proposed mechanism of action involves an oxidative pathway (Fenton-type reaction), which produces harmful reactive species, like hydroxyl radicals.
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11
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Hahn MB, Meyer S, Schröter MA, Kunte HJ, Solomun T, Sturm H. DNA protection by ectoine from ionizing radiation: molecular mechanisms. Phys Chem Chem Phys 2018; 19:25717-25722. [PMID: 28913528 DOI: 10.1039/c7cp02860a] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ectoine, a compatible solute and osmolyte, is known to be an effective protectant of biomolecules and whole cells against heating, freezing and extreme salinity. Protection of cells (human keratinocytes) by ectoine against ultraviolet radiation has also been reported by various authors, although the underlying mechanism is not yet understood. We present the first electron irradiation of DNA in a fully aqueous environment in the presence of ectoine and at high salt concentrations. The results demonstrate effective protection of DNA by ectoine against the induction of single-strand breaks by ionizing radiation. The effect is explained by an increase in low-energy electron scattering at the enhanced free-vibrational density of states of water due to ectoine, as well as the use of ectoine as an ˙OH-radical scavenger. This was demonstrated by Raman spectroscopy and electron paramagnetic resonance (EPR).
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Affiliation(s)
- Marc Benjamin Hahn
- Free University Berlin, Department of Physics, D-14195 Berlin, Germany. and Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Susann Meyer
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and University of Potsdam, Institute of Biochemistry and Biology, D-14476 Potsdam, Germany
| | | | - Hans-Jörg Kunte
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Tihomir Solomun
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany.
| | - Heinz Sturm
- Bundesanstalt für Materialforschung und Prüfung, D-12205 Berlin, Germany. and Technical University Berlin, D-10587 Berlin, Germany
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12
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Hilbert BJ, Hayes JA, Stone NP, Xu RG, Kelch BA. The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain. Nucleic Acids Res 2017; 45:3591-3605. [PMID: 28082398 PMCID: PMC5389665 DOI: 10.1093/nar/gkw1356] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 01/05/2017] [Indexed: 01/07/2023] Open
Abstract
Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the adenosine triphosphatase (ATPase) that powers DNA translocation and an endonuclease that cleaves the concatemeric genome at both initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage remains mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nuclease activity. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of DNA cleavage suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the capsid upon completion of packaging unlocks the nuclease domains to cleave DNA.
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Affiliation(s)
- Brendan J. Hilbert
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Janelle A. Hayes
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nicholas P. Stone
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Rui-Gang Xu
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, UK
| | - Brian A. Kelch
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA,To whom correspondence should be addressed. Tel: +1 508 856 8322; Fax: +1 508 856 6464;
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13
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Oliveira VA, Iglesias BA, Auras BL, Neves A, Terenzi H. Photoactive meso-tetra(4-pyridyl)porphyrin-tetrakis-[chloro(2,2′bipyridine)platinum(ii) derivatives recognize and cleave DNA upon irradiation. Dalton Trans 2017; 46:1660-1669. [DOI: 10.1039/c6dt04634g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Photoactive platinum porphyrins may be interesting as photosensitizers in photodynamic therapy and photochemotherapy, and we demonstrate their activity towards DNA cleavage under exposure to light.
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Affiliation(s)
- Vanessa A. Oliveira
- Centro de Biologia Molecular Estrutural
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | | | - Bruna L. Auras
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Ademir Neves
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
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14
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Auras BL, Oliveira VA, Terenzi H, Neves A, Iglesias BA. meso-Mono-[4-(1,4,7-triazacyclononanyl)]-tri(phenyl)]porphyrin and the respective zinc(ii)-complex: complete characterization and biomolecules binding abilities. Photochem Photobiol Sci 2016; 15:564-79. [DOI: 10.1039/c6pp00016a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We aimed to synthesize a new series of triazacyclononanyl-porphyrins (4and5) with the potential ability to bind DNA.
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Affiliation(s)
- Bruna L. Auras
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Vanessa A. Oliveira
- Centro de Biologia Molecular Estrutural
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Hernán Terenzi
- Centro de Biologia Molecular Estrutural
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Ademir Neves
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
| | - Bernardo A. Iglesias
- Departamento de Química
- Universidade Federal de Santa Catarina
- Florianópolis
- Brazil
- Departamento de Química
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15
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Kathiresan S, Mugesh S, Murugan M, Ahamed F, Annaraj J. Mixed-ligand copper(ii)-phenolate complexes: structure and studies on DNA/protein binding profiles, DNA cleavage, molecular docking and cytotoxicity. RSC Adv 2016. [DOI: 10.1039/c5ra20607c] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Copper(ii) complexes with simple and mixed ligands, [Cu(L)(ClO4)] and [Cu(L)(diimine)]ClO4 were synthesized and characterized by elemental analysis, UV-vis, FT-IR, electrospray ionization-mass spectrometry (ESI-MS) and electrochemical studies.
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Affiliation(s)
- Sellamuthu Kathiresan
- Department of Materials Science
- School of Chemistry
- Madurai Kamaraj University
- Madurai 625021
- India
| | - Subramanian Mugesh
- Department of Microbial Technology
- School of Biological Sciences
- Madurai Kamaraj University
- Madurai-625 021
- India
| | - Maruthamuthu Murugan
- Department of Microbial Technology
- School of Biological Sciences
- Madurai Kamaraj University
- Madurai-625 021
- India
| | - Feroze Ahamed
- Department of Microbial Technology
- School of Biological Sciences
- Madurai Kamaraj University
- Madurai-625 021
- India
| | - Jamespandi Annaraj
- Department of Materials Science
- School of Chemistry
- Madurai Kamaraj University
- Madurai 625021
- India
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16
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Meenongwa A, Brissos RF, Soikum C, Chaveerach P, Gamez P, Trongpanich Y, Chaveerach U. Effects of N,N-heterocyclic ligands on the in vitro cytotoxicity and DNA interactions of copper(ii) chloride complexes from amidino-O-methylurea ligands. NEW J CHEM 2016. [DOI: 10.1039/c5nj03439f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four novel copper(ii) complexes based on guanidine derivatives have been synthesized by addition of N,N-heterocyclic ligands, and their interesting biological activities have been evaluated.
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Affiliation(s)
- Atittaya Meenongwa
- Materials Chemistry Research Center
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
| | - Rosa F. Brissos
- Departament de Química Inorgànica
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Chaiyaporn Soikum
- Department of Veterinary Public Health
- Faculty of Veterinary Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Prapansak Chaveerach
- Department of Veterinary Public Health
- Faculty of Veterinary Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Patrick Gamez
- Departament de Química Inorgànica
- Universitat de Barcelona
- 08028 Barcelona
- Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
| | - Yanee Trongpanich
- Department of Biochemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Unchulee Chaveerach
- Materials Chemistry Research Center
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
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Meenongwa A, Brissos RF, Soikum C, Chaveerach P, Gamez P, Trongpanich Y, Chaveerach U. DNA-interacting and biological properties of copper(ii) complexes from amidino-O-methylurea. NEW J CHEM 2015. [DOI: 10.1039/c4nj01377h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two copper(ii) complexes from the water-soluble amidino-O-methylureas exhibit interesting activities which are of paramount importance for biological applications.
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Affiliation(s)
- Atittaya Meenongwa
- Materials Chemistry Research Center
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
| | - Rosa F. Brissos
- Departament de Química Inorgànica
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - Chaiyaporn Soikum
- Department of Veterinary Public Health
- Faculty of Veterinary Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Prapansak Chaveerach
- Department of Veterinary Public Health
- Faculty of Veterinary Medicine
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Patrick Gamez
- Departament de Química Inorgànica
- Universitat de Barcelona
- 08028 Barcelona
- Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)
| | - Yanee Trongpanich
- Department of Biochemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
- Thailand
| | - Unchulee Chaveerach
- Materials Chemistry Research Center
- Department of Chemistry and Center of Excellence for Innovation in Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002
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18
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Tycon MA, Dial CF, Faison K, Melvin W, Fecko CJ. Quantification of dye-mediated photodamage during single-molecule DNA imaging. Anal Biochem 2012; 426:13-21. [PMID: 22484041 DOI: 10.1016/j.ab.2012.03.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2012] [Revised: 03/26/2012] [Accepted: 03/28/2012] [Indexed: 11/30/2022]
Abstract
Single-molecule fluorescence imaging of DNA-binding proteins has enabled detailed investigations of their interactions. However, the intercalating dyes used to visually locate DNA molecules have the undesirable effect of photochemically damaging the DNA through radical intermediaries. Unfortunately, this damage occurs as single-strand breaks (SSBs), which are visually undetectable but can heavily influence protein behavior. We investigated the formation of SSBs on DNA molecules by the dye YOYO-1 using complementary single-molecule imaging and gel electrophoresis-based damage assays. The single-molecule assay imaged hydrodynamically elongated lambda DNA, enabling the real-time detection of double-strand breaks (DSBs). The gel assay, which used supercoiled plasmid DNA, was sensitive to both SSBs and DSBs. This enabled the quantification of SSBs that precede DSB formation. Using the parameters determined from the gel damage assay, we applied a model of stochastic DNA damage to the time-resolved DNA breakage data, extracting the rates of single-strand breakage at two dye staining ratios and measuring the damage reduction from the radical scavengers ascorbic acid and β-mercaptoethanol. These results enable the estimation of the number of SSBs that occur during imaging and are scalable over a wide range of laser intensities used in fluorescence microscopy.
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Affiliation(s)
- Michael A Tycon
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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19
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Tian M, Ihmels H, Brötz E. DNA cleavage by the Cu(ii) complex of the DNA-intercalating 9-bis(pyridin-2-ylmethyl)aminobenzo[b]quinolizinium. Dalton Trans 2010; 39:8195-202. [DOI: 10.1039/c0dt00238k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Molloy MJ, Hall VS, Bailey SI, Griffin KJ, Faulkner J, Uden M. Effective and robust plasmid topology analysis and the subsequent characterization of the plasmid isoforms thereby observed. Nucleic Acids Res 2004; 32:e129. [PMID: 15358833 PMCID: PMC519125 DOI: 10.1093/nar/gnh124] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Within the biopharmaceutical industry, recombinant plasmid DNA is used both as a raw material (e.g. in lentiviral and AAV vector production) as well as an active ingredient (e.g. in DNA vaccines). Consequently, many analytical laboratories are routinely involved with plasmid DNA topoisoform qualitative analysis and quantification. In order to reliably determine plasmid topology, one must ensure that the methodology employed can reliably, precisely and accurately measure qualitatively and quantitatively all topological isoforms. Presented here are an anion-exchange high-performance liquid chromatography (AEC) and an agarose gel electrophoresis (AGE)-based method developed for this purpose. The strategies undertaken to overcome the respective typical problems of limited linear range of quantitation (for AGE) and isoform resolution (for AEC) are described. Also presented is a subsequent direct comparison (for assay precision/accuracy) of these two methods, as well as a package of species characterization [by chloroquine-AGE, enzymatic digestion, multi-angle laser light-scattering (MALLS) and electron microscopy] undertaken to confirm the identity of a minor supercoiled dimeric concatamer observed by both approaches.
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Affiliation(s)
- Michael J Molloy
- Department of Analytical Sciences, Biopharmaceutical Centre of Excellence for Drug Discovery (Beckenham), GlaxoSmithKline, Beckenham, Kent BR3 3BS, UK
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Abstract
Bacterial RecA protein is required for repair of two-strand DNA lesions that disable whole chromosomes. recA mutants are viable, suggesting a considerable cellular capacity to avoid these chromosome-disabling lesions. recA-dependent mutants reveal chromosomal lesion avoidance pathways. Here we characterize one such mutant, rdgB/yggV, deficient in a putative inosine/xanthosine triphosphatase, conserved throughout kingdoms of life. The rdgB recA lethality is suppressed by inactivation of endonuclease V (gpnfi) specific for DNA-hypoxanthines/xanthines, suggesting that RdgB either intercepts improper DNA precursors dITP/dXTP or works downstream of EndoV in excision repair of incorporated hypoxathines/xanthines. We find that DNA isolated from rdgB mutants contains EndoV-recognizable modifications, whereas DNA from nfi mutants does not, substantiating the dITP/dXTP interception by RdgB. rdgB recBC cells are inviable, whereas rdgB recF cells are healthy, suggesting that chromosomes in rdgB mutants suffer double-strand breaks. Chromosomal fragmentation is indeed observed in rdgB recBC mutants and is suppressed in rdgB recBC nfi mutants. Thus, one way to avoid chromosomal lesions is to prevent hypoxanthine/xanthine incorporation into DNA via interception of dITP/dXTP.
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Affiliation(s)
- Jill S Bradshaw
- Department of Microbiology, University of Illinois at Urbana-Champaign, B103 C&LSL, 601 South Goodwin Ave., 61801-3709, USA
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22
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Jaspan HB, Richard Gaumer H, Garry RF. Quantitative competitive reverse transcription polymerase chain reaction is not a useful method for quantification of CD4 and CD8 cell status during HIV infection. J Negat Results Biomed 2003; 2:2. [PMID: 12702212 PMCID: PMC153544 DOI: 10.1186/1477-5751-2-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2002] [Accepted: 03/12/2003] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND A polymerase chain reaction (PCR)-based method for quantitating CD4 and CD8 mRNA could provide a means of assessing immune status of AIDS patients and other immunologically compromised persons without requiring large blood draws, and could be exquisitely sensitive. Such a method would also be useful in assessing the immune status of patients retrospectively. RESULTS Quantitative competitive reverse transcription PCR (QC-RT-PCR) assays were developed for measurement of CD4 and CD8 mRNA. Samples were obtained from HIV-positive and negative patients whose CD4 and CD8 counts had been determined via Flow Cytometry. The quantity of CD4 (n = 13) and CD8 (n = 28) mRNA standardized according to GAPDH mRNA quantities, all determined by QC-RT-PCR, were compared to cell number as determined by flow cytometry. There was no correlation between CD4 and CD8 cell counts and mRNA levels of CD4 and CD8 as determined by QC-RT-PCR. There is no correlation between CD4 and CD8 mRNA levels and the number of cells expressing these proteins on their surface. CONCLUSION QC-RT-PCR, and related methodologies are not useful substitutes for assessment of CD4 and CD8 cell numbers in HIV-infected persons.
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Affiliation(s)
- Heather B Jaspan
- Interdisciplinary Program in Molecular and Cellular Biology Tulane University School of Medicine New Orleans LA, 70112, USA
| | - H Richard Gaumer
- Department of Pathology Louisiana State University Medical Center New Orleans LA, 70112, USA
| | - Robert F Garry
- Interdisciplinary Program in Molecular and Cellular Biology Tulane University School of Medicine New Orleans LA, 70112, USA
- Department of Microbiology and Immunology Tulane University School of Medicine New Orleans LA, 70112, USA
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Adam W, Arnold MA, Nau WM, Pischel U, Saha-Möller CR. Structure-dependent reactivity of oxyfunctionalized acetophenones in the photooxidation of DNA: base oxidation and strand breaks through photolytic radical formation (spin trapping, EPR spectroscopy, transient kinetics) versus photosensitization (electron transfer, hydrogen-atom abstraction). Nucleic Acids Res 2001; 29:4955-62. [PMID: 11812825 PMCID: PMC97623 DOI: 10.1093/nar/29.24.4955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The photooxidative damage of DNA, specifically guanine oxidation and strand-break formation, by sidechain-oxyfunctionalized acetophenones (hydroxy, methoxy, tert-butoxy and acetoxy derivatives), has been examined. The involvement of triplet-excited ketones and their reactivity towards DNA has been determined by time-resolved laser-flash spectroscopy. The generation of carbon-centered radical species upon Norrish-type I cleavage has been assessed by spin-trapping experiments with 5,5-dimethyl-1-pyrroline N-oxide, coupled with electron paramagnetic resonance spectroscopy. The observed DNA-base oxidation and strand-break formation is discussed in terms of the peroxyl radicals derived from the triplet-excited ketones by alpha cleavage and molecular oxygen trapping, as well as direct interaction of the excited states by electron transfer and hydrogen-atom abstraction. It is concluded that acetophenone derivatives, which produce radicals upon photolysis, in particular the hydroxy (AP-OH) and tert-butoxy (AP-O(t)Bu) derivatives, are more effective in oxidizing DNA.
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Affiliation(s)
- W Adam
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany.
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Abstract
Various cleavage agents interact with circular double-stranded DNA molecules to convert the closed-circular form (form-I) to the open-circular (form-II) and linear (form-III) forms, and ultimately to small DNA fragments. The various cutting processes which take place in the DNA pool are here analyzed kinetically, and, by solving the kinetic equations, expressions are derived for the amounts of the closed-circular, open-circular, and linear forms of DNA as a function of reaction time and concentration of cleavage agent. Conversions between subspecies of forms II and III, differing in numbers of internal cuts, are taken into account. The only assumption required to solve the kinetic equations is that the concentration of cleavage agent obeys [D] = D0 f(t) where the function of time f(t) is independent of D0, the initial concentration of cleavage agent. By choosing parameters in the expressions for the calculated amounts of forms I, II and III to give the best fit to the measured amounts, one obtains information about the rates and rate constants for the conversions. The rate constants in turn give important information about the specificity and mechanism of action of the cleavage agents. The analysis is applied to the cleavage of pBR322, SV-40 and PM2 DNAs by DNase I, Fe-EDTA, and the antitumor agents calicheamicin and bleomycin. Cleavage rate constants are derived and discussed for these systems.
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Affiliation(s)
- J Goodisman
- Department of Chemistry, Syracuse University, NY 13244-4100, USA
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