1
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Concentration-Dependent Study of Nucleic Acid Blockers Used for Sequence-Specificity Enhancement in Nucleic Acids Detection. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022. [DOI: 10.1007/s13369-022-06972-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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2
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Signal-on/signal-off bead-based assays for the multiplexed monitoring of base excision repair activities by flow cytometry. Anal Bioanal Chem 2022; 414:2029-2040. [DOI: 10.1007/s00216-021-03849-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/03/2021] [Accepted: 12/13/2021] [Indexed: 11/01/2022]
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3
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Ramírez N, Serey M, Illanes A, Piumetti M, Ottone C. Immobilization strategies of photolyases: Challenges and perspectives for DNA repairing application. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 215:112113. [PMID: 33383556 DOI: 10.1016/j.jphotobiol.2020.112113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/27/2020] [Accepted: 12/19/2020] [Indexed: 02/08/2023]
Abstract
Photolyases are enzymes that repair DNA damage caused by solar radiation. Due to their photorepair potential, photolyases added in topical creams and used in medical treatments has allowed to reverse skin damage and prevent the development of different diseases, including actinic keratosis, premature photoaging and cancer. For this reason, research has been oriented to the study of new photolyases performing in extreme environments, where high doses of UV radiation may be a key factor for these enzymes to have perfected their photorepair potential. Generally, the extracted enzymes are first encapsulated and then added to the topical creams to increase their stability. However, other well consolidated immobilization methods are interesting strategies to be studied that may improve the biocatalyst performance. This review aims to go through the different Antarctic organisms that have exhibited photoreactivation activity, explaining the main mechanisms of photolyase DNA photorepair. The challenges of immobilizing these enzymes on porous and nanostructured supports is also discussed. The comparison of the most reported immobilization methods with respect to the structure of photolyases show that both covalent and ionic immobilization methods produced an increase in their stability. Moreover, the use of nanosized materials as photolyase support would permit the incorporation of the biocatalyst into the target cell, which is a technological requirement that photolyase based biocatalysts must fulfill.
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Affiliation(s)
- Nicolás Ramírez
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Marcela Serey
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Andrés Illanes
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile
| | - Marco Piumetti
- Department of Applied Science and Technology, Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino, Italy.
| | - Carminna Ottone
- Escuela de Ingeniería Bioquímica, Pontificia Universidad Católica de Valparaíso, Avenida Brasil 2085, Valparaíso, Chile.
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4
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Vallejos-Almirall A, Folch-Cano C, Rosas A, Vergara C. Development of liquid chromatography tandem mass spectrometry method to quantify cyclobutane pyrimidine dimer photolyase activity by detection of 15mer oligonucleotide as reaction product. J Chromatogr A 2019; 1611:460577. [PMID: 31591040 DOI: 10.1016/j.chroma.2019.460577] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 06/11/2019] [Accepted: 09/26/2019] [Indexed: 11/15/2022]
Abstract
Ultraviolet radiation from sunlight causes DNA damage in skin cells by formation of photoproducts, mainly cyclobutane pyrimidine dimers (CPD), which are reverted by exogenous CPD-photolyase, preventing photoaging and skin cancer. High performance liquid chromatography tandem mass spectrometry method for quantification of CPD-photolyase activity was developed to search new enzymes sources for dermatology or clinical studies. The method was based in the enzymatic conversion of a 15mer oligonucleotide, containing a center cyclobutane thymidine dimer, to the restored 15mer oligonucleotide. Three ion pair reagent were evaluated by response surface methodology to increase mass intensities. Additionally, chromatographic separation of oligonucleotides was performed. The selected mobile phase was 15 mM diisopropylethylamine/20 mM hexafluoroisopropanol in methanol. The method allowed total separation between the oligonucleotides studied (resolution of 2.3) by using the core shell technology, which reduce the diffusion time of the analyte into the column, increasing the efficiency and minimizing the analysis time at 7 min. The mass spectrometry detection allowed a high selectivity and sensitivity. This is the first time where MRM modality has been employed with this specific purpose. Oligonucleotides recovery from reaction mixture was ∼ 94% and the limit of quantification was 13.4 nM for 15mer. The method was evaluated with a recombinant CPD-photolyase from Synechococcus leopoliensis using purified and crude protein extract. CPD-photolyase could be measured in terms of activity for enzymatic kinetics studies, for evaluation of UV-R effects in (micro)organisms and to identify new enzymes.
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Affiliation(s)
- A Vallejos-Almirall
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile; Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - C Folch-Cano
- Departamento de Agroindustrias, Facultad de Ingeniería Agrícola, Universidad de Concepción, Chillán, Chile
| | - A Rosas
- Departamento de Suelos y Recursos Naturales, Facultad de Agronomía, Universidad de Concepción, Chillán, Chile
| | - C Vergara
- Departamento de Análisis Instrumental, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile.
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Vendrell-Criado V, Rodríguez-Muñiz GM, Lhiaubet-Vallet V, Cuquerella MC, Miranda MA. The (6-4) Dimeric Lesion as a DNA Photosensitizer. Chemphyschem 2016; 17:1979-82. [PMID: 26990589 DOI: 10.1002/cphc.201600154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/08/2022]
Abstract
Based on our previous investigations into the photophysical properties of the 5-methyl-2-pyrimidone (Pyo) chromophore, we now extend our studies to the photobehavior of the dimeric (6-4) thymine photoproducts (6-4 PP) to evaluate their capability to act as instrinsic DNA photosensitizers. The lesion presents significant absorption in the UVB/UVA region, weak fluorescence emission, a singlet-excited-state energy of approximately 351 kJ mol(-1) , and a triplet-excited-state energy of 297 kJ mol(-1) . Its triplet transient absorption has a maximum at 420-440 nm, a lifetime of around 7 μs, and a high formation quantum yield, ΦISC =0.86. This species is efficiently quenched by thymidine. Its DNA photosensitizing properties are demonstrated by a series of experiments run on a pBR322 plasmid. The lesion photoinduces both single-strand breaks and the formation of cyclobutane thymine dimers. Altogether, these results show that, the substitution of the pyrimidone ring at C4 by a 5-hydroxy-5,6-dihydrothymine does not cancel out the photosensitization properties of the chromophore.
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Affiliation(s)
- Victoria Vendrell-Criado
- Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Gemma M Rodríguez-Muñiz
- Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - Virginie Lhiaubet-Vallet
- Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022, Valencia, Spain
| | - M Consuelo Cuquerella
- Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022, Valencia, Spain.
| | - Miguel A Miranda
- Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Avenida de los Naranjos s/n, 46022, Valencia, Spain.
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Gines G, Saint-Pierre C, Gasparutto D. On-bead fluorescent DNA nanoprobes to analyze base excision repair activities. Anal Chim Acta 2014; 812:168-75. [PMID: 24491778 DOI: 10.1016/j.aca.2013.12.038] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Revised: 12/18/2013] [Accepted: 12/28/2013] [Indexed: 12/25/2022]
Abstract
DNA integrity is constantly threatened by endogenous and exogenous agents that can modify its physical and chemical structure. Changes in DNA sequence can cause mutations sparked by some genetic diseases or cancers. Organisms have developed efficient defense mechanisms able to specifically repair each kind of lesion (alkylation, oxidation, single or double strand break, mismatch, etc). Here we report the adjustment of an original assay to detect enzymes' activity of base excision repair (BER), that supports a set of lesions including abasic sites, alkylation, oxidation or deamination products of bases. The biosensor is characterized by a set of fluorescent hairpin-shaped nucleic acid probes supported on magnetic beads, each containing a selective lesion targeting a specific BER enzyme. We have studied the DNA glycosylase alkyl-adenine glycosylase (AAG) and the human AP-endonuclease (APE1) by incorporating within the DNA probe a hypoxanthine lesion or an abasic site analog (tetrahydrofuran), respectively. Enzymatic repair activity induces the formation of a nick in the damaged strand, leading to probe's break, that is detected in the supernatant by fluorescence. The functional assay allows the measurement of DNA repair activities from purified enzymes or in cell-free extracts in a fast, specific, quantitative and sensitive way, using only 1 pmol of probe for a test. We recorded a detection limit of 1 μg mL(-1) and 50 μg mL(-1) of HeLa nuclear extracts for APE1 and AAG enzymes, respectively. Finally, the on-bead assay should be useful to screen inhibitors of DNA repair activities.
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Affiliation(s)
- Guillaume Gines
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France
| | - Christine Saint-Pierre
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France
| | - Didier Gasparutto
- Laboratoire des Lésions des Acides Nucléiques, SCIB-UMR E3 CEA-UJF/INAC/CEA Grenoble, Grenoble Cedex 09 38054, France.
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7
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Toga T, Kuraoka I, Yasui A, Iwai S. A transfection reporter for the prevention of false-negative results in molecular beacon experiments. Anal Biochem 2013; 440:9-11. [PMID: 23685051 DOI: 10.1016/j.ab.2013.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 04/30/2013] [Indexed: 11/26/2022]
Abstract
We previously developed a molecular beacon-type probe to detect the strand scission in cellular base excision repair and found that the phosphodiester linkages in the fluorophore/quencher linkers were cleaved. This reaction was applied to a transfection reporter, which contained the unmodified phosphodiester in the linker to another type of fluorophore. After cotransfection of cells with the probe and the reporter, the signals were used to detect the incision and to confirm the proper transfection, respectively. This method will contribute to the prevention of false-negative results in experiments using molecular beacon-type probes.
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Affiliation(s)
- Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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8
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Svilar D, Vens C, Sobol RW. Quantitative, real-time analysis of base excision repair activity in cell lysates utilizing lesion-specific molecular beacons. J Vis Exp 2012:e4168. [PMID: 22895410 DOI: 10.3791/4168] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
We describe a method for the quantitative, real-time measurement of DNA glycosylase and AP endonuclease activities in cell nuclear lysates using base excision repair (BER) molecular beacons. The substrate (beacon) is comprised of a deoxyoligonucleotide containing a single base lesion with a 6-Carboxyfluorescein (6-FAM) moiety conjugated to the 5'end and a Dabcyl moiety conjugated to the 3' end of the oligonucleotide. The BER molecular beacon is 43 bases in length and the sequence is designed to promote the formation of a stem-loop structure with 13 nucleotides in the loop and 15 base pairs in the stem. When folded in this configuration the 6-FAM moiety is quenched by Dabcyl in a non-fluorescent manner via Förster Resonance Energy Transfer (FRET). The lesion is positioned such that following base lesion removal and strand scission the remaining 5 base oligonucleotide containing the 6-FAM moiety is released from the stem. Release and detachment from the quencher (Dabcyl) results in an increase of fluorescence that is proportionate to the level of DNA repair. By collecting multiple reads of the fluorescence values, real-time assessment of BER activity is possible. The use of standard quantitative real-time PCR instruments allows the simultaneous analysis of numerous samples. The design of these BER molecular beacons, with a single base lesion, is amenable to kinetic analyses, BER quantification and inhibitor validation and is adaptable for quantification of DNA Repair activity in tissue and tumor cell lysates or with purified proteins. The analysis of BER activity in tumor lysates or tissue aspirates using these molecular beacons may be applicable to functional biomarker measurements. Further, the analysis of BER activity with purified proteins using this quantitative assay provides a rapid, high-throughput method for the discovery and validation of BER inhibitors.
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Affiliation(s)
- David Svilar
- Department of Pharmacology & Chemical Biology, University of Pittsburgh School of Medicine, USA
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9
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Haiser K, Fingerhut BP, Heil K, Glas A, Herzog TT, Pilles BM, Schreier WJ, Zinth W, de Vivie-Riedle R, Carell T. Mechanismus der UV-induzierten Bildung von Dewar-Schäden in DNA. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201106231] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Haiser K, Fingerhut BP, Heil K, Glas A, Herzog TT, Pilles BM, Schreier WJ, Zinth W, de Vivie-Riedle R, Carell T. Mechanism of UV-induced formation of Dewar lesions in DNA. Angew Chem Int Ed Engl 2011; 51:408-11. [PMID: 22109845 DOI: 10.1002/anie.201106231] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Indexed: 11/11/2022]
Abstract
The importance of a backbone: The mechanism of formation of Dewar lesions has been investigated by using femtosecond IR spectroscopy and ab initio calculations of the exited state. The 4π electrocyclization is rather slow, occurs with an unusual high quantum yield, and--surprisingly--is controlled by the phosphate backbone.
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Affiliation(s)
- Karin Haiser
- Faculty of Physics, Center for Integrative Protein Science, Ludwig Maximilians University Munich, Oettingenstrasse 67, 80538 Munich, Germany
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11
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Heil K, Pearson D, Carell T. Chemical investigation of light induced DNA bipyrimidine damage and repair. Chem Soc Rev 2010; 40:4271-8. [PMID: 21076781 DOI: 10.1039/c000407n] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In all organisms, genetic information is stored in DNA and RNA. Both of these macromolecules are damaged by many exogenous and endogenous events, with UV irradiation being one of the major sources of damage. The major photolesions formed are the cyclobutane pyrimidine dimers (CPD), pyrimidine-pyrimidone-(6-4)-photoproducts, Dewar valence isomers and, for dehydrated spore DNA, 5-(α-thyminyl)-5,6-dihydrothymine (SP). In order to be able to investigate how nature's repair and tolerance mechanisms protect the integrity of genetic information, oligonucleotides containing sequence and site-specific UV lesions are essential. This tutorial review provides an overview of synthetic procedures by which these oligonucleotides can be generated, either through phosphoramidite chemistry or direct irradiation of DNA. Moreover, a brief summary on their usage in analysing repair and tolerance processes as well as their biological effects is provided.
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Affiliation(s)
- Korbinian Heil
- Center for Integrative Protein Science CiPSM at the Department of Chemistry and Biochemistry, Ludwig-Maximilians University Munich, Butenandtstr. 5-13, D-81377 Munich, Germany
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12
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Yamamoto J, Nishiguchi K, Manabe K, Masutani C, Hanaoka F, Iwai S. Photosensitized [2 + 2] cycloaddition of N-acetylated cytosine affords stereoselective formation of cyclobutane pyrimidine dimer. Nucleic Acids Res 2010; 39:1165-75. [PMID: 20880992 PMCID: PMC3035463 DOI: 10.1093/nar/gkq855] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Photocycloaddition between two adjacent bases in DNA produces a cyclobutane pyrimidine dimer (CPD), which is one of the major UV-induced DNA lesions, with either the cis-syn or trans-syn structure. In this study, we investigated the photosensitized intramolecular cycloaddition of partially-protected thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxy-5-methylcytidine, to clarify the effect of the base modification on the cycloaddition reaction. The reaction resulted in the stereoselective formation of the trans-syn CPD, followed by hydrolysis of the acetylamino group. The same result was obtained for the photocycloaddition of thymidylyl-(3'→5')-N(4)-acetyl-2'-deoxycytidine, whereas both the cis-syn and trans-syn CPDs were formed from thymidylyl-(3'→5')-thymidine. Kinetic analyses revealed that the activation energy of the acid-catalyzed hydrolysis is comparable to that reported for the thymine-cytosine CPD. These findings provided a new strategy for the synthesis of oligonucleotides containing the trans-syn CPD. Using the synthesized oligonucleotide, translesion synthesis by human DNA polymerase η was analyzed.
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Affiliation(s)
- Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
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Oladepo SA, Loppnow GR. Self-quenching smart probes as a platform for the detection of sequence-specific UV-induced DNA photodamage. Anal Bioanal Chem 2010; 397:2949-57. [DOI: 10.1007/s00216-010-3896-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/29/2010] [Accepted: 05/30/2010] [Indexed: 11/30/2022]
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Abstract
Trp-DNA adducts resulting from UV irradiation of pyrimidine bases and nucleotides in the presence of tryptophan (Trp) have been the subject of previous research. However, the relative yield of the adducts compared with the UV screening effect of Trp has not been previously considered. To determine whether Trp-DNA adduct formation or absorption "screening" by Trp is the predominant process when DNA solutions are irradiated with UV light in the presence of Trp, we irradiated Trp-containing DNA oligonucleotide solutions with UVC light and incubated aliquots of those solutions with molecular beacons (MBs) to detect the damage. We observed a rapid decay of fluorescence of the MBs for pure DNA solutions, thereby indicating damage. However, in the presence of Trp, the fluorescence decay is prolonged, with time constants that increase exponentially with Trp concentration. The results are discussed in terms of a beneficial in vivo cellular protection rather than harmful adduct formation and suggest a net sacrificial absorption of UV light by Trp which actually protects the DNA from UV damage.
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Affiliation(s)
- Sulayman A Oladepo
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
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15
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Boussicault F, Robert M. Electron Transfer in DNA and in DNA-Related Biological Processes. Electrochemical Insights. Chem Rev 2008; 108:2622-45. [DOI: 10.1021/cr0680787] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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16
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Yarasi S, McConachie C, Loppnow GR. Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶. Photochem Photobiol 2007. [DOI: 10.1111/j.1751-1097.2005.tb00209.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Trkulja I, Biner SM, Langenegger SM, Häner R. A Molecular Probe for the Detection of Homopurine Sequences. Chembiochem 2007; 8:25-7. [PMID: 17121403 DOI: 10.1002/cbic.200600378] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Ivan Trkulja
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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18
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Mu W, Han Q, Luo Z, Wang Y. Production of cis-syn thymine-thymine cyclobutane dimer oligonucleotide in the presence of acetone photosensitizer. Anal Biochem 2006; 353:117-23. [PMID: 16581009 DOI: 10.1016/j.ab.2006.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2006] [Revised: 02/18/2006] [Accepted: 03/03/2006] [Indexed: 11/17/2022]
Abstract
cis-syn Cyclobutane pyrimidine dimer (CPD) oligonucleotide was produced by UV irradiation in the presence of acetone photosensitizer. Acetone could enhance the productivity but evidently induced the photocleavage of oligonucleotide under a long time irradiation. A statistical approach of orthogonal design was applied to optimize the preparation condition for the production of the modified oligonucleotide. Optimal conditions for maximal cis-syn CPD oligonucleotide productivity were determined based on three factors: acetone concentration, initial oligonucleotide concentration, and irradiation time at several different levels. The optimal modified oligonucleotide that this optimization could produce was 32.7%. Through analysis of 20% polyacrylamide gel electrophoresis, it was found that modified oligonucleotide migrated slightly more slowly than the parent oligonucleotide. The photoreactivation of cis-syn thymine-thymine dimer oligonucleotide displayed the selectivity of the substrate specificity of DNA photolyase with high-performance liquid chromatography (HPLC) analysis.
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Affiliation(s)
- Wanmeng Mu
- School of Life Sciences, University of Science and Technology of China, Hefei
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19
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Wagenknecht HA. Electron transfer processes in DNA: mechanisms, biological relevance and applications in DNA analytics. Nat Prod Rep 2006; 23:973-1006. [PMID: 17119642 DOI: 10.1039/b504754b] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In principle, DNA-mediated charge transfer processes can be categorized as oxidative hole transfer and reductive electron transfer. With respect to the routes of DNA damage most of the past research has been focused on the investigation of oxidative hole transfer or transport. On the other hand, the transport or transfer of excess electrons has a large potential for biomedical applications, mainly for DNA chip technology.
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Affiliation(s)
- Hans-Achim Wagenknecht
- University of Regensburg, Institute for Organic Chemistry, D-93040, Regensburg, Germany.
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20
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Mu W, Zhang D, Xu L, Luo Z, Wang Y. Activity assay of His-tagged E. coli DNA photolyase by RP-HPLC and SE-HPLC. ACTA ACUST UNITED AC 2005; 63:111-24. [PMID: 15916808 DOI: 10.1016/j.jbbm.2005.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2005] [Accepted: 03/13/2005] [Indexed: 11/30/2022]
Abstract
Escherichia coli DNA photolyase was expressed as C-terminal 6x histidine-fused protein. Purification of His-tagged E. coli DNA photolyase was developed using immobilized metal affinity chromatography with Chelating Sepharose Fast Flow. By one-step affinity chromatography, approximate 4.6 mg DNA photolyase was obtained from 400 ml E. coli culture. The purified His-tagged enzyme was combined with two chromophors, FADH and MTHF. Using the oligonucleotide containing cyclobutane pyrimidine dimer as substrate, both reversed-phase high-performance liquid chromatography and size-exclusion high-performance liquid chromatography were developed to measure the enzyme activity. The enzyme was found to be able to repair the cyclobutane pyrimidine dimer with the turnover rate of 2.4 dimers/photolyase molecule/min.
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Affiliation(s)
- Wanmeng Mu
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, PR China
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21
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DeRosa MC, Sancar A, Barton JK. Electrically monitoring DNA repair by photolyase. Proc Natl Acad Sci U S A 2005; 102:10788-92. [PMID: 16043698 PMCID: PMC1182438 DOI: 10.1073/pnas.0503527102] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclobutane pyrimidine dimers are the major DNA photoproducts produced upon exposure to UV radiation. If left unrepaired, these lesions can lead to replication errors, mutation, and cell death. Photolyase is a light-activated flavoenzyme that binds to pyrimidine dimers in DNA and repairs them in a reaction triggered by electron transfer from the photoexcited flavin cofactor to the dimer. Using gold electrodes modified with DNA duplexes containing a cyclobutane thymine dimer (T<>T), here we probe the electrochemistry of the flavin cofactor in Escherichia coli photolyase. Cyclic and square-wave voltammograms of photolyase deposited on these electrodes show a redox signal at 40 mV versus normal hydrogen electrode, consistent with electron transfer to and from the flavin in the DNA-bound protein. This signal is dramatically attenuated on surfaces where the pi-stacking of the DNA bases is perturbed by the presence of an abasic site below the T<>T, an indication that the redox pathway is DNA-mediated. DNA repair can, moreover, be monitored electrically. Exposure of photolyase on T<>T-damaged DNA films to near-UV/blue light leads to changes in the flavin signal consistent with repair, as confirmed by parallel HPLC experiments. These results demonstrate the exquisite sensitivity of DNA electrochemistry to perturbations in base pair stacking and the applicability of this chemistry to probe reactions of proteins with DNA.
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Affiliation(s)
- Maria C DeRosa
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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Crey-Desbiolles C, Ahn DR, Leumann CJ. Molecular beacons with a homo-DNA stem: improving target selectivity. Nucleic Acids Res 2005; 33:e77. [PMID: 15879349 PMCID: PMC1090445 DOI: 10.1093/nar/gni076] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Molecular beacons (MBs) are stem–loop DNA probes used for identifying and reporting the presence and localization of nucleic acid targets in vitro and in vivo via target-dependent dequenching of fluorescence. A drawback of conventional MB design is present in the stem sequence that is necessary to keep the MBs in a closed conformation in the absence of a target, but that can participate in target binding in the open (target-on) conformation, giving rise to the possibility of false-positive results. In order to circumvent these problems, we designed MBs in which the stem was replaced by an orthogonal DNA analog that does not cross-pair with natural nucleic acids. Homo-DNA seemed to be specially suited, as it forms stable adenine-adenine base pairs of the reversed Hoogsteen type, potentially reducing the number of necessary building blocks for stem design to one. We found that MBs in which the stem part was replaced by homo-adenylate residues can easily be synthesized using conventional automated DNA synthesis. As conventional MBs, such hybrid MBs show cooperative hairpin to coil transitions in the absence of a DNA target, indicating stable homo-DNA base pair formation in the closed conformation. Furthermore, our results show that the homo-adenylate stem is excluded from DNA target binding, which leads to a significant increase in target binding selectivity.
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Affiliation(s)
| | | | - Christian J. Leumann
- To whom correspondence should be addressed. Tel: +41 0 31 631 4355; Fax: +41 0 31 631 3422;
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Nakayama T, Todo T, Notsu S, Nakazono M, Zaitsu K. Assay method for Escherichia coli photolyase activity using single-strand cis-syn cyclobutane pyrimidine dimer DNA as substrate. Anal Biochem 2005; 329:263-8. [PMID: 15158485 DOI: 10.1016/j.ab.2004.03.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2003] [Indexed: 11/21/2022]
Abstract
A high-performance liquid chromatography method for the assay of Escherichia coli photolyase activity was developed. When cis-syn cyclobutane pyrimidine dimer was used as substrate, the Michaelis constant (K(m)) value for the photolyase activity was 100 nM. The linear range of the calibration curve of the photolyase activity was 0.026-6.64 microU/assay tube. The correlation coefficient for this linearity was 0.998. The limit of detection (S/N = 3) was 26 nU/assay tube. The photolyase activity was increased 1.6-fold in the presence of 5,10-methenyltetrahydrofolic acid in the enzyme reaction mixture.
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Affiliation(s)
- Takuya Nakayama
- Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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Yarasi S, McConachie C, Loppnow GR. Molecular Beacon Probes of Photodamage in Thymine and Uracil Oligonucleotides¶. Photochem Photobiol 2005. [DOI: 10.1562/2004-09-02-ra-301.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kundu LM, Linne U, Marahiel M, Carell T. RNA Is More UV Resistant than DNA: The Formation of UV-Induced DNA Lesions is Strongly Sequence and Conformation Dependent. Chemistry 2004; 10:5697-705. [PMID: 15472947 DOI: 10.1002/chem.200305731] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA and RNA hairpins, which represent well-folded oligonucleotide structures, were irradiated and the amount of damaged hairpins was directly quantified by using ion-exchange HPLC. The types of photoproducts formed in the hairpins were determined by ESI-HPLC-MS/MS experiments. Irradiation of hairpins with systematically varied sequences and conformations (A versus B) revealed remarkable differences regarding the amount of photolesions formed. UV-damage formation is, therefore, a strongly sequence and conformation dependent process.
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Affiliation(s)
- Lal Mohan Kundu
- Department Chemie, Ludwig-Maximilians University, Butenandtstrasse 5-13, 81377 Munich, Germany
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