1
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Pan TT, Jiang S, Yuan H, Wang ZY, He MT, Zhang CY. Construction of a chemiluminescent biosensor based on enzymatic extension and click chemistry for sensitive measurement of MGMT activity in human breast tissues. Talanta 2024; 282:127009. [PMID: 39383723 DOI: 10.1016/j.talanta.2024.127009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 09/29/2024] [Accepted: 10/05/2024] [Indexed: 10/11/2024]
Abstract
O6-methylguanine methyltransferase (MGMT) is responsible for dealkylation of naturally occurring O6-methylguanines, and it is closely related with DNA replication, transcription, and cancers. Herein, we develop a chemiluminescent biosensor based on enzymatic extension and click chemistry for sensitive measurement of MGMT activity. When MGMT is present, the MGMT-catalyzed demethylation reaction initiates the cleavage of biotinylated dumbbell probes by PvuII restrictive enzyme, releasing two DNA fragments with 3'-OH end. The resultant DNA fragments can trigger terminal transferase (TdT)- and click chemistry-assisted isothermal amplification to obtain abundant G-rich sequences. The G-rich sequences can be captured by magnetic beads to produce a high chemiluminescence signal. This biosensor can greatly amplify the chemiluminescence signal, facilitating label-free and template-free measurement of MGMT. Especially, the introduction of dumbbell probe and PvuII enzyme can efficiently eliminate the false positive and improve the assay specificity. This biosensor possesses high sensitivity with a detection limit of 1.4 × 10-9 ng/μL, and it may accurately quantify the intracellular MGMT. Importantly, this biosensor can be used to screen the MGMT inhibitors and distinguish the MGMT level in breast tumor tissues and normal tissues, with great potential in drug discovery and cancer diagnosis.
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Affiliation(s)
- Ting-Ting Pan
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Huimin Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Mao-Tao He
- School of Basic Medicine Sciences, Shandong Second Medical University, Weifang, 261053, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 211189, China.
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2
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Ayan S, Rotaru AM, Kaye EG, Juneau G, Das S, Wilds CJ, Beharry AA. A chloromethyl-triazole fluorescent chemosensor for O 6-methylguanine DNA methyltransferase. Org Biomol Chem 2024; 22:2749-2753. [PMID: 38502038 DOI: 10.1039/d4ob00120f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Fluorescent chemosensors offer a direct means of measuring enzyme activity for cancer diagnosis, predicting drug resistance, and aiding in the discovery of new anticancer drugs. O6-methylguanine DNA methyltransferase (MGMT) is a predictor of resistance towards anticancer alkylating agents such as temozolomide. Using the fluorescent molecular rotor, 9-(2-carboxy-2-cyanovinyl)julolidine (CCVJ), we synthesized, and evaluated a MGMT fluorescent chemosensor derived from a chloromethyl-triazole covalent inhibitor, AA-CW236, a non-pseudosubstrate of MGMT. Our fluorescence probe covalently labelled the MGMT active site C145, producing a 18-fold increase in fluorescence. Compared to previous fluorescent probes derived from a substrate-based inhibitor, our probe had improved binding and reaction rate. Overall, our chloromethyl triazole-based fluorescence MGMT probe is a promising tool for measuring MGMT activity to predict temozolomide resistance.
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Affiliation(s)
- Seylan Ayan
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Adrian M Rotaru
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Esther G Kaye
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
| | - Gabrielle Juneau
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St W., Montréal, Québec, H4B 1R6, Canada
| | - Sunit Das
- Keenan Chair in Surgery, Division of Neurosurgery, St Michael's Hospital, University of Toronto, Ontario, M5B 1W8, Canada
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, 7141 Sherbrooke St W., Montréal, Québec, H4B 1R6, Canada
| | - Andrew A Beharry
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario, L5L 1C6, Canada.
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3
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Fillion A, Franco Pinto J, Granzhan A. Harnessing an emissive guanine surrogate to design small-molecule fluorescent chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT). Org Biomol Chem 2022; 20:1888-1892. [PMID: 35174383 DOI: 10.1039/d2ob00208f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
The fluorescence properties of an emissive guanine surrogate, thienoguanine (thGN, 2-aminothieno[3,4-d]pyrimidin-4(3H)-one), were exploited to design two real-time chemosensors of O6-methylguanine-DNA-methyltransferase (MGMT), a key DNA repair enzyme involved in the resistance to DNA-alkylating anti-cancer drugs though direct reversal of O6-alkylated guanine adducts.
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Affiliation(s)
- Alexandra Fillion
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France.
- CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Jaime Franco Pinto
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France.
- CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, Inserm U1196, Institut Curie, PSL Research University, 91405 Orsay, France.
- CNRS UMR9187, Inserm U1196, Université Paris Saclay, 91405 Orsay, France
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4
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang J. “Repaired and Activated” DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
| | - Jian‐Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics College of Chemistry and Chemical Engineering College of biology Hunan University Changsha 410082 China
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5
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Wang X, Yi X, Huang Z, He J, Wu Z, Chu X, Jiang JH. "Repaired and Activated" DNAzyme Enables the Monitoring of DNA Alkylation Repair in Live Cells. Angew Chem Int Ed Engl 2021; 60:19889-19896. [PMID: 34165234 DOI: 10.1002/anie.202106557] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/16/2021] [Indexed: 12/31/2022]
Abstract
Direct measurement of DNA repair is critical for the annotation of their clinical relevance and the discovery of drugs for cancer therapy. Here we reported a "repaired and activated" DNAzyme (RADzyme) by incorporating a single methyl lesion (O6 MeG, 3MeC, or 1MeA) at designated positions through systematic screening. We found that the catalytic activity of the RADzyme was remarkably suppressed and could be restored via enzyme-mediated DNA repair. Benefit from these findings, a fluorogenic RADzyme sensor was developed for the monitoring of MGMT-mediated repair of O6 MeG lesion. Importantly, the sensor allowed the evaluation of MGMT repair activity in different cells and under drugs treatment. Furthermore, another RADzyme sensor was engineered for the monitoring of ALKBH2-mediated repair of 3MeC lesion. This strategy provides a simple and versatile tool for the study of the basic biology of DNA repair, clinical diagnosis and therapeutic assessment.
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Affiliation(s)
- Xiangnan Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xin Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhimei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jianjun He
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Zhenkun Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of biology, Hunan University, Changsha, 410082, China
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6
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding-upon-Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021; 60:7283-7289. [PMID: 33415794 PMCID: PMC8783695 DOI: 10.1002/anie.202016223] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Indexed: 09/28/2023]
Abstract
We present a new class of DNA-based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding-upon-repair DNA nanoswitches are synthetic DNA sequences containing O6 -methyl-guanine (O6 -MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of the O6 -MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding-upon-repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors.
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Affiliation(s)
- Nada Farag
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Giulia Palermo
- Department of Bioengineering, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
- Department of Chemistry, University of California Riverside, 900 University Avenue, Riverside, CA, 52512, USA
| | - Alessandro Porchetta
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131, Naples, Italy
| | - Francesco Ricci
- Department of Chemistry, University of Rome Tor Vergata, Via della Ricerca Scientifica, 00133, Rome, Italy
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7
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Farag N, Mattossovich R, Merlo R, Nierzwicki Ł, Palermo G, Porchetta A, Perugino G, Ricci F. Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016223] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Nada Farag
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Rosanna Mattossovich
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Rosa Merlo
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Łukasz Nierzwicki
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Giulia Palermo
- Department of Bioengineering University of California Riverside 900 University Avenue Riverside CA 52512 USA
- Department of Chemistry University of California Riverside 900 University Avenue Riverside CA 52512 USA
| | - Alessandro Porchetta
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources National Research Council of Italy Via Pietro Castellino 111 80131 Naples Italy
| | - Francesco Ricci
- Department of Chemistry University of Rome Tor Vergata Via della Ricerca Scientifica 00133 Rome Italy
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8
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Mattossovich R, Merlo R, Miggiano R, Valenti A, Perugino G. O6-alkylguanine-DNA Alkyltransferases in Microbes Living on the Edge: From Stability to Applicability. Int J Mol Sci 2020; 21:E2878. [PMID: 32326075 PMCID: PMC7216122 DOI: 10.3390/ijms21082878] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/09/2020] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
The genome of living cells is continuously exposed to endogenous and exogenous attacks, and this is particularly amplified at high temperatures. Alkylating agents cause DNA damage, leading to mutations and cell death; for this reason, they also play a central role in chemotherapy treatments. A class of enzymes known as AGTs (alkylguanine-DNA-alkyltransferases) protects the DNA from mutations caused by alkylating agents, in particular in the recognition and repair of alkylated guanines in O6-position. The peculiar irreversible self-alkylation reaction of these enzymes triggered numerous studies, especially on the human homologue, in order to identify effective inhibitors in the fight against cancer. In modern biotechnology, engineered variants of AGTs are developed to be used as protein tags for the attachment of chemical ligands. In the last decade, research on AGTs from (hyper)thermophilic sources proved useful as a model system to clarify numerous phenomena, also common for mesophilic enzymes. This review traces recent progress in this class of thermozymes, emphasizing their usefulness in basic research and their consequent advantages for in vivo and in vitro biotechnological applications.
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Affiliation(s)
- Rosanna Mattossovich
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Rosa Merlo
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy;
| | - Anna Valenti
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
| | - Giuseppe Perugino
- Institute of Bioscience and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy; (R.M.); (R.M.)
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9
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Raghavan S, Baskin DS, Sharpe MA. A "Clickable" Probe for Active MGMT in Glioblastoma Demonstrates Two Discrete Populations of MGMT. Cancers (Basel) 2020; 12:cancers12020453. [PMID: 32075134 PMCID: PMC7072665 DOI: 10.3390/cancers12020453] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 01/19/2023] Open
Abstract
Various pathways can repair DNA alkylation by chemotherapeutic agents such as temozolomide (TMZ). The enzyme O6-methylguanine methyltransferase (MGMT) removes O6-methylated DNA adducts, leading to the failure of chemotherapy in resistant glioblastomas. Because of the anti-chemotherapeutic activities of MGMT previously described, estimating the levels of active MGMT in cancer cells can be a significant predictor of response to alkylating agents. Current methods to detect MGMT in cells are indirect, complicated, time-intensive, or utilize molecules that require complex and multistep chemistry synthesis. Our design simulates DNA repair by the transfer of a clickable propargyl group from O6-propargyl guanine to active MGMT and subsequent attachment of fluorescein-linked PEG linker via "click chemistry." Visualization of active MGMT levels reveals discrete active and inactive MGMT populations with biphasic kinetics for MGMT inactivation in response to TMZ-induced DNA damage.
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Affiliation(s)
- Sudhir Raghavan
- Correspondence: (S.R.); (M.A.S.); Tel.: +1-713-441-8822 (S.R.); +1-713-363-6995 (M.A.S.)
| | | | - Martyn A. Sharpe
- Correspondence: (S.R.); (M.A.S.); Tel.: +1-713-441-8822 (S.R.); +1-713-363-6995 (M.A.S.)
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10
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Hsu SH, Chen SH, Kuo CC, Chang JY. Ubiquitin-conjugating enzyme E2 B regulates the ubiquitination of O 6-methylguanine-DNA methyltransferase and BCNU sensitivity in human nasopharyngeal carcinoma cells. Biochem Pharmacol 2018; 158:327-338. [PMID: 30449727 DOI: 10.1016/j.bcp.2018.10.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/25/2018] [Indexed: 02/06/2023]
Abstract
O6-Methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme that removes the alkyl groups from the O6 position of guanine and is then degraded via ubiquitin-mediated degradation. Previous studies indicated that 1,3-bis(2-chloroethyl)-1-nitrosourea (BCNU) facilitates the ubiquitination and degradation of MGMT in several types of cancer cells. However, the underlying mechanism of MGMT ubiquitination remains unclear. In this study, we demonstrated for the first time that ubiquitin-conjugating enzyme E2 B (UBE2B) is a novel regulator of MGMT ubiquitination mediated by BCNU in nasopharyngeal carcinoma (NPC) cells. The E3 ubiquitin ligase RAD18, a partner of UBE2B, is also involved in BCNU-mediated MGMT ubiquitination. Overexpression/knockdown of UBE2B enhanced/reduced BCNU-mediated MGMT ubiquitination. Surprisingly, UBE2B knockdown significantly increased BCNU cytotoxicity in NPC cells. Therefore, loss of UBE2B seems to disrupt ubiquitin-mediated degradation of alkylated MGMT. We found that UBE2B knockdown reduced MGMT activity, suggesting that loss of UBE2B leads to the accumulation of deactivated MGMT and suppresses MGMT protein turnover in BCNU-treated cells. These findings indicate that UBE2B modulates sensitivity to BCNU in NPC cells by regulating MGMT ubiquitination.
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Affiliation(s)
- Shih-Han Hsu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Shang-Hung Chen
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Chuan Kuo
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Jang-Yang Chang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan; Division of Hematology/Oncology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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11
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Zhang Y, Tu J, Wang D, Zhu H, Maity SK, Qu X, Bogaert B, Pei H, Zhang H. Programmable and Multifunctional DNA-Based Materials for Biomedical Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1703658. [PMID: 29389041 DOI: 10.1002/adma.201703658] [Citation(s) in RCA: 130] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 09/09/2017] [Indexed: 06/07/2023]
Abstract
DNA encodes the genetic information; recently, it has also become a key player in material science. Given the specific Watson-Crick base-pairing interactions between only four types of nucleotides, well-designed DNA self-assembly can be programmable and predictable. Stem-loops, sticky ends, Holliday junctions, DNA tiles, and lattices are typical motifs for forming DNA-based structures. The oligonucleotides experience thermal annealing in a near-neutral buffer containing a divalent cation (usually Mg2+ ) to produce a variety of DNA nanostructures. These structures not only show beautiful landscape, but can also be endowed with multifaceted functionalities. This Review begins with the fundamental characterization and evolutionary trajectory of DNA-based artificial structures, but concentrates on their biomedical applications. The coverage spans from controlled drug delivery to high therapeutic profile and accurate diagnosis. A variety of DNA-based materials, including aptamers, hydrogels, origamis, and tetrahedrons, are widely utilized in different biomedical fields. In addition, to achieve better performance and functionality, material hybridization is widely witnessed, and DNA nanostructure modification is also discussed. Although there are impressive advances and high expectations, the development of DNA-based structures/technologies is still hindered by several commonly recognized challenges, such as nuclease instability, lack of pharmacokinetics data, and relatively high synthesis cost.
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Affiliation(s)
- Yuezhou Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Jing Tu
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Dongqing Wang
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | - Haitao Zhu
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
| | | | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Bram Bogaert
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 200241, Shanghai, P. R. China
| | - Hongbo Zhang
- Department of Pharmaceutical Science Laboratory, Åbo Akademi University, 20520, Turku, Finland
- Department of Radiology, Affiliated Hospital of Jiangsu University Jiangsu University, 212001, Zhenjiang, P. R. China
- Turku Center for Biotechnology, Åbo Akademi University, 20520, Turku, Finland
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12
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Miggiano R, Valenti A, Rossi F, Rizzi M, Perugino G, Ciaramella M. Every OGT Is Illuminated … by Fluorescent and Synchrotron Lights. Int J Mol Sci 2017; 18:ijms18122613. [PMID: 29206193 PMCID: PMC5751216 DOI: 10.3390/ijms18122613] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 11/28/2017] [Accepted: 11/30/2017] [Indexed: 12/23/2022] Open
Abstract
O6-DNA-alkyl-guanine-DNA-alkyl-transferases (OGTs) are evolutionarily conserved, unique proteins that repair alkylation lesions in DNA in a single step reaction. Alkylating agents are environmental pollutants as well as by-products of cellular reactions, but are also very effective chemotherapeutic drugs. OGTs are major players in counteracting the effects of such agents, thus their action in turn affects genome integrity, survival of organisms under challenging conditions and response to chemotherapy. Numerous studies on OGTs from eukaryotes, bacteria and archaea have been reported, highlighting amazing features that make OGTs unique proteins in their reaction mechanism as well as post-reaction fate. This review reports recent functional and structural data on two prokaryotic OGTs, from the pathogenic bacterium Mycobacterium tuberculosis and the hyperthermophilic archaeon Sulfolobus solfataricus, respectively. These studies provided insight in the role of OGTs in the biology of these microorganisms, but also important hints useful to understand the general properties of this class of proteins.
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Affiliation(s)
- Riccardo Miggiano
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Anna Valenti
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Franca Rossi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Menico Rizzi
- DSF-Dipartimento di Scienze del Farmaco, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy.
| | - Giuseppe Perugino
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
| | - Maria Ciaramella
- Institute of Biosciences and BioResources, National Research Council of Italy, Via Pietro Castellino 111, 80131 Naples, Italy.
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13
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Fluorogenic Real-Time Reporters of DNA Repair by MGMT, a Clinical Predictor of Antitumor Drug Response. PLoS One 2016; 11:e0152684. [PMID: 27035132 PMCID: PMC4818092 DOI: 10.1371/journal.pone.0152684] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/17/2016] [Indexed: 01/26/2023] Open
Abstract
Common alkylating antitumor drugs, such as temozolomide, trigger their cytotoxicity by methylating the O6-position of guanosine in DNA. However, the therapeutic effect of these drugs is dampened by elevated levels of the DNA repair enzyme, O6-methylguanine DNA methyltransferase (MGMT), which directly reverses this alkylation. As a result, assessing MGMT levels in patient samples provides an important predictor of therapeutic response; however, current methods available to measure this protein are indirect, complex and slow. Here we describe the design and synthesis of fluorescent chemosensors that report directly on MGMT activity in a single step within minutes. The chemosensors incorporate a fluorophore and quencher pair, which become separated by the MGMT dealkylation reaction, yielding light-up responses of up to 55-fold, directly reflecting repair activity. Experiments show that the best-performing probe retains near-native activity at mid-nanomolar concentrations. A nuclease-protected probe, NR-1, was prepared and tested in tumor cell lysates, demonstrating an ability to evaluate relative levels of MGMT repair activity in twenty minutes. In addition, a probe was employed to evaluate inhibitors of MGMT, suggesting utility for discovering new inhibitors in a high-throughput manner. Probe designs such as that of NR-1 may prove valuable to clinicians in selection of patients for alkylating drug therapies and in assessing resistance that arises during treatment.
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Tintoré M, Mazzini S, Polito L, Marelli M, Latorre A, Somoza Á, Aviñó A, Fàbrega C, Eritja R. Gold-Coated Superparamagnetic Nanoparticles for Single Methyl Discrimination in DNA Aptamers. Int J Mol Sci 2015; 16:27625-39. [PMID: 26593913 PMCID: PMC4661904 DOI: 10.3390/ijms161126046] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 12/16/2022] Open
Abstract
Au- and iron-based magnetic nanoparticles (NPs) are promising NPs for biomedical applications due to their unique properties. The combination of a gold coating over a magnetic core puts together the benefits from adding the magnetic properties to the robust chemistry provided by the thiol functionalization of gold. Here, the use of Au-coated magnetic NPs for molecular detection of a single methylation in DNA aptamer is described. Binding of α-thrombin to two aptamers conjugated to these NPs causes aggregation, a phenomenon that can be observed by UV, DLS and MRI. These techniques discriminate a single methylation in one of the aptamers, preventing aggregation due to the inability of α-thrombin to recognize it. A parallel study with gold and ferromagnetic NPs is detailed, concluding that the Au coating of FexOy NP does not affect their performance and that they are suitable as complex biosensors. These results prove the high detection potency of Au-coated SPIONs for biomedical applications especially for DNA repair detection.
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Affiliation(s)
- Maria Tintoré
- Department of Chemical and Biomolecular Nanotechnology, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, C/Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), Division of Chemistry and Molecular Biology, University of Milan, Via Celoria 2, 20133 Milan, Italy.
| | - Laura Polito
- Department Institute of Molecular Science and Technologies, ISTM-CNR, Via G. Fantoli 16/15, 20138 Milan, Italy.
| | - Marcello Marelli
- Department Institute of Molecular Science and Technologies, ISTM-CNR, Via G. Fantoli 16/15, 20138 Milan, Italy.
| | - Alfonso Latorre
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia), Asociada al Centro Nacional de Biotecnología (CSIC), C/Faraday 9, 28049 Madrid, Spain.
| | - Álvaro Somoza
- IMDEA Nanociencia & Nanobiotecnología (IMDEA-Nanociencia), Asociada al Centro Nacional de Biotecnología (CSIC), C/Faraday 9, 28049 Madrid, Spain.
| | - Anna Aviñó
- Department of Chemical and Biomolecular Nanotechnology, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, C/Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Carme Fàbrega
- Department of Chemical and Biomolecular Nanotechnology, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, C/Jordi Girona 18-26, 08034 Barcelona, Spain.
| | - Ramon Eritja
- Department of Chemical and Biomolecular Nanotechnology, IQAC-CSIC, CIBER-BBN Networking Centre on Bioengineering, Biomaterials and Nanomedicine, C/Jordi Girona 18-26, 08034 Barcelona, Spain.
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15
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Tintoré M, Grijalvo S, Eritja R, Fàbrega C. Synthesis of oligonucleotides carrying fluorescently labelled O(6)-alkylguanine for measuring hAGT activity. Bioorg Med Chem Lett 2015; 25:5208-11. [PMID: 26459209 DOI: 10.1016/j.bmcl.2015.09.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 09/23/2015] [Accepted: 09/26/2015] [Indexed: 01/17/2023]
Abstract
O(6)-alkylguanine-DNA-alkyltransferase (hAGT) activity provides resistance to cancer chemotherapeutic agents and its inhibition enhances chemotherapy. We herein present the development of a novel fluorescence assay for the detection of hAGT activity. We designed a dsDNA sequence containing a fluorophore-quencher pair, where the fluorophore was attached to an O(6)-benzylguanine. This precursor was synthesized using the Mitsunobu reaction to introduce the benzyl group. The alkyl-fluorophore group is transferred to the active site during the dealkylation, producing an increase in fluorescence which is correlated to hAGT activity. This assay can be used for the evaluation of potential inhibitors of hAGT in a straightforward manner.
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Affiliation(s)
- Maria Tintoré
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Santiago Grijalvo
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/ Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Carme Fàbrega
- Institute for Advanced Chemistry of Catalonia (IQAC), Spanish National Research Council (CSIC), Spain; Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), C/ Jordi Girona 18-26, 08034 Barcelona, Spain.
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16
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Tintoré M, Eritja R, Fábrega C. DNA Nanoarchitectures: Steps towards Biological Applications. Chembiochem 2014; 15:1374-90. [DOI: 10.1002/cbic.201402014] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Indexed: 12/26/2022]
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17
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Doluca O, Withers JM, Filichev VV. Molecular engineering of guanine-rich sequences: Z-DNA, DNA triplexes, and G-quadruplexes. Chem Rev 2013; 113:3044-83. [PMID: 23391174 DOI: 10.1021/cr300225q] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osman Doluca
- Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand
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Perugino G, Vettone A, Illiano G, Valenti A, Ferrara MC, Rossi M, Ciaramella M. Activity and regulation of archaeal DNA alkyltransferase: conserved protein involved in repair of DNA alkylation damage. J Biol Chem 2011; 287:4222-31. [PMID: 22167184 DOI: 10.1074/jbc.m111.308320] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Agents that form methylation adducts in DNA are highly mutagenic and carcinogenic, and organisms have evolved specialized cellular pathways devoted to their repair, including DNA alkyltransferases. These are proteins conserved in eucarya, bacteria and archaea, acting by a unique reaction mechanism, which leads to direct repair of DNA alkylation damage and irreversible protein alkylation. The alkylated form of DNA alkyltransferases is inactive, and in eukaryotes, it is rapidly directed to degradation. We report here in vitro and in vivo studies on the DNA alkyltransferase from the thermophilic archaeon Sulfolobus solfataricus (SsOGT). The development of a novel, simple, and sensitive fluorescence-based assay allowed a careful characterization of the SsOGT biochemical and DNA binding activities. In addition, transcriptional and post-translational regulation of SsOGT by DNA damage was studied. We show that although the gene transcription is induced by alkylating agent treatment, the protein is degraded in vivo by an alkylation-dependent mechanism. These experiments suggest a striking conservation, from archaea to humans, of this important pathway safeguarding genome stability.
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Affiliation(s)
- Giuseppe Perugino
- Institute of Protein Biochemistry, Consiglio Nazionale delle Ricerche, Via P. Castellino 111, 80131 Naples, Italy
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