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Yang H, Eremeeva E, Abramov M, Jacquemyn M, Groaz E, Daelemans D, Herdewijn P. CRISPR-Cas9 recognition of enzymatically synthesized base-modified nucleic acids. Nucleic Acids Res 2023; 51:1501-1511. [PMID: 36611237 PMCID: PMC9976875 DOI: 10.1093/nar/gkac1147] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/09/2022] [Accepted: 11/17/2022] [Indexed: 01/09/2023] Open
Abstract
An enzymatic method has been successfully established enabling the generation of partially base-modified RNA (previously named RZA) constructs, in which all G residues were replaced by isomorphic fluorescent thienoguanosine (thG) analogs, as well as fully modified RZA featuring thG, 5-bromocytosine, 7-deazaadenine and 5-chlorouracil. The transcriptional efficiency of emissive fully modified RZA was found to benefit from the use of various T7 RNA polymerase variants. Moreover, dthG could be incorporated into PCR products by Taq DNA polymerase together with the other three base-modified nucleotides. Notably, the obtained RNA products containing thG as well as thG together with 5-bromocytosine could function as effectively as natural sgRNAs in an in vitro CRISPR-Cas9 cleavage assay. N1-Methylpseudouridine was also demonstrated to be a faithful non-canonical substitute of uridine to direct Cas9 nuclease cleavage when incorporated in sgRNA. The Cas9 inactivation by 7-deazapurines indicated the importance of the 7-nitrogen atom of purines in both sgRNA and PAM site for achieving efficient Cas9 cleavage. Additional aspects of this study are discussed in relation to the significance of sgRNA-protein and PAM--protein interactions that were not highlighted by the Cas9-sgRNA-DNA complex crystal structure. These findings could expand the impact and therapeutic value of CRISPR-Cas9 and other RNA-based technologies.
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Affiliation(s)
- Hui Yang
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Elena Eremeeva
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,Queensland University of Technology, Centre for Agriculture and the Bioeconomy, Molecular Engineering Group, George Street 2, 4000 Brisbane, Queensland, Australia
| | - Mikhail Abramov
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Maarten Jacquemyn
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Elisabetta Groaz
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium.,University of Padova, Department of Pharmaceutical and Pharmacological Sciences, Via Marzolo 5, 35131 Padova, Italy
| | - Dirk Daelemans
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, Herestraat 49, Box 1043, 3000 Leuven, Belgium
| | - Piet Herdewijn
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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Chakraborty G, Chattaraj S, Pal H. pH assisted modulation in the binding affinity for BODIPY-benzimidazole conjugate with anionic cyclodextrin. J Photochem Photobiol A Chem 2023. [DOI: 10.1016/j.jphotochem.2022.114266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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3
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Excited-State Dynamics of Imiquimod in Aqueous Solutions. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.113998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Thienoguanosine, a unique non-perturbing reporter for investigating rotational dynamics of DNA duplexes and their complexes with proteins. Int J Biol Macromol 2022; 213:210-225. [DOI: 10.1016/j.ijbiomac.2022.05.162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/23/2022] [Indexed: 11/05/2022]
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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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Bucardo MS, Wu Y, Ludford PT, Li Y, Fin A, Tor Y. Real-Time Monitoring of Human Guanine Deaminase Activity by an Emissive Guanine Analog. ACS Chem Biol 2021; 16:1208-1214. [PMID: 34190533 PMCID: PMC9109600 DOI: 10.1021/acschembio.1c00232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Guanine deaminase (GDA) deaminates guanine to xanthine. Despite its significance, the study of human GDA remains limited compared to other metabolic deaminases. As a result, its substrate and inhibitor repertoire are limited, and effective real-time activity, inhibitory, and discovery assays are missing. Herein, we explore two emissive heterocyclic cores, based on thieno[3,4-d]pyrimidine (thN) and isothiazole[4,3-d]pyrimidine (tzN), as surrogate GDA substrates. We demonstrate that, unlike the thieno analog, thGN, the isothiazolo guanine surrogate, tzGN, does undergo effective enzymatic deamination by GDA and yields the spectroscopically distinct xanthine analog, tzXN. Further, we showcase the potential of this fluorescent nucleobase surrogate to provide a visible spectral window for a real-time study of GDA and its inhibition.
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Affiliation(s)
- Marcela S Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - You Wu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yao Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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Kuchlyan J, Martinez-Fernandez L, Mori M, Gavvala K, Ciaco S, Boudier C, Richert L, Didier P, Tor Y, Improta R, Mély Y. What Makes Thienoguanosine an Outstanding Fluorescent DNA Probe? J Am Chem Soc 2020; 142:16999-17014. [PMID: 32915558 DOI: 10.1021/jacs.0c06165] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Thienoguanosine (thG) is an isomorphic guanosine (G) surrogate that almost perfectly mimics G in nucleic acids. To exploit its full potential and lay the foundation for future applications, 20 DNA duplexes, where the bases facing and neighboring thG were systematically varied, were thoroughly studied using fluorescence spectroscopy, molecular dynamics simulations, and mixed quantum mechanical/molecular mechanics calculations, yielding a comprehensive understanding of its photophysics in DNA. In matched duplexes, thG's hypochromism was larger for flanking G/C residues but its fluorescence quantum yield (QY) and lifetime values were almost independent of the flanking bases. This was attributed to high duplex stability, which maintains a steady orientation and distance between nucleobases, so that a similar charge transfer (CT) mechanism governs the photophysics of thG independently of its flanking nucleobases. thG can therefore replace any G residue in matched duplexes, while always maintaining similar photophysical features. In contrast, the local destabilization induced by a mismatch or an abasic site restores a strong dependence of thG's QY and lifetime values on its environmental context, depending on the CT route efficiency and solvent exposure of thG. Due to this exquisite sensitivity, thG appears ideal for monitoring local structural changes and single nucleotide polymorphism. Moreover, thG's dominant fluorescence lifetime in DNA is unusually long (9-29 ns), facilitating its selective measurement in complex media using a lifetime-based or a time-gated detection scheme. Taken together, our data highlight thG as an outstanding emissive substitute for G with good QY, long fluorescence lifetimes, and exquisite sensitivity to local structural changes.
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Affiliation(s)
- Jagannath Kuchlyan
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Mattia Mori
- Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Krishna Gavvala
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France.,Department of Biotechnology, Chemistry, and Pharmacy, University of Siena, Via Aldo Moro 2, 53100 Siena, Italy
| | - Christian Boudier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Ludovic Richert
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto Biostrutture e Bioimmagini, Via Mezzocannone 16, 80134 Napoli, Italy
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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