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Koplūnaitė M, Butkutė K, Stankevičiūtė J, Meškys R. Exploring the Mutated Kinases for Chemoenzymatic Synthesis of N4-Modified Cytidine Monophosphates. Molecules 2024; 29:3767. [PMID: 39202847 PMCID: PMC11357392 DOI: 10.3390/molecules29163767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Revised: 08/07/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024] Open
Abstract
Nucleosides, nucleotides, and their analogues are an important class of molecules that are used as substrates in research of enzymes and nucleic acid, or as antiviral and antineoplastic agents. Nucleoside phosphorylation is usually achieved with chemical methods; however, enzymatic phosphorylation is a viable alternative. Here, we present a chemoenzymatic synthesis of modified cytidine monophosphates, where a chemical synthesis of novel N4-modified cytidines is followed by an enzymatic phosphorylation of the nucleosides by nucleoside kinases. To enlarge the substrate scope, multiple mutant variants of Drosophila melanogaster deoxynucleoside kinase (DmdNK) (EC:2.7.1.145) and Bacillus subtilis deoxycytidine kinase (BsdCK) (EC:2.7.1.74) have been created and tested. It has been determined that certain point mutations in the active sites of the kinases alter their substrate specificities noticeably and allow phosphorylation of compounds that had been otherwise not phosphorylated by the wild-type DmdNK or BsdCK.
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Affiliation(s)
| | | | | | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Sauletekio Av. 7, LT-10257 Vilnius, Lithuania; (K.B.); (J.S.)
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2
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Li Y, Zhou Y, Zhou D, Jiang Y, Butt M, Yang H, Que Y, Li Z, Chen G. Regioselective Homolytic C 2-H Borylation of Unprotected Adenosine and Adenine Derivatives via Minisci Reaction. J Am Chem Soc 2024; 146:21428-21441. [PMID: 39051926 DOI: 10.1021/jacs.4c03865] [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: 07/27/2024]
Abstract
A Minisci-type borylation of unprotected adenosine, adenine nucleotide, and adenosine analogues was successfully achieved through photocatalysis or thermal activation. Despite the challenges posed by the presence of two potential reactive sites (C2 and C8) in the purine motif, the unique nucleophilic amine-ligated boryl radicals effortlessly achieved excellent C2 site selectivity and simultaneously avoided the formation of multifunctionalized products. This protocol proved effective for the late-stage borylation of some important biomolecules as well as a few antiviral and antitumor drug molecules, such as AMP, cAMP, Vidarabine, Cordycepin, Tenofovir, Adefovir, GS-441524, etc. Theoretical calculations shed light on the site selectivity, revealing that the free energy barriers for the C2-Minisci addition are further lowered through the chelation of additive Mg2+ to N3 and furyl oxygen. This phenomenon has been confirmed by an IGMH analysis. Preliminary antitumor evaluation, derivation of the C2-borylated adenosine to other analogues with high-value functionalities, along with the CuAAC click reactions, suggest the potential application of this methodology in drug molecular optimization studies and chemical biology.
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Affiliation(s)
- Yangyan Li
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yutong Zhou
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Green and High-value Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, Qinghai, P. R. China
| | - Dazhi Zhou
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Yujie Jiang
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Madiha Butt
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Hui Yang
- Key Laboratory of Biocatalysis and Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Department of Pharmacy, Zunyi Medical University, Zunyi 563000, P. R. China
| | - Yingchuan Que
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Zhiming Li
- Department of Chemistry, Fudan University, Shanghai 200438, P. R. China
| | - Gang Chen
- Shanghai Key Laboratory for Molecular Engineering of Chiral Drugs, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
- Key Laboratory of Green and High-value Utilization of Salt Lake Resources, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, Qinghai, P. R. China
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3
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Arora A, Kumar S, Kumar S, Dua A, Singh BK. Synthesis, characterization and photophysical studies of dual-emissive base-modified fluorescent nucleosides. Org Biomol Chem 2024; 22:4922-4939. [PMID: 38808609 DOI: 10.1039/d4ob00749b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2024]
Abstract
A straightforward and efficient methodology has been employed for the synthesis of a diverse set of base-modified fluorescent nucleoside conjugates via Cu(I)-catalysed cycloaddition reaction of 5-ethynyl-2',3',5'-tri-O-acetyluridine/3',5'-di-O-acetyl-2'-deoxyuridine with 4-(azidomethyl)-N9-(4'-aryl)-9,10-dihydro-2H,8H-chromeno[8,7-e][1,3]oxazin-2-ones in tBuOH to afford the desired 1,2,3-triazoles in 92-95% yields. Treatment with NaOMe/MeOH resulted in the final deprotected nucleoside analogues. The synthesized 1,2,3-triazoles demonstrated a significant emission spectrum, featuring two robust bands in the region from 350-500 nm (with excitation at 300 nm) in fluorescence studies. Photophysical investigations revealed a dual-emissive band with high fluorescence intensity, excellent Stokes shift (140-164 nm) and superior quantum yields (0.068-0.350). Furthermore, the electronic structures of the synthesized triazoles have been further verified by DFT studies. Structural characterization of all synthesized compounds was carried out using various analytical techniques, including IR, 1H-NMR, 13C-NMR, 1H-1H COSY, 1H-13C HETCOR experiments, and HRMS measurements. The dual-emissive nature of these nucleosides would be a significant contribution to nucleoside chemistry as there are limited literature reports on the same.
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Affiliation(s)
- Aditi Arora
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sumit Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
| | - Sandeep Kumar
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
- Department of Chemistry, Ramjas College, University of Delhi, Delhi-110007, India
| | - Amita Dua
- Department of Chemistry, Dyal Singh College, University of Delhi, Delhi-110007, India
| | - Brajendra K Singh
- Bioorganic Laboratory, Department of Chemistry, University of Delhi, Delhi-110007, India.
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4
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Stachelska-Wierzchowska A, Wierzchowski J. Chemo-Enzymatic Generation of Highly Fluorescent Nucleoside Analogs Using Purine-Nucleoside Phosphorylase. Biomolecules 2024; 14:701. [PMID: 38927104 PMCID: PMC11201700 DOI: 10.3390/biom14060701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Chemo-enzymatic syntheses of strongly fluorescent nucleoside analogs, potentially applicable in analytical biochemistry and cell biology are reviewed. The syntheses and properties of fluorescent ribofuranosides of several purine, 8-azapurine, and etheno-purine derivatives, obtained using various types of purine nucleoside phosphorylase (PNP) as catalysts, as well as α-ribose-1-phosphate (r1P) as a second substrate, are described. In several instances, the ribosylation sites are different to the canonical purine N9. Some of the obtained ribosides show fluorescence yields close to 100%. Possible applications of the new analogs include assays of PNP, nucleoside hydrolases, and other enzyme activities both in vitro and within living cells using fluorescence microscopy.
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Affiliation(s)
| | - Jacek Wierzchowski
- Department of Physics and Biophysics, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
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5
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Gonçalves JM, Gonçalves JND, Sousa LF, Rodrigues LR, Correia-de-Sá P, Coutinho PJG, Castanheira EMS, Oliveira R, Dias AM. 2,4,5-Triaminopyrimidines as blue fluorescent probes for cell viability monitoring: synthesis, photophysical properties, and microscopy applications. Org Biomol Chem 2024; 22:2252-2263. [PMID: 38390694 DOI: 10.1039/d4ob00092g] [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: 02/24/2024]
Abstract
Monitoring cell viability is critical in cell biology, pathology, and drug discovery. Most cell viability assays are cell-destructive, time-consuming, expensive, and/or hazardous. Herein, we present a series of newly synthesized 2,4,5-triaminopyrimidine derivatives able to discriminate between live and dead cells. To our knowledge, these compounds are the first fluorescent nucleobase analogues (FNAs) with cell viability monitoring potential. These new fluorescent molecules are synthesized using highly efficient and cost-effective methods and feature unprecedented photophysical properties (longer absorption and emission wavelengths, environment-sensitive emission, and unprecedented brightness within FNAs). Using a live-dead Saccharomyces cerevisiae cell and theoretical assays, the fluorescent 2,4,5-triaminopyrimidine derivatives were found to specifically accumulate inside dead cells by interacting with dsDNA grooves, thus paving the way for the emergence of novel and safe fluorescent cell viability markers emitting in the blue region. As the majority of commercially available viability dyes emit in the green to red region of the visible spectrum, these novel markers might be useful to meet the needs of blue markers for co-staining combinations.
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Affiliation(s)
- Jorge M Gonçalves
- CQ-UM - Centre of Chemistry of University of Minho, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
- CF-UM-UP - Physics Centre of Minho and Porto Universities and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), Campus de Gualtar, 4710-057, Braga, Portugal
| | - João N D Gonçalves
- CQ-UM - Centre of Chemistry of University of Minho, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Luís F Sousa
- CQ-UM - Centre of Chemistry of University of Minho, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
- CF-UM-UP - Physics Centre of Minho and Porto Universities and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Lígia R Rodrigues
- CEB - Centre of Biological Engineering, Department of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- LABBELS - Associate Laboratory, Guimarães, Braga, Portugal
| | - Paulo Correia-de-Sá
- Laboratório de Farmacologia e Neurobiologia, Center for Drug Discovery and Innovative Medicines (MedInUP), Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, R. Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Paulo J G Coutinho
- CF-UM-UP - Physics Centre of Minho and Porto Universities and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Elisabete M S Castanheira
- CF-UM-UP - Physics Centre of Minho and Porto Universities and LaPMET (Laboratory of Physics for Materials and Emergent Technologies), Campus de Gualtar, 4710-057, Braga, Portugal
| | - Rui Oliveira
- CBMA - Centre of Molecular and Environmental Biology, Department of Biology, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Alice M Dias
- CQ-UM - Centre of Chemistry of University of Minho, Department of Chemistry, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.
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6
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Lang F, Rönicke F, Wagenknecht HA. Aminophthalimide as a mimetic of purines and a fluorescent RNA base surrogate for RNA imaging. Org Biomol Chem 2023; 21:3079-3082. [PMID: 36943317 DOI: 10.1039/d3ob00302g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Aminophthalimide and N,N-dimethylaminophthalimide are used as fluorescent mimetics of purines due to their similar size and their possibility for hydrogen bonding. Their C-nucleotides were synthetically incorporated into RNA by means of phosphoramidite chemistry, behave as nonspecific fluorescent base analogs with flexible hydrogen bonding capabilities, and show solvatochromic fluorescence that is suitable for RNA imaging in live cells.
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Affiliation(s)
- Fabian Lang
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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7
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Lakshman MK. Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond. CHEM REC 2023; 23:e202200182. [PMID: 36166699 DOI: 10.1002/tcr.202200182] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 08/26/2022] [Indexed: 01/24/2023]
Abstract
Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.
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Affiliation(s)
- Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 Fifth Avenue, New York, NY 10016, USA
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8
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He Y, Liu M, Teng S, Wojtas L, Gu G, Shi X. Synthesis and Characterization of Fluorescence Active G 4-Quartet and Direct Evaluation of Self-Assembly Impact on Emission. CHINESE CHEM LETT 2022; 33:4203-4207. [PMID: 38107831 PMCID: PMC10723654 DOI: 10.1016/j.cclet.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fluorescence (FL) active 8-aryl guanosine derivatives were prepared and applied for cation mediated self-assembly to form the H-bonded G8-quadruplexes. The p-cyano (p-CN) and 8-anthracene (8-An) substituted guanosines were identified to give the strongest fluorescence with the formation of G8-octamers (G8) both in solution (NMR) and solid state (X-ray). This well-defined G8-octamer system has provided the first direct evidence on the self-assembled G-quadruplex fluorescence emission with aggregation-induced emission (AIE), which could be applied as the foundation for FL molecular probe design toward G-quadruplex recognition.
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Affiliation(s)
- Ying He
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Mengjia Liu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Shun Teng
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Lukasz Wojtas
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Guangxin Gu
- Department of Materials Science, Fudan University, 2005 Songhu Rd., Shanghai, 200438, PR China
| | - Xiaodong Shi
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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9
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Krul SE, Costa GJ, Hoehn SJ, Valverde D, Oliveira LMF, Borin AC, Crespo-Hernández CE. Resolving Ultrafast Photoinitiated Dynamics of the Hachimoji 5-Aza-7-Deazaguanine Nucleobase: Impact of Synthetically Expanding the Genetic Alphabet. Photochem Photobiol 2022; 99:693-705. [PMID: 35938218 DOI: 10.1111/php.13688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/05/2022] [Indexed: 11/29/2022]
Abstract
The guanine derivative, 5-aza-7-deazaguanine (5N7C G) has recently been proposed as one of four unnatural bases, termed Hachimoji (8-letter) to expand the genetic code. We apply steady-state and time-resolved spectroscopy to investigate its electronic relaxation mechanism and probe the effect of atom substitution on the relaxation mechanism in polar protic and polar aprotic solvents. Mapping of the excited state potential energy surfaces is performed, from which the critical points are optimized by using the state-of-art Extended Multi-State Complete Active Space Second-Order Perturbation Theory. It is demonstrated that excitation to the lowest energy 1 ππ* state of 5N7C G results in complex dynamics leading to ca. 10 to 30-fold slower relaxation (depending on solvent) compared to guanine. A significant conformational change occurs at the S1 minimum, resulting in a 10-fold greater fluorescence quantum yield compared to guanine. The fluorescence quantum yield and S1 decay lifetime increase going from water to acetonitrile to propanol. The solvent-dependent results are supported by the quantum chemical calculations showing an increase in the energy barrier between the S1 minimum and the S1 /S0 conical intersection going from water to propanol. The longer lifetimes might make 5N7C G more photochemical active to adjacent nucleobases than guanine or other nucleobases within DNA.
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Affiliation(s)
- Sarah E Krul
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Gustavo J Costa
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Sean J Hoehn
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
| | - Danillo Valverde
- Unité de Chimie Physique Theorique et Structurale, Namur Institute of Structured Matter, Université de Namur, B-5000, Namur, Belgium
| | - Leonardo M F Oliveira
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000. São Paulo, SP, Brazil
| | - Carlos E Crespo-Hernández
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio, 44106, United States
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10
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Appy L, Peyrottes S, Roy B. Supported Synthesis of Adenosine Nucleotides and Derivatives on a Benzene‐Centered Tripodal Soluble Support. European J Org Chem 2022. [DOI: 10.1002/ejoc.202100544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lucie Appy
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
| | - Suzanne Peyrottes
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
| | - Béatrice Roy
- Nucleosides & Phosphorylated Effectors Team Institute for Biomolecules Max Mousseron (IBMM) UMR 5247 CNRS University of Montpellier, ENSCM Campus Triolet cc 1705, Place Eugène Bataillon 34095 Montpellier France
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11
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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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12
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Abstract
A new fluorescent ribonucleoside alphabet (mth N) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (th N) and isothiazole[4,3-d]pyrimidine (tz N) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding mth N/mth NTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the mth N alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Shenghua Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Marcela S Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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13
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Akula HK, Bae S, Pradhan P, Yang L, Zajc B, Lakshman MK. Diversely C8-functionalized adenine nucleosides via their underexplored carboxaldehydes. Chem Commun (Camb) 2022; 58:1744-1747. [PMID: 35029254 DOI: 10.1039/d1cc06686b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potentially versatile N-unprotected 8-formyl derivatives of adenosine and 2'-deoxyadenosine are highly underexploited for C8 modifications of these nucleosides. Only in situ formation of 8-formyladenosine is known and a single application of an N-benzoyl derivative has been reported. On the other hand, 8-formyl-2'-deoxyadenosine and its applications remain unknown. Herein, we report straightforward, scalable syntheses of both N-unprotected 8-formyladenine nucleoside derivatives, and demonstrate broad diversification at the C8 position by hydroxymethylation, azidation, CuAAC ligation, reductive amination, as well as olefination and fluoroolefination with modified Julia and a Horner-Wadsworth-Emmons reagents.
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Affiliation(s)
- Hari K Akula
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Suyeal Bae
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Padmanava Pradhan
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Lijia Yang
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA.
| | - Barbara Zajc
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA. .,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, NY 10031, USA. .,The PhD Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
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14
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Koboku S, Tsukada T, Oku Y, Kobayashi S, Saito Y. FRET-based dual-labeled oligonucleotide probe detects target DNA by probing a minor groove environment. Org Biomol Chem 2022; 20:1699-1706. [DOI: 10.1039/d2ob00027j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel amino-modifier ESF nucleoside AM37zA (1) containing trifluoroacetyl (TFA)-protected amino group is designed for the functionalization of ODN probe after oligonucleotide synthesis. AM37zA (1) demonstrated remarkable solvatochromicity and ODN...
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15
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Balasubramaniyam T, Oh KI, Jin HS, Ahn HB, Kim BS, Lee JH. Non-Canonical Helical Structure of Nucleic Acids Containing Base-Modified Nucleotides. Int J Mol Sci 2021; 22:9552. [PMID: 34502459 PMCID: PMC8430589 DOI: 10.3390/ijms22179552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 12/12/2022] Open
Abstract
Chemically modified nucleobases are thought to be important for therapeutic purposes as well as diagnosing genetic diseases and have been widely involved in research fields such as molecular biology and biochemical studies. Many artificially modified nucleobases, such as methyl, halogen, and aryl modifications of purines at the C8 position and pyrimidines at the C5 position, are widely studied for their biological functions. DNA containing these modified nucleobases can form non-canonical helical structures such as Z-DNA, G-quadruplex, i-motif, and triplex. This review summarizes the synthesis of chemically modified nucleotides: (i) methylation, bromination, and arylation of purine at the C8 position and (ii) methylation, bromination, and arylation of pyrimidine at the C5 position. Additionally, we introduce the non-canonical structures of nucleic acids containing these modifications.
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Affiliation(s)
- Thananjeyan Balasubramaniyam
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Kwnag-Im Oh
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Ho-Seong Jin
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Hye-Bin Ahn
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
| | - Byeong-Seon Kim
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
- Department of Chemistry Education, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
| | - Joon-Hwa Lee
- Department of Chemistry, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea; (T.B.); (K.-I.O.); (H.-S.J.); (H.-B.A.)
- The Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, Gyeongnam, Korea
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16
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Sengupta S, Das P. Application of diazonium chemistry in purine modifications: A focused review. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Saumitra Sengupta
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
| | - Parthasarathi Das
- Department of Chemistry Indian Institute of Technology (Indian School of Mines) Dhanbad India
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17
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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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18
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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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19
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20
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Baraniak D, Boryski J. Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry. Biomedicines 2021; 9:628. [PMID: 34073038 PMCID: PMC8229351 DOI: 10.3390/biomedicines9060628] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/26/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.
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Affiliation(s)
- Dagmara Baraniak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland;
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21
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Podder A, Lee HJ, Kim BH. Fluorescent Nucleic Acid Systems for Biosensors. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Arup Podder
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Ha Jung Lee
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Korea
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22
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Site-Specific Fluorescent Labeling of RNA Interior Positions. Molecules 2021; 26:molecules26051341. [PMID: 33802273 PMCID: PMC7959133 DOI: 10.3390/molecules26051341] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 02/08/2023] Open
Abstract
The introduction of fluorophores into RNA for both in vitro and in cellulo studies of RNA function and cellular distribution is a subject of great current interest. Here I briefly review methods, some well-established and others newly developed, which have been successfully exploited to site-specifically fluorescently label interior positions of RNAs, as a guide to investigators seeking to apply this approach to their studies. Most of these methods can be applied directly to intact RNAs, including (1) the exploitation of natural posttranslational modifications, (2) the repurposing of enzymatic transferase reactions, and (3) the nucleic acid-assisted labeling of intact RNAs. In addition, several methods are described in which specifically labeled RNAs are prepared de novo.
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23
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Le HN, Brazard J, Barnoin G, Vincent S, Michel BY, Leonard J, Burger A. Control of Intermolecular Photoinduced Electron Transfer in Deoxyadenosine-Based Fluorescent Probes. Chemistry 2021; 27:1364-1373. [PMID: 32767410 DOI: 10.1002/chem.202003456] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Indexed: 12/12/2022]
Abstract
In this work, we report on the Photoinduced Electron Transfer (PET) reaction between a donor (adenine analogue) and an acceptor (3-methoxychromone dye, 3MC) in the context of designing efficient fluorescent probes as DNA sensors. Firstly, Gibbs energy was investigated in disconnected donor-acceptor systems by Rehm-Weller equation. The oxidation potential of the adenine derivative was responsible for exergonicity of the PET reaction in separated combinations. Then, the PET reaction in donor-π-acceptor conjugates was investigated using steady-state fluorescence spectroscopy, acid-mediated PET inhibition and transient absorption techniques. In conjugated systems, PET is a favorable pathway of fluorescent quenching when an electron-rich adenine analogue (d7A) was connected to the fluorophore (3MC). We found that formation of ground-state complexes even at nm concentration range dominated the dye photophysics and generated poorly emissive species likely through intermolecular PET from d7A to 3MC. On the other hand, solution acidification disrupts complexation and turns on the dye emission. Bridging an electron-poor adenine analogue with high oxidation potential (8 d7A) to 3MC presenting low reduction potential is another alternative to prevent complex formation and produce highly emissive monomer conjugates.
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Affiliation(s)
- Hoang-Ngoan Le
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Johanna Brazard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France.,Present address: Université de Genève, Département de Chimie Physique, 1211, Genève, France
| | - Guillaume Barnoin
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Steve Vincent
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Benoît Y Michel
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
| | - Jérémie Leonard
- Université de Strasbourg, Institut de Physique et Chimie, des Matériaux de Strasbourg and Labex NIE, UMR 7504, CNRS, 67200, Strasbourg, France
| | - Alain Burger
- Université Côte d'Azur, Institut de Chimie de Nice, UMR 7272, CNRS, Parc Valrose, 06108, Nice cedex 2, France
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24
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Kumar S, Kumar S, Maity J, Kumar B, Bali Mehta S, Prasad AK. Synthesis and photophysical properties of 5-(3′′-alkyl/aryl-amino-1′′-azaindolizin-2′′-yl)-2′-deoxyuridines. NEW J CHEM 2021. [DOI: 10.1039/d1nj02423j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Groebke–Blackburn–Bienayame (GBB) reaction has been used for the efficient synthesis of novel fluorescent 5-azaindolizino-2′-deoxyuridines starting from commercially available thymidine following two strategies.
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Affiliation(s)
- Sandeep Kumar
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
| | - Sumit Kumar
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen's College, University of Delhi, Delhi, India
| | - Banty Kumar
- Department of Chemistry, Rajdhani College, University of Delhi, Delhi, India
| | | | - Ashok K. Prasad
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
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25
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Kapdi AR, Bhilare S, Kori S, Shet H, Balaram G, Mahendar K, Sanghvi YS. Scale-Up of a Heck Alkenylation Reaction: Application to the Synthesis of an Amino-Modifier Nucleoside ‘Ruth Linker’. SYNTHESIS-STUTTGART 2020. [DOI: 10.1055/s-0040-1707260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
AbstractRuth linker is a C5 pyrimidine modified nucleoside analogue widely utilized for the incorporation of a primary amine in a synthetic oligonucleotide. The increasing demand for non-radioactive labeling, detection of biomolecules, and assembly of COVID-19 test kits has triggered a need for scale-up of Ruth linker. Herein, an efficient protocol involving a palladium-catalyzed Heck alkenylation is described. The synthesis has been optimized with a goal of low catalyst concentration, column-free isolation, high product purity, reproducibility, and shorter reaction time. The scalability and utility of the process have been demonstrated successfully on a 100 g scale (starting material). Additionally, for scale-up of the Heck alkenylation protocol, 7-phospha-1,3,5-triaza-adamantanebutane sulfonate (PTABS) as the coordinating caged phosphine ligand was also synthesized on a multigram scale after careful optimization of the conditions.
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Affiliation(s)
- Anant R. Kapdi
- Department of Chemistry, Institute of Chemical Technology
| | | | - Santosh Kori
- Department of Chemistry, Institute of Chemical Technology
- Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre
| | - Harshita Shet
- Department of Chemistry, Institute of Chemical Technology
- Institute of Chemical Technology-Indian Oil Odisha Campus, IIT Kharagpur Extension Centre
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26
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Sanches de Araújo AV, Valverde D, Canuto S, Borin AC. Solvation Structures and Deactivation Pathways of Luminescent Isothiazole-Derived Nucleobases: tzA, tzG, and tzI. J Phys Chem A 2020; 124:6834-6844. [PMID: 32786984 DOI: 10.1021/acs.jpca.0c03398] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The photophysical relaxation pathways of tzA, tzG, and tzI luminescent nucleobases were investigated with the MS-CASPT2 quantum-chemical method and double-ζ basis sets (cc-pVDZ) in gas and condensed phases (1,4-dioxane and water) with the sequential Monte Carlo/CASPT2 and free energy gradient (FEG) methods. Solvation shell structures, in the ground and excited states, were examined with the pairwise radial distribution function (G(r)) and solute-solvent hydrogen-bond networks. Site-specific hydrogen bonding analysis evidenced relevant changes between both electronic states. The three luminescent nucleobases share a common photophysical pattern, summarized as the lowest-lying 1(ππ*) bright state that is populated directly after the absorption of radiation and evolves barrierless to the minimum energy structure, from where the excess of energy is released by fluorescence. From the 1(ππ*)min region, the conical intersection with the ground state ((ππ*/GS)CI) is not accessible due to the presence of high energetic barriers. By combining the present results with those reported earlier by us for the pyrimidine fluorescent nucleobases, we present a comprehensive description of the photophysical properties of this important class of new fluorescent nucleosides.
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Affiliation(s)
| | - Danillo Valverde
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Sylvio Canuto
- Institute of Physics, University of São Paulo, Rua do Matão 1371, 05508-090 São Paulo, SP, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, SP, Brazil
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27
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Wierzchowski J, Smyk B. Excited-State Proton Transfer in 8-Azapurines I: A Kinetic Analysis of 8-Azaxanthine Fluorescence. Molecules 2020; 25:molecules25122740. [PMID: 32545696 PMCID: PMC7356501 DOI: 10.3390/molecules25122740] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 01/30/2023] Open
Abstract
A super-continuum white laser with a half-pulse width of ~75 ps was used to observe the kinetics of a postulated excited-state proton transfer in 8-azaxanthine and its 8-methyl derivative. Both compounds exhibited dual emissions in weakly acidified alcoholic media, but only one band was present in aqueous solutions, exhibiting an abnormal Stokes shift (>12,000 cm−1). It was shown that long-wavelength emissions were delayed relative to the excitation pulse within alcoholic media. The rise time was calculated to be 0.4–0.5 ns in both methanol and deuterated methanol. This is equal to the main component of the fluorescence decay in the short-wavelength band (340 nm). Time-resolved emission spectra (TRES) indicated a two-state photo-transformation model in both compounds. Global analysis of the time dependence revealed three exponential components in each compound, one of which had an identical rise-time, with the second attributed to a long-wavelength band decay (6.4 ns for aza-xanthine and 8.3 ns for its 8-methyl derivative). The origin of the third, intermediate decay time (1.41 ns for aza-xanthine and 0.87 ns for 8-methyl-azaxanthine) is uncertain, but decay-associated spectra (DAS) containing both bands suggest the participation of a contact ion pair. These results confirm the model of phototautomerism proposed earlier, but the question of the anomalous isotope effect remains unsolved.
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28
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2-Ethynylnaphthalene-modified 8-aza-3,7-dideaza-2′-deoxyadenosine derivative discriminates thymine in target DNA via changes in the fluorescence wavelength. Tetrahedron Lett 2020. [DOI: 10.1016/j.tetlet.2020.151841] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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30
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Grosjean S, Julienne K, Gouin SG, Deniaud D. Approach to Artificial Nucleosides from Glycoside Isothiocyanates: Synthesis of Original N‐Glycosylated Heterostructures by Cyclocondensation Reactions. ChemistrySelect 2019. [DOI: 10.1002/slct.201903391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sylvain Grosjean
- Karlsruhe Institute of Technology (KIT)University of Karlsruhe (TH)
| | | | | | - David Deniaud
- Univ NantesCNRSCEISAM (UMR 6230) F-44000 Nantes France
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31
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Leonard P, Kondhare D, Jentgens X, Daniliuc C, Seela F. Nucleobase-Functionalized 5-Aza-7-deazaguanine Ribo- and 2′-Deoxyribonucleosides: Glycosylation, Pd-Assisted Cross-Coupling, and Photophysical Properties. J Org Chem 2019; 84:13313-13328. [DOI: 10.1021/acs.joc.9b01347] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Xenia Jentgens
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
| | - Constantin Daniliuc
- Institut für Organische Chemie, Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany
- Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069 Osnabrück, Germany
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32
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Shelkovnikov VV, Kargapolova IY, Korotaev SV, Orlova NA, Rybalova TV, Chuikov IP. Three-color luminescent transformation of the julolidine pyrylo/pyridocyanine dyes in the adsorbed state. J Photochem Photobiol A Chem 2019. [DOI: 10.1016/j.jphotochem.2019.02.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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33
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Takeda T, Yanagi M, Suzuki A, Katoh R, Saito Y. Synthesis of ethynylpyrene-modified 3-deaza-2′-deoxyguanosines as environmentally sensitive fluorescent nucleosides: Target DNA-sequence detection via changes in the fluorescence wavelength. Tetrahedron Lett 2019. [DOI: 10.1016/j.tetlet.2019.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ludford PT, Rovira AR, Fin A, Tor Y. Fluorescing Isofunctional Ribonucleosides: Assessing Adenosine Deaminase Activity and Inhibition. Chembiochem 2019; 20:718-726. [PMID: 30566279 DOI: 10.1002/cbic.201800665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Indexed: 12/12/2022]
Abstract
The enzymatic conversion of isothiazolo[4,3-d]pyrimidine-based adenosine (tz A) and 2-aminoadenosine (tz 2-AA) analogues to the corresponding isothiazolo[4,3-d]pyrimidine-based inosine (tz I) and guanosine (tz G) derivatives is evaluated and compared to the conversion of native adenosine to inosine. Henri-Michaelis-Menten analyses provides the foundation for a high-throughput screening assay, and the efficacy of the assay is showcased by fluorescence-based analysis of tz A conversion to tz I in the presence of known and newly synthesized inhibitors.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0358, USA
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Kanamori T, Masaki Y, Oda Y, Ohzeki H, Ohkubo A, Sekine M, Seio K. DNA triplex-based fluorescence turn-on sensors for adenosine using a fluorescent molecular rotor 5-(3-methylbenzofuran-2-yl) deoxyuridine. Org Biomol Chem 2019; 17:2077-2080. [DOI: 10.1039/c8ob02747a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescence turn-on detection of adenosine based on microenvironmental and conformational changes of a fluorescent molecular rotor in the DNA triplex is reported.
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Affiliation(s)
- Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Yuki Oda
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Hiroki Ohzeki
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Akihiro Ohkubo
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Yokohama 226-8501
- Japan
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Teppang KL, Lee RW, Burns DD, Turner MB, Lokensgard ME, Cooksy AL, Purse BW. Electronic Modifications of Fluorescent Cytidine Analogues Control Photophysics and Fluorescent Responses to Base Stacking and Pairing. Chemistry 2018; 25:1249-1259. [PMID: 30338571 DOI: 10.1002/chem.201803653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Indexed: 11/07/2022]
Abstract
The rational design of fluorescent nucleoside analogues is greatly hampered by the lack of a general method to predict their photophysics, a problem that is especially acute when base pairing and stacking change fluorescence. To better understand these effects, a series of tricyclic cytidine (tC and tCO ) analogues ranging from electron-rich to electron-deficient was designed and synthesized. They were then incorporated into oligonucleotides, and photophysical responses to base pairing and stacking were studied. When inserted into double-stranded DNA oligonucleotides, electron-rich analogues exhibit a fluorescence turn-on effect, in contrast with the electron-deficient compounds, which show diminished fluorescence. The magnitude of these fluorescence changes is correlated with the oxidation potential of nearest neighbor nucleobases. Moreover, matched base pairing enhances fluorescence turn-on for the electron-rich compounds, and it causes a fluorescence decrease for the electron-deficient compounds. For the tCO compounds, the emergence of vibrational fine structure in the fluorescence spectra in response to base pairing and stacking was observed, offering a potential new tool for studying nucleic acid structure and dynamics. These results, supported by DFT calculations, help to rationalize fluorescence changes in the base stack and will be useful for selecting the best fluorescent nucleoside analogues for a desired application.
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Affiliation(s)
- Kristine L Teppang
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Raymond W Lee
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Dillon D Burns
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - M Benjamin Turner
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Melissa E Lokensgard
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Andrew L Cooksy
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
| | - Byron W Purse
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, 92182, USA
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Matarazzo A, Brow J, Hudson RH. Synthesis and photophysical evaluation of new fluorescent 7-arylethynyl-7-deazaadenosine analogs. CAN J CHEM 2018. [DOI: 10.1139/cjc-2018-0303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Three new fluorescent 7-deaza-2′-deoxyadenosine analogs were synthesized via the Sonogashira cross-coupling reaction of 7-iodo-7-deaza-2′-deoxyadenosine with 1-ethynylpyrene, 2-ethynyl-6-methoxynaphthalene, and 9-ethynylphenanthrene. The spectral properties of these analogs were evaluated in dioxane, EtOH, and H2O to determine their potential for use as environmentally sensitive fluorescent probes. All three analogs displayed large solvatofluorochromicity in H2O, relative to their emission wavelengths in dioxane or EtOH. Moreover, all three analogs exhibited microenvironmental sensitivity of their fluorescence emission intensity, being moderate to high quantum yields in dioxane and EtOH and significantly lower in H2O. Various attempts to perform domino cross-coupling and annuation reactions on 7-deaza-7-alkynyladenine derivatives to form a new fused tricyclic adenine analog were unsuccessful.
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Affiliation(s)
- Augusto Matarazzo
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Justin Brow
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Robert H.E. Hudson
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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