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Paez‐Perez M, Kuimova MK. Molecular Rotors: Fluorescent Sensors for Microviscosity and Conformation of Biomolecules. Angew Chem Int Ed Engl 2024; 63:e202311233. [PMID: 37856157 PMCID: PMC10952837 DOI: 10.1002/anie.202311233] [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: 08/03/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/20/2023]
Abstract
The viscosity and crowding of biological environment are considered vital for the correct cellular function, and alterations in these parameters are known to underly a number of pathologies including diabetes, malaria, cancer and neurodegenerative diseases, to name a few. Over the last decades, fluorescent molecular probes termed molecular rotors proved extremely useful for exploring viscosity, crowding, and underlying molecular interactions in biologically relevant settings. In this review, we will discuss the basic principles underpinning the functionality of these probes and will review advances in their use as sensors for lipid order, protein crowding and conformation, temperature and non-canonical nucleic acid structures in live cells and other relevant biological settings.
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Affiliation(s)
- Miguel Paez‐Perez
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
| | - Marina K. Kuimova
- Department of Chemistry, Imperial College London, MSRHImperial College LondonWood LaneLondonW12 0BZUK
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Johnson RE, Murray MT, Bycraft LJ, Myler P, Wetmore SD, Manderville RA. Harnessing a 4-Formyl-Aniline Handle to Tune the Stability of a DNA Aptamer-Protein Complex via Fluorescent Surrogates. Bioconjug Chem 2023; 34:2066-2076. [PMID: 37857354 DOI: 10.1021/acs.bioconjchem.3c00373] [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: 10/21/2023]
Abstract
Interactions between DNA aptamers and protein targets hold promise for the development of pharmaceuticals and diagnostics. As such, the utilization of fluorescent nucleobase surrogates in studying aptamer-protein interactions is a powerful tool due to their ability to provide site-specific information through turn-on fluorescence. Unfortunately, previously described turn-on probes serving as nucleobase replacements have only been strongly disruptive to the affinity of aptamer-protein interactions. Herein, we present a modified TBA15 aptamer for thrombin containing a fluorescent surrogate that provides site-specific turn-on emission with low nanomolar affinity. The modification, referred to as AnBtz, was substituted at position T3 and provided strong turn-on emission (Irel ≈ 4) and brightness (ε·Φ > 20 000 cm-1 M-1) with an apparent dissociation constant (Kd) of 15 nM to afford a limit of detection (LOD) of 10 nM for thrombin in 20% human serum. The probe was selected through a modular "on-strand" synthesis process that utilized a 4-formyl-aniline (4FA) handle. Using this platform, we were able to enhance the affinity of the final aptamer conjugate by ∼30-fold in comparison with the initial conjugate design. Molecular dynamics simulations provide insight into the structural basis for this phenomenon and highlight the importance of targeting hydrophobic protein binding sites with fluorescent nucleobase surrogates to create new contacts with protein targets.
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Affiliation(s)
- Ryan E Johnson
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Makay T Murray
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Lucas J Bycraft
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Peter Myler
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta T1K 3M4, Canada
| | - Richard A Manderville
- Departments of Chemistry & Toxicology, University of Guelph, Guelph, ON N1G 2W1, Canada
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Sawyer JM, Passow KT, Harki DA. Synthesis and photophysical characterization of fluorescent indole nucleoside analogues. RSC Adv 2023; 13:16369-16376. [PMID: 37266506 PMCID: PMC10230516 DOI: 10.1039/d3ra03457g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/03/2023] Open
Abstract
Fluorescent nucleosides are useful chemical tools for biochemical research and are frequently incorporated into nucleic acids for a variety of applications. The most widely utilized fluorescent nucleoside is 2-aminopurine-2'-deoxyribonucleoside (2APN). However, 2APN is limited by a moderate Stokes shift, molar extinction coefficient, and quantum yield. We recently reported 4-cyanoindole-2'-deoxyribonucleoside (4CIN), which offers superior photophysical characteristics in comparison to 2APN. To further improve upon 4CIN, a focused library of additional analogues combining the structural features of 2APN and 4CIN were synthesized and their photophysical properties were quantified. Nucleosides 2-6 were found to possess diverse photophysical properties with some features superior to 4CIN. In addition, the structure-function relationship data gained from 1-6 can inform the design of next-generation fluorescent indole nucleosides.
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Affiliation(s)
- Jacob M Sawyer
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
| | - Daniel A Harki
- Department of Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
- Department of Medicinal Chemistry, University of Minnesota Minneapolis Minnesota 55455 USA
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Yang C, Slavětínská LP, Fleuti M, Klepetářová B, Tichý M, Gurská S, Pavliš P, Džubák P, Hajdúch M, Hocek M. Synthesis of Polycyclic Hetero-Fused 7-Deazapurine Heterocycles and Nucleosides through C-H Dibenzothiophenation and Negishi Coupling. J Am Chem Soc 2022; 144:19437-19446. [PMID: 36245092 PMCID: PMC9619403 DOI: 10.1021/jacs.2c07517] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
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A new approach for synthesizing polycyclic heterofused
7-deazapurine
heterocycles and the corresponding nucleosides was developed based
on C–H functionalization of diverse (hetero)aromatics with
dibenzothiophene-S-oxide followed by the Negishi
cross-cooupling with bis(4,6-dichloropyrimidin-5-yl)zinc. This cross-coupling
afforded a series of (het)aryl-pyrimidines that were converted to
fused deazapurine heterocycles through azidation and thermal cyclization.
The fused heterocycles were glycosylated to the corresponding 2′-deoxy-
and ribonucleosides, and a series of derivatives were prepared by
nucleophilic substitutions at position 4. Four series of new polycyclic
thieno-fused 7-deazapurine nucleosides were synthesized using this
strategy. Most of the deoxyribonucleosides showed good cytotoxic activity,
especially for the CCRF-CEM cell line. Phenyl- and thienyl-substituted
thieno-fused 7-deazapurine nucleosides were fluorescent, and the former
one was converted to 2′-deoxyribonucleoside triphosphate for
enzymatic synthesis of labeled oligonucleotides.
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Affiliation(s)
- Chao Yang
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Marianne Fleuti
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Blanka Klepetářová
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Michal Tichý
- Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
| | - Soňa Gurská
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Pavliš
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Petr Džubák
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Marián Hajdúch
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry
& Czech Advanced Technology and Research Institute, Palacky University and University Hospital in Olomouc, Hněvotínská
5, CZ-77515 Olomouc, Czech Republic
| | - Michal Hocek
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic,Institute
of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic,E-mail:
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