1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Chawla M, Poater A, Oliva R, Cavallo L. Unveiling structural and energetic characterization of the emissive RNA alphabet anchored in the methylthieno[3,4- d]pyrimidine heterocycle core. Phys Chem Chem Phys 2024; 26:16358-16368. [PMID: 38805177 DOI: 10.1039/d3cp06136a] [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: 05/29/2024]
Abstract
This study presents a comprehensive theoretical exploration of the fluorescent non-natural emissive nucleobases- mthA, mthG, mthC, and mthU derived from the methylthieno[3,4-d]pyrimidine heterocycle. Our calculations, aligning with experimental findings, reveal that these non-natural bases exert minimal influence on the geometry of classical Watson-Crick base pairs within an RNA duplex, maintaining H-bonding akin to natural bases. In terms of energy, the impact of the modified bases, but for mthG, is also found to be little significant. We delved into an in-depth analysis of the photophysical properties of these non-natural bases. This investigation unveiled a correlation between their absorption/emission peaks and the substantial impact of the modification on the energy levels of the highest unoccupied molecular orbitals (HOMO) and the lowest unoccupied molecular orbital (LUMO). Notably, this alteration in energy levels resulted in a significant reduction of the HOMO-LUMO gap, from approximately 5.4-5.5 eV in the natural bases, to roughly 3.9-4.7 eV in the modified bases. This shift led to a consequential change in absorption and emission spectra towards longer wavelengths, elucidating their bathochromic shift.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
| | - Albert Poater
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, c/Ma Aurèlia Capmany 69, Girona 17003, Catalonia, Spain
| | - Romina Oliva
- Department of Sciences and Technologies, University Parthenope of Naples, Centro Direzionale Isola C4, Naples, I-80143, Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
| |
Collapse
|
3
|
Tor Y. Isomorphic Fluorescent Nucleosides. Acc Chem Res 2024; 57:1325-1335. [PMID: 38613490 PMCID: PMC11079976 DOI: 10.1021/acs.accounts.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/15/2024]
Abstract
In 1960, Weber prophesied that "There are many ways in which the properties of the excited state can be utilized to study points of ignorance of the structure and function of proteins". This has been realized, illustrating that an intrinsic and highly responsive fluorophore such as tryptophan can alter the course of an entire scientific discipline. But what about RNA and DNA? Adapting Weber's protein photophysics prophecy to nucleic acids requires the development of intrinsically emissive nucleoside surrogates as, unlike Trp, the canonical nucleobases display unusually low emission quantum yields, which render nucleosides, nucleotides, and oligonucleotides practically dark for most fluorescence-based applications.Over the past decades, we have developed emissive nucleoside surrogates that facilitate the monitoring of nucleoside-, nucleotide-, and nucleic acid-based transformations at a nucleobase resolution in real time. The premise underlying our approach is the identification of minimal atomic/structural perturbations that endow the synthetic analogs with favorable photophysical features while maintaining native conformations and pairing. As illuminating probes, the photophysical parameters of such isomorphic nucleosides display sensitivity to microenvironmental factors. Responsive isomorphic analogs that function similarly to their native counterparts in biochemical contexts are defined as isofunctional.Early analogs included pyrimidines substituted with five-membered aromatic heterocycles at their 5 position and have been used to assess the polarity of the major groove in duplexes. Polarized quinazolines have proven useful in assembling FRET pairs with established fluorophores and have been used to study RNA-protein and RNA-small-molecule binding. Completing a fluorescent ribonucleoside alphabet, composed of visibly emissive purine (thA, thG) and pyrimidine (thU, thC) analogs, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, was a major breakthrough. To further augment functionality, a second-generation emissive RNA alphabet based on an isothiazolo[4,3-d]pyrimidine core (thA, tzG, tzU, and tzC) was fabricated. This single-atom "mutagenesis" restored the basic/coordinating nitrogen corresponding to N7 in the purine skeleton and elevated biological recognition.The isomorphic emissive nucleosides and nucleotides, particularly the purine analogs, serve as substrates for diverse enzymes. Beyond polymerases, we have challenged the emissive analogs with metabolic and catabolic enzymes, opening optical windows into the biochemistry of nucleosides and nucleotides as metabolites as well as coenzymes and second messengers. Real-time fluorescence-based assays for adenosine deaminase, guanine deaminase, and cytidine deaminase have been fabricated and used for inhibitor discovery. Emissive cofactors (e.g., SthAM), coenzymes (e.g., NtzAD+), and second messengers (e.g., c-di-tzGMP) have been enzymatically synthesized, using xyNTPs and native enzymes. Both their biosynthesis and their transformations can be fluorescently monitored in real time.Highly isomorphic and isofunctional emissive surrogates can therefore be fabricated and judiciously implemented. Beyond their utility, side-by-side comparison to established analogs, particularly to 2-aminopurine, the workhorse of nucleic acid biophysics over 5 decades, has proven prudent as they refined the scope and limitations of both the new analogs and their predecessors. Challenges, however, remain. Associated with such small heterocycles are relatively short emission wavelengths and limited brightness. Recent advances in multiphoton spectroscopy and further structural modifications have shown promise for overcoming such barriers.
Collapse
Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
| |
Collapse
|
4
|
Khatik SY, Roy S, Srivatsan SG. Synthesis and Enzymatic Incorporation of a Dual-App Nucleotide Probe That Reports Antibiotics-Induced Conformational Change in the Bacterial Ribosomal Decoding Site RNA. ACS Chem Biol 2024; 19:687-695. [PMID: 38407057 DOI: 10.1021/acschembio.3c00676] [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: 02/27/2024]
Abstract
Natural nucleosides are nonfluorescent and do not have intrinsic labels that can be readily utilized for analyzing nucleic acid structure and recognition. In this regard, researchers typically use the so-called "one-label, one-technique" approach to study nucleic acids. However, we envisioned that a responsive dual-app nucleoside system that harnesses the power of two complementing biophysical techniques namely, fluorescence and 19F NMR, will allow the investigation of nucleic acid conformations more comprehensively than before. We recently introduced a nucleoside analogue by tagging trifluoromethyl-benzofuran at the C5 position of 2'-deoxyuridine, which serves as an excellent fluorescent and 19F NMR probe to study G-quadruplex and i-motif structures. Taking forward, here, we report the development of a ribonucleotide version of the dual-app probe to monitor antibiotics-induced conformational changes in RNA. The ribonucleotide analog is derived by conjugating trifluoromethyl-benzofuran at the C5 position of uridine (TFBF-UTP). The analog is efficiently incorporated by T7 RNA polymerase to produce functionalized RNA transcripts. Detailed photophysical and 19F NMR of the nucleoside and nucleotide incorporated into RNA oligonucleotides revealed that the analog is structurally minimally invasive and can be used for probing RNA conformations by fluorescence and 19F NMR techniques. Using the probe, we monitored and estimated aminoglycoside antibiotics binding to the bacterial ribosomal decoding site RNA (A-site, a very important RNA target). While 2-aminopurine, a famous fluorescent nucleic acid probe, fails to detect structurally similar aminoglycoside antibiotics binding to the A-site, our probe reports the binding of different aminoglycosides to the A-site. Taken together, our results demonstrate that TFBF-UTP is a very useful addition to the nucleic acid analysis toolbox and could be used to devise discovery platforms to identify new RNA binders of therapeutic potential.
Collapse
Affiliation(s)
- Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| |
Collapse
|
5
|
Le HN, Kuchlyan J, Baladi T, Albinsson B, Dahlén A, Wilhelmsson LM. Synthesis and photophysical characterization of a pH-sensitive quadracyclic uridine (qU) analogue. Chemistry 2024:e202303539. [PMID: 38230625 DOI: 10.1002/chem.202303539] [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] [Received: 10/26/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/18/2024]
Abstract
Fluorescent base analogues (FBAs) have become useful tools for applications in biophysical chemistry, chemical biology, live-cell imaging, and RNA therapeutics. Herein, two synthetic routes towards a novel FBA of uracil named qU (quadracyclic uracil/uridine) are described. The qU nucleobase bears a tetracyclic fused ring system and is designed to allow for specific Watson-Crick base pairing with adenine. We find that qU absorbs light in the visible region of the spectrum and emits brightly with a quantum yield of 27 % and a dual-band character in a wide pH range. With evidence, among other things, from fluorescence lifetime measurements we suggest that this dual emission feature results from an excited-state proton transfer (ESPT) process. Furthermore, we find that both absorption and emission of qU are highly sensitive to pH. The high brightness in combination with excitation in the visible and pH responsiveness makes qU an interesting native-like nucleic acid label in spectroscopy and microscopy applications in, for example, the field of mRNA and antisense oligonucleotide (ASO) therapeutics.
Collapse
Affiliation(s)
- Hoang-Ngoan Le
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Jagannath Kuchlyan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Tom Baladi
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - Bo Albinsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| | - Anders Dahlén
- Cell Gene and RNA Therapy, Discovery Science, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Kemivägen 10, SE-41296, Gothenburg, Sweden
| |
Collapse
|
6
|
Wojtczak BA, Bednarczyk M, Sikorski PJ, Wojtczak A, Surynt P, Kowalska J, Jemielity J. Synthesis and Evaluation of Diguanosine Cap Analogs Modified at the C8-Position by Suzuki-Miyaura Cross-Coupling: Discovery of 7-Methylguanosine-Based Molecular Rotors. J Org Chem 2023. [PMID: 37209102 DOI: 10.1021/acs.joc.3c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chemical modifications of the mRNA cap structure can enhance the stability, translational properties, and half-life of mRNAs, thereby altering the therapeutic properties of synthetic mRNA. However, cap structure modification is challenging because of the instability of the 5'-5'-triphosphate bridge and N7-methylguanosine. The Suzuki-Miyaura cross-coupling reaction between boronic acid and halogen compound is a mild, convenient, and potentially applicable approach for modifying biomolecules. Herein, we describe two methods to synthesize C8-modified cap structures using the Suzuki-Miyaura cross-coupling reaction. Both methods employed phosphorimidazolide chemistry to form the 5',5'-triphosphate bridge. However, in the first method, the introduction of the modification via the Suzuki-Miyaura cross-coupling reaction at the C8 position occurs postsynthetically, at the dinucleotide level, whereas in the second method, the modification was introduced at the level of the nucleoside 5'-monophosphate, and later, the triphosphate bridge was formed. Both methods were successfully applied to incorporate six different groups (methyl, cyclopropyl, phenyl, 4-dimethylaminophenyl, 4-cyanophenyl, and 1-pyrene) into either the m7G or G moieties of the cap structure. Aromatic substituents at the C8-position of guanosine form a push-pull system that exhibits environment-sensitive fluorescence. We demonstrated that this phenomenon can be harnessed to study the interaction with cap-binding proteins, e.g., eIF4E, DcpS, Nudt16, and snurportin.
Collapse
Affiliation(s)
- Blazej A Wojtczak
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Marcelina Bednarczyk
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Pawel J Sikorski
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| | - Anna Wojtczak
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Piotr Surynt
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Joanna Kowalska
- Faculty of Physics, University of Warsaw; L. Pasteura 5, 02-093, Warsaw, Poland
| | - Jacek Jemielity
- Centre of New Technologies, University of Warsaw; S. Banacha 2c, 02-097 Warsaw, Poland
| |
Collapse
|
7
|
Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
Collapse
Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| |
Collapse
|
8
|
Yang QL, Liu Y, Luo YR, Li ZH, Jia HW, Fu YB, Qu GR, Guo HM. Rhodium(III)-Catalyzed Synthesis of Diverse Fluorescent Polycyclic Purinium Salts from 6-Arylpurine Nucleosides and Alkynes. Org Lett 2022; 24:4234-4239. [PMID: 35658480 DOI: 10.1021/acs.orglett.2c01546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Described herein is an efficient strategy for assembling a new library of functionalized polycyclic purinium salts with a wide range of anions through RhIII-catalyzed C-H activation/annulation of 6-arylpurine nucleosides with alkynes under mild reaction conditions. The resulting products displayed tunable photoluminescence covering most of the visible spectrum. Mechanistic insights delineated the rhodium catalyst's mode of action. A purinoisoquinolinium-coordinated rhodium(I) sandwich complex was well characterized and identified as the key intermediate.
Collapse
Affiliation(s)
- Qi-Liang Yang
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Ying Liu
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Yi-Rui Luo
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Zhi-Hao Li
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Hong-Wei Jia
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Ya-Bo Fu
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Gui-Rong Qu
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| | - Hai-Ming Guo
- Henan Key Laboratory of Organic Functional Molecules and Drug Innovation, Collaborative Innovation Center of Henan Province for Green Manufacturing of Fine Chemicals, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
| |
Collapse
|
9
|
Zhou H, Li Y, Gan Y, Wang R. Total RNA Synthesis and its Covalent Labeling Innovation. Top Curr Chem (Cham) 2022; 380:16. [PMID: 35218412 DOI: 10.1007/s41061-022-00371-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/24/2022] [Indexed: 12/16/2022]
Abstract
RNA plays critical roles in a wide range of physiological processes. For example, it is well known that RNA plays an important role in regulating gene expression, cell proliferation, and differentiation, and many other chemical and biological processes. However, the research community still suffers from limited approaches that can be applied to readily visualize a specific RNA-of-interest (ROI). Several methods can be used to track RNAs; these rely mainly on biological properties, namely, hybridization, aptamer, reporter protein, and protein binding. With respect to covalent approaches, very few cases have been reported. Happily, several new methods for efficient labeling studies of ROIs have been demonstrated successfully in recent years. Additionally, methods employed for the detection of ROIs by RNA modifying enzymes have also proved feasible. Several approaches, namely, phosphoramidite chemistry, in vitro transcription reactions, co-transcription reactions, chemical post-modification, RNA modifying enzymes, ligation, and other methods targeted at RNA labeling have been revealed in the past decades. To illustrate the most recent achievements, this review aims to summarize the most recent research in the field of synthesis of RNAs-of-interest bearing a variety of unnatural nucleosides, the subsequent RNA labeling research via biocompatible ligation, and beyond.
Collapse
Affiliation(s)
- Hongling Zhou
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Li
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Youfang Gan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Rui Wang
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Hubei Key Laboratory of Natural Medicinal Chemistry and Resource Evaluation, Huazhong University of Science and Technology, Wuhan, 430030, China. .,Key Laboratory of Natural Product and Resource, Shanghai Institute of Organic Chemistry, Shanghai, 230030, China.
| |
Collapse
|
10
|
He X, Kuang S, Gao Q, Xie Y, Ming X. Bright fluorescent purine analogues as promising probes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:45-60. [PMID: 34806926 DOI: 10.1080/15257770.2021.2004418] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Modified bright fluorescent nucleosides that respond to the microenvironment have great potential as probes. A series of novel 8-(phenylethynyl)phenylated 2-amino-2'-deoxyadenosine and 2'-deoxyisoguanosine derivatives have been synthesized by Sonogashira-type coupling reaction and Suzuki reaction. The maximum emission of the new compounds is in the visible region, with strong solvatochromicity and pH-dependent fluorescent properties. Furthermore, some of them exhibit bright fluorescence emissions in various solvents (ε × Φ = 4000-39,000 cm-1 M-1). These consequences indicate that purine analogues could respond to the microenvironment and serve as promising fluorescent probes.Supplemental data for this article is available online at https://doi.org/10.1080/15257770.2021.2004418 .
Collapse
Affiliation(s)
- Xin He
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Shuang Kuang
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Qian Gao
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - YuXin Xie
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China
| | - Xin Ming
- School of Pharmacy, Chengdu Medical College, Chengdu, Sichuan, China.,Study on the Structure-Specific Small Molecular Drug in Sichuan Province College Key Laboratory, Chengdu Medical College, Chengdu, Sichuan, China
| |
Collapse
|
11
|
Xie Y, Fang Z, Yang W, He Z, Chen K, Heng P, Wang B, Zhou X. 6-Iodopurine as a Versatile Building Block for RNA Purine Architecture Modifications. Bioconjug Chem 2022; 33:353-362. [PMID: 35119264 DOI: 10.1021/acs.bioconjchem.1c00595] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Natural modified bases in RNA were found to be indispensable for basic biological processes. In addition, artificial RNA modifications have been a versatile toolbox for the study of RNA interference, structure, and dynamics. Here, we present a chemical method for the facile synthesis of RNA containing C6-modified purine. 6-Iodopurine, as a postsynthetic building block with high reactivity, was used for metal-free construction of C-N, C-O, and C-S bonds under mild conditions and C-C bond formation by Suzuki-Miyaura cross-coupling. Our strategy provides a convenient approach for the synthesis of various RNA modifications, especially for oligonucleotides containing specific structures.
Collapse
Affiliation(s)
- Yalun Xie
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhentian Fang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Wei Yang
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Zhiyong He
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Kun Chen
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Panpan Heng
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Baoshan Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiang Zhou
- Key Laboratory of Biomedical Polymers of Ministry of Education, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| |
Collapse
|
12
|
Walunj MB, Srivatsan SG. Heterocycle-modified 2'-Deoxyguanosine Nucleolipid Analogs Stabilize Guanosine Gels and Self-assemble to Form Green Fluorescent Gels. Chem Asian J 2021; 17:e202101163. [PMID: 34817121 DOI: 10.1002/asia.202101163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 11/22/2021] [Indexed: 11/08/2022]
Abstract
Nucleoside-lipid conjugates are very useful supramolecular building blocks to construct self-assembled architectures suited for biomedical and material applications. Such nucleoside derivatives can be further synthetically manipulated to endow additional functionalities that could augment the assembling process and impart interesting properties. Here, we report the design, synthesis and self-assembling process of multifunctional supramolecular nucleolipid synthons containing an environment-sensitive fluorescent guanine. The amphiphilic synthons are composed of an 8-(2-(benzofuran-2-yl)vinyl)-guanine core and alkyl chains attached to 3'-O and 5'-O-positions of 2'-deoxyguanosine. The 2-(benzofuran-2-yl)vinyl (BFV) moiety attached at the C8 position of the nucleobase adopted a syn conformation about the glycosidic bond, which facilitated the self-assembly process through the formation of a G-tetrad as the basic unit. While 3',5'-diacylated BFV-modified dG analog stabilized the guanosine hydrogel by hampering the crystallization process and imparted fluorescence, BFV-modified dGs containing longer alkyl chains formed a green fluorescent organogel, which transformed into a yellow fluorescent gel in the presence of a complementary non-fluorescent cytidine nucleolipid. The ability of the dG analog containing short alkyl chains to modulate the mechanical property of a gel, and interesting fluorescence properties and self-assembling behavior exhibited by the dG analogs containing long alkyl chains in response to heat and complementary base underscore the potential use of these new supramolecular synthons in material applications.
Collapse
Affiliation(s)
- Manisha B Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
13
|
Khan AM, Agnihotri NK, Singh VK, Mohapatra SC, Mathur D, Kumar M, Kumar R. Biocatalyst-mediated selective acylation and deacylation chemistry on the secondary hydroxyl/amine groups of nucleosides. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:1220-1236. [PMID: 34636267 DOI: 10.1080/15257770.2021.1986222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Nucleosides play a pivotal role in biological systems and therefore have attracted a lot of interest as chemotherapeutic agents in drug discovery. Over the years biocatalysts have emerged as a sustainable alternative to conventional synthetic catalysts. As a nature's catalyst, they exhibit excellent selectivity, remarkable tolerance, and help in carrying out eco-friendly benign processes. The use of a biocatalyst as a regio- and enantioselective catalyst is particularly relevant in the transformations of nucleosides and their analogs because of the presence of multiple chiral centres. Herein, we discuss the recent advances in the Pseudomonas Cepacia Lipase mediated selective acylation and deacylation reactions of the secondary hydroxyl and amino groups of nucleosides and their analogs.
Collapse
Affiliation(s)
- Amarendra Mohan Khan
- Department of Chemistry, Motilal Nehru College, University of Delhi, Delhi, India
| | | | - Vinay Kumar Singh
- Department of Chemistry, Sri Aurobindo College, University of Delhi, Delhi, India
| | | | - Divya Mathur
- Department of Chemistry, Daulat Ram College, University of Delhi, Delhi, India
| | - Manish Kumar
- Department of Chemistry, Motilal Nehru College, University of Delhi, Delhi, India
| | - Rajesh Kumar
- Department of Chemistry, R.D.S. College, B. R. A. Bihar University, Muzaffarpur, India
| |
Collapse
|
14
|
Depmeier H, Hoffmann E, Bornewasser L, Kath‐Schorr S. Strategies for Covalent Labeling of Long RNAs. Chembiochem 2021; 22:2826-2847. [PMID: 34043861 PMCID: PMC8518768 DOI: 10.1002/cbic.202100161] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/26/2021] [Indexed: 12/17/2022]
Abstract
The introduction of chemical modifications into long RNA molecules at specific positions for visualization, biophysical investigations, diagnostic and therapeutic applications still remains challenging. In this review, we present recent approaches for covalent internal labeling of long RNAs. Topics included are the assembly of large modified RNAs via enzymatic ligation of short synthetic oligonucleotides and synthetic biology approaches preparing site-specifically modified RNAs via in vitro transcription using an expanded genetic alphabet. Moreover, recent approaches to employ deoxyribozymes (DNAzymes) and ribozymes for RNA labeling and RNA methyltransferase based labeling strategies are presented. We discuss the potentials and limits of the individual methods, their applicability for RNAs with several hundred to thousands of nucleotides in length and indicate future directions in the field.
Collapse
Affiliation(s)
- Hannah Depmeier
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Eva Hoffmann
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | - Lisa Bornewasser
- University of CologneDepartment of ChemistryGreinstr. 450939CologneGermany
| | | |
Collapse
|
15
|
Parameswaran P, Ranjan N, Flora SJS. New Approaches in Sensing and Targeting Bacterial rRNA A-site. Med Chem 2021; 17:299-309. [PMID: 31660840 DOI: 10.2174/1573406415666191011160035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/06/2019] [Accepted: 09/11/2019] [Indexed: 11/22/2022]
Abstract
New chemical agents that could combat increasing antibiotic resistance are urgently needed. In this mini-review, an old but highly relevant RNA sequence which is crucial for the continuation of bacterial life-cycle is covered. Some of the most significant advances of the last decade in sensing and targeting the bacterial rRNA A-site: a well-validated binding site of proverbially known aminoglycoside antibiotics are described. Some of the major advances in direct sensing of the bacterial decoding side (A-site) are described and also new fluorescent molecules that are capable of detecting lead compounds through high-throughput assays by displacement of fluorescent probe molecules are highlighted. Lastly, some of the recently discovered non-aminoglycoside small molecule binders of bacterial rRNA A-site as a new class of molecules that could provide future scaffolds and molecules for developing new antibacterial agents have been discussed.
Collapse
Affiliation(s)
- Preethi Parameswaran
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)- Raebareli, New Transit Campus, Lucknow 226002, India
| | - Nihar Ranjan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER)- Raebareli, New Transit Campus, Lucknow 226002, India
| | - Swaran J S Flora
- Department of Pharmacology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, New Transit Campus, Lucknow 226002, India
| |
Collapse
|
16
|
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.
Collapse
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.
| |
Collapse
|
17
|
Baladi T, Nilsson JR, Gallud A, Celauro E, Gasse C, Levi-Acobas F, Sarac I, Hollenstein MR, Dahlén A, Esbjörner EK, Wilhelmsson LM. Stealth Fluorescence Labeling for Live Microscopy Imaging of mRNA Delivery. J Am Chem Soc 2021; 143:5413-5424. [PMID: 33797236 PMCID: PMC8154517 DOI: 10.1021/jacs.1c00014] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Methods for tracking
RNA inside living cells without perturbing
their natural interactions and functions are critical within biology
and, in particular, to facilitate studies of therapeutic RNA delivery.
We present a stealth labeling approach that can efficiently, and with
high fidelity, generate RNA transcripts, through enzymatic incorporation
of the triphosphate of tCO, a fluorescent tricyclic cytosine
analogue. We demonstrate this by incorporation of tCO in
up to 100% of the natural cytosine positions of a 1.2 kb mRNA encoding
for the histone H2B fused to GFP (H2B:GFP). Spectroscopic characterization
of this mRNA shows that the incorporation rate of tCO is
similar to cytosine, which allows for efficient labeling and controlled
tuning of labeling ratios for different applications. Using live cell
confocal microscopy and flow cytometry, we show that the tCO-labeled mRNA is efficiently translated into H2B:GFP inside human
cells. Hence, we not only develop the use of fluorescent base analogue
labeling of nucleic acids in live-cell microscopy but also, importantly,
show that the resulting transcript is translated into the correct
protein. Moreover, the spectral properties of our transcripts and
their translation product allow for their straightforward, simultaneous
visualization in live cells. Finally, we find that chemically transfected
tCO-labeled RNA, unlike a state-of-the-art fluorescently
labeled RNA, gives rise to expression of a similar amount of protein
as its natural counterpart, hence representing a methodology for studying
natural, unperturbed processing of mRNA used in RNA therapeutics and
in vaccines, like the ones developed against SARS-CoV-2.
Collapse
Affiliation(s)
- Tom Baladi
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden.,Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Audrey Gallud
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Emanuele Celauro
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - Cécile Gasse
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 91057 Evry, France
| | - Fabienne Levi-Acobas
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Ivo Sarac
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Marcel R Hollenstein
- Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, Institut Pasteur, 28, Rue du Docteur Roux, 75724 Paris CEDEX 15, France
| | - Anders Dahlén
- Medicinal Chemistry, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elin K Esbjörner
- Department of Biology and Biological Engineering, Chemical Biology, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden
| |
Collapse
|
18
|
Espinasse A, Lembke HK, Cao AA, Carlson EE. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. RSC Chem Biol 2020; 1:333-351. [PMID: 33928252 PMCID: PMC8081287 DOI: 10.1039/d0cb00078g] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Modified nucleoside triphosphates (NTPs) are invaluable tools to probe bacterial enzymatic mechanisms, develop novel genetic material, and engineer drugs and proteins with new functionalities. Although the impact of nucleobase alterations has predominantly been studied due to their importance for protein recognition, sugar and phosphate modifications have also been investigated. However, NTPs are cell impermeable due to their negatively charged phosphate tail, a major hurdle to achieving live bacterial studies. Herein, we review the recent advances made to investigate and evolve bacteria and their processes with the use of modified NTPs by exploring alterations in one of the three moieties: the nucleobase, the sugar and the phosphate tail. We also present the innovative methods that have been devised to internalize NTPs into bacteria for in vivo applications.
Collapse
Affiliation(s)
- Adeline Espinasse
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Hannah K. Lembke
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Angela A. Cao
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
| | - Erin E. Carlson
- Department of Chemistry, University of Minnesota207 Pleasant Street SEMinneapolisMinnesota 55455USA
- Department of Medicinal Chemistry, University of Minnesota208 Harvard Street SEMinneapolisMinnesota 55454USA
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota321 Church St SEMinneapolisMinnesota 55454USA
| |
Collapse
|
19
|
George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
Collapse
Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
| | | |
Collapse
|
20
|
Li J, Fang X, Ming X. Visibly Emitting Thiazolyl-Uridine Analogues as Promising Fluorescent Probes. J Org Chem 2020; 85:4602-4610. [DOI: 10.1021/acs.joc.9b03208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Jinsi Li
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, Sichuan 610500, P. R. China
| | - Xuerong Fang
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, Sichuan 610500, P. R. China
| | - Xin Ming
- Department of Pharmacy, Chengdu Medical College, No. 783 Xindu Avenue, Chengdu, Sichuan 610500, P. R. China
| |
Collapse
|
21
|
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).
Collapse
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
| |
Collapse
|
22
|
Flamme M, McKenzie LK, Sarac I, Hollenstein M. Chemical methods for the modification of RNA. Methods 2019; 161:64-82. [PMID: 30905751 DOI: 10.1016/j.ymeth.2019.03.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
RNA is often considered as being the vector for the transmission of genetic information from DNA to the protein synthesis machinery. However, besides translation RNA participates in a broad variety of fundamental biological roles such as gene expression and regulation, protein synthesis, and even catalysis of chemical reactions. This variety of function combined with intricate three-dimensional structures and the discovery of over 100 chemical modifications in natural RNAs require chemical methods for the modification of RNAs in order to investigate their mechanism, location, and exact biological roles. In addition, numerous RNA-based tools such as ribozymes, aptamers, or therapeutic oligonucleotides require the presence of additional chemical functionalities to strengthen the nucleosidic backbone against degradation or enhance the desired catalytic or binding properties. Herein, the two main methods for the chemical modification of RNA are presented: solid-phase synthesis using phosphoramidite precursors and the enzymatic polymerization of nucleoside triphosphates. The different synthetic and biochemical steps required for each method are carefully described and recent examples of practical applications based on these two methods are discussed.
Collapse
Affiliation(s)
- Marie Flamme
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France; Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Luke K McKenzie
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Ivo Sarac
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France.
| |
Collapse
|
23
|
Milisavljevič N, Perlíková P, Pohl R, Hocek M. Enzymatic synthesis of base-modified RNA by T7 RNA polymerase. A systematic study and comparison of 5-substituted pyrimidine and 7-substituted 7-deazapurine nucleoside triphosphates as substrates. Org Biomol Chem 2019; 16:5800-5807. [PMID: 30063056 DOI: 10.1039/c8ob01498a] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We synthesized a small library of eighteen 5-substituted pyrimidine or 7-substituted 7-deazapurine nucleoside triphosphates bearing methyl, ethynyl, phenyl, benzofuryl or dibenzofuryl groups through cross-coupling reactions of nucleosides followed by triphosphorylation or through direct cross-coupling reactions of halogenated nucleoside triphosphates. We systematically studied the influence of the modification on the efficiency of T7 RNA polymerase catalyzed synthesis of modified RNA and found that modified ATP, UTP and CTP analogues bearing smaller modifications were good substrates and building blocks for the RNA synthesis even in difficult sequences incorporating multiple modified nucleotides. Bulky dibenzofuryl derivatives of ATP and GTP were not substrates for the RNA polymerase. In the case of modified GTP analogues, a modified procedure using a special promoter and GMP as initiator needed to be used to obtain efficient RNA synthesis. The T7 RNA polymerase synthesis of modified RNA can be very efficiently used for synthesis of modified RNA but the method has constraints in the sequence of the first three nucleotides of the transcript, which must contain a non-modified G in the +1 position.
Collapse
Affiliation(s)
- Nemanja Milisavljevič
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic.
| | | | | | | |
Collapse
|
24
|
Wen Z, Tuttle PR, Howlader AH, Vasilyeva A, Gonzalez L, Tangar A, Lei R, Laverde EE, Liu Y, Miksovska J, Wnuk SF. Fluorescent 5-Pyrimidine and 8-Purine Nucleosides Modified with an N-Unsubstituted 1,2,3-Triazol-4-yl Moiety. J Org Chem 2019; 84:3624-3631. [PMID: 30806513 DOI: 10.1021/acs.joc.8b03135] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Cu(I)- or Ag(I)-catalyzed cycloaddition between 8-ethynyladenine or guanine nucleosides and TMSN3 gave 8-(1- H-1,2,3-triazol-4-yl) nucleosides in good yields. On the other hand, reactions of 5-ethynyluracil or cytosine nucleosides with TMSN3 led to the chemoselective formation of triazoles via Cu(I)-catalyzed cycloaddition or vinyl azides via Ag(I)-catalyzed hydroazidation. These nucleosides with a minimalistic triazolyl modification showed excellent fluorescent properties with 8-(1- H-1,2,3-triazol-4-yl)-2'-deoxyadenosine (8-TrzdA), exhibiting a quantum yield of 44%. The 8-TrzdA 5'-triphosphate was incorporated into duplex DNA containing a one-nucleotide gap by DNA polymerase β.
Collapse
Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Paloma R Tuttle
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - A Hasan Howlader
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Anna Vasilyeva
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Laura Gonzalez
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Antonija Tangar
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Ruipeng Lei
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Eduardo E Laverde
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Yuan Liu
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Jaroslava Miksovska
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| | - Stanislaw F Wnuk
- Department of Chemistry and Biochemistry , Florida International University , Miami , Florida 33199 , United States
| |
Collapse
|
25
|
Radhakrishnan K, Das S, Kundu LM. Synthesis of Size‐Expanded Nucleobase Analogues for Artificial Base‐Pairing Using a Ligand‐Free, Microwave‐Assisted Copper(I)‐Catalyzed Reaction. ChemistrySelect 2018. [DOI: 10.1002/slct.201802455] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- K Radhakrishnan
- Department of ChemistryIndian Institute of Technology Guwahati 781039 Assam India
| | - Soumi Das
- Department of ChemistryIndian Institute of Technology Guwahati 781039 Assam India
| | - Lal Mohan Kundu
- Department of ChemistryIndian Institute of Technology Guwahati 781039 Assam India
| |
Collapse
|
26
|
Seio K, Kanamori T, Masaki Y. Synthesis of Fluorescent Nucleic Acids bearing Nucleobases Modified with Heteroaryl Group and Fluorophores. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Kohji Seio
- Department of Life Science and Technology, Tokyo Institute of Technology
| | | | | |
Collapse
|
27
|
Walunj MB, Tanpure AA, Srivatsan SG. Post-transcriptional labeling by using Suzuki-Miyaura cross-coupling generates functional RNA probes. Nucleic Acids Res 2018; 46:e65. [PMID: 29546376 PMCID: PMC6009664 DOI: 10.1093/nar/gky185] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 02/12/2018] [Accepted: 03/01/2018] [Indexed: 12/21/2022] Open
Abstract
Pd-catalyzed C-C bond formation, an important vertebra in the spine of synthetic chemistry, is emerging as a valuable chemoselective transformation for post-synthetic functionalization of biomacromolecules. While methods are available for labeling protein and DNA, development of an analogous procedure to label RNA by cross-coupling reactions remains a major challenge. Herein, we describe a new Pd-mediated RNA oligonucleotide (ON) labeling method that involves post-transcriptional functionalization of iodouridine-labeled RNA transcripts by using Suzuki-Miyaura cross-coupling reaction. 5-Iodouridine triphosphate (IUTP) is efficiently incorporated into RNA ONs at one or more sites by T7 RNA polymerase. Further, using a catalytic system made of Pd(OAc)2 and 2-aminopyrimidine-4,6-diol (ADHP) or dimethylamino-substituted ADHP (DMADHP), we established a modular method to functionalize iodouridine-labeled RNA ONs in the presence of various boronic acid and ester substrates under very mild conditions (37°C and pH 8.5). This method is highly chemoselective, and offers direct access to RNA ONs labeled with commonly used fluorescent and affinity tags and new fluorogenic environment-sensitive nucleoside probes in a ligand-controlled stereoselective fashion. Taken together, this simple approach of generating functional RNA ON probes by Suzuki-Miyaura coupling will be a very important addition to the resources and tools available for analyzing RNA motifs.
Collapse
Affiliation(s)
- Manisha B Walunj
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| |
Collapse
|
28
|
Seio K, Kanamori T, Masaki Y. Solvent- and environment-dependent fluorescence of modified nucleobases. Tetrahedron Lett 2018. [DOI: 10.1016/j.tetlet.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
29
|
Suzol S, Howlader AH, Wen Z, Ren Y, Laverde EE, Garcia C, Liu Y, Wnuk SF. Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA. ACS OMEGA 2018; 3:4276-4288. [PMID: 29732453 PMCID: PMC5928487 DOI: 10.1021/acsomega.8b00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 05/28/2023]
Abstract
Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(β-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary β-sulfonylvinylamines gave 5-(β-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5'-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions.
Collapse
Affiliation(s)
- Sazzad
H. Suzol
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - A. Hasan Howlader
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Zhiwei Wen
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yaou Ren
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Eduardo E. Laverde
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Carol Garcia
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yuan Liu
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Stanislaw F. Wnuk
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
30
|
Patel B, Zunk DM, Grant DG, Rudrawar S. Solid‐Phase Microwave‐Assisted Ligand‐Free Suzuki‐Miyaura Cross‐Coupling of 5‐Iodouridine. ChemistrySelect 2018. [DOI: 10.1002/slct.201703111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Bhautikkumar Patel
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Dr Matthew Zunk
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Dr Gary Grant
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
| | - Santosh Rudrawar
- Menzies Health Institute Queensland Griffith University Gold Coast QLD 4222 Australia
- School of Pharmacy and Pharmacology Griffith University Gold Coast QLD 4222 Australia
- Quality Use of Medicines Network Griffith University Gold Coast QLD 4222 Australia
- School of Chemistry The University of Sydney Sydney NSW 2006 Australia
| |
Collapse
|
31
|
Hopkins PA, McCoy LS, Tor Y. Enzymatic incorporation and utilization of an emissive 6-azauridine. Org Biomol Chem 2018; 15:684-690. [PMID: 27981333 DOI: 10.1039/c6ob02080a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To display favorable fluorescent properties, the non-emissive native nucleosides need to be modified. Here we present a motif that relies on conjugating 5-membered aromatic heterocycles (e.g., thiophene) to a 6-azapyrimidine (1,2,4-triazine) core. Synthetic accessibility and desirable photophysical properties make these nucleosides attractive candidates for enzymatic incorporation and biochemical assays. While 6-azauridine triphosphate is known to be poorly tolerated by polymerases in RNA synthesis, we illustrate that conjugating a thiophene ring at position 5 overcomes such limitations, facilitating its T7 RNA polymerase-mediated in vitro transcription incorporation into RNA constructs. We further show that the modified transcripts can be ligated to longer oligonucleotides to form singly modified RNAs, as illustrated for an A-site hairpin model RNA construct, which was employed to visualize aminoglycoside antibiotics binding.
Collapse
Affiliation(s)
- Patrycja A Hopkins
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Lisa S McCoy
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
| |
Collapse
|
32
|
Chawla M, Autiero I, Oliva R, Cavallo L. Energetics and dynamics of the non-natural fluorescent 4AP:DAP base pair. Phys Chem Chem Phys 2018; 20:3699-3709. [DOI: 10.1039/c7cp07400j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Quantum mechanics and molecular dynamics methods are used to compare the non-natural 4AP–DAP base pair to natural base pairs.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Ida Autiero
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| | - Romina Oliva
- Department of Sciences and Technologies
- University Parthenope of Naples
- Centro Direzionale Isola C4
- Naples
- Italy
| | - Luigi Cavallo
- King Abdullah University of Science and Technology (KAUST)
- Physical Sciences and Engineering Division
- Thuwal 23955-6900
- Saudi Arabia
| |
Collapse
|
33
|
Synthesis of two 6-aza-uridines modified by benzoheterocycle as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.05.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
34
|
Rajapaksha SM, Mlsna TE, Pittman CU. A Regioselective Synthesis of 6-Alkyl- and 6-Aryluracils by Cs 2CO 3- or K 3PO 4-Promoted Dimerization of 3-Alkyl- and 3-Aryl-2-Propynamides. J Org Chem 2017; 82:5678-5688. [PMID: 28488857 DOI: 10.1021/acs.joc.7b00508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A regioselective synthesis of 6-alkyl- and 6-aryluracils was developed by the dimerization of 3-alkyl- and 3-aryl-2-propynamides promoted by either Cs2CO3 or K3PO4. A range of 3-aryl-2-propynamides, with both electron-deficient and electron-rich 3-aryl substituents, were successfully reacted in high yields. Cs+ acts as a soft Lewis acid to polarize the carbon-carbon triple bond, and solid K3PO4 interacts with carbonyl oxygen, promoting intermolecular nucleophilic attack by the only weakly nucleophilic amide nitrogen. Experiments were conducted to support the proposed mechanism.
Collapse
Affiliation(s)
- Suranga M Rajapaksha
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Todd E Mlsna
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| | - Charles U Pittman
- Department of Chemistry, Mississippi State University , Mississippi State, Mississippi 39762, United States
| |
Collapse
|
35
|
George JT, Srivatsan SG. Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA. Bioconjug Chem 2017; 28:1529-1536. [PMID: 28406614 DOI: 10.1021/acs.bioconjchem.7b00169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.
Collapse
Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|
36
|
Wen Z, Suzol SH, Peng J, Liang Y, Snoeck R, Andrei G, Liekens S, Wnuk SF. Antiviral and Cytostatic Evaluation of 5-(1-Halo-2-sulfonylvinyl)- and 5-(2-Furyl)uracil Nucleosides. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201700023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Sazzad H. Suzol
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Jufang Peng
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Yong Liang
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Robert Snoeck
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| |
Collapse
|
37
|
Custer TC, Walter NG. In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines. Protein Sci 2017; 26:1363-1379. [PMID: 28028853 PMCID: PMC5477532 DOI: 10.1002/pro.3108] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 12/20/2022]
Abstract
RNA plays a fundamental, ubiquitous role as either substrate or functional component of many large cellular complexes-"molecular machines"-used to maintain and control the readout of genetic information, a functional landscape that we are only beginning to understand. The cellular mechanisms for the spatiotemporal organization of the plethora of RNAs involved in gene expression are particularly poorly understood. Intracellular single-molecule fluorescence microscopy provides a powerful emerging tool for probing the pertinent mechanistic parameters that govern cellular RNA functions, including those of protein coding messenger RNAs (mRNAs). Progress has been hampered, however, by the scarcity of efficient high-yield methods to fluorescently label RNA molecules without the need to drastically increase their molecular weight through artificial appendages that may result in altered behavior. Herein, we employ T7 RNA polymerase to body label an RNA with a cyanine dye, as well as yeast poly(A) polymerase to strategically place multiple 2'-azido-modifications for subsequent fluorophore labeling either between the body and tail or randomly throughout the tail. Using a combination of biochemical and single-molecule fluorescence microscopy approaches, we demonstrate that both yeast poly(A) polymerase labeling strategies result in fully functional mRNA, whereas protein coding is severely diminished in the case of body labeling.
Collapse
Affiliation(s)
- Thomas C Custer
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, 48109.,Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109
| |
Collapse
|
38
|
Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017; 56:2640-2644. [PMID: 28156044 PMCID: PMC5397316 DOI: 10.1002/anie.201611700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/17/2017] [Indexed: 12/22/2022]
Abstract
Comprehensive understanding of the structure–function relationship of RNA both in real time and at atomic level will have a profound impact in advancing our understanding of RNA functions in biology. Here, we describe the first example of a multifunctional nucleoside probe, containing a conformation‐sensitive fluorophore and an anomalous X‐ray diffraction label (5‐selenophene uracil), which enables the correlation of RNA conformation and recognition under equilibrium and in 3D. The probe incorporated into the bacterial ribosomal RNA decoding site, fluorescently reports antibiotic binding and provides diffraction information in determining the structure without distorting native RNA fold. Further, by comparing solution binding data and crystal structure, we gained insight on how the probe senses ligand‐induced conformational change in RNA. Taken together, our nucleoside probe represents a new class of biophysical tool that would complement available tools for functional RNA investigations.
Collapse
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Mark A Boerneke
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry, Center for Drug Discovery Innovation, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| |
Collapse
|
39
|
Nuthanakanti A, Boerneke MA, Hermann T, Srivatsan SG. Structure of the Ribosomal RNA Decoding Site Containing a Selenium-Modified Responsive Fluorescent Ribonucleoside Probe. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201611700] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| | - Mark A. Boerneke
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Thomas Hermann
- Department of Chemistry and Biochemistry; Center for Drug Discovery Innovation; University of California, San Diego; 9500 Gilman Drive La Jolla CA 92093 USA
| | - Seergazhi G. Srivatsan
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune 411008 India
| |
Collapse
|
40
|
Li Y, Fin A, McCoy L, Tor Y. Polymerase-Mediated Site-Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2017; 56:1303-1307. [PMID: 28000329 PMCID: PMC5241218 DOI: 10.1002/anie.201609327] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 11/10/2016] [Indexed: 12/22/2022]
Abstract
An enzyme-mediated approach for the assembly of singly modified RNA constructs in which specific G residues are replaced with th G, an emissive isomorphic G surrogate, is reported. Transcription in the presence of th G and native nucleoside triphosphates enforces initiation with the unnatural analogue, yielding 5'-end modified transcripts that can be mono-phosphorylated and ligated to provide longer site-specifically modified RNA constructs. The scope of this unprecedented enzymatic approach to non-canonical purine-containing RNAs is explored via the assembly of several altered hammerhead (HH) ribozymes and a singly modified HH substrate. By strategically modifying key positions, a mechanistic insight into the ribozyme-mediated cleavage is gained. Additionally, the emissive features of the modified nucleoside and its responsiveness to environmental changes can be used to monitor cleavage in real time by steady state fluorescence spectroscopy.
Collapse
Affiliation(s)
- Yao Li
- 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
| | - Lisa McCoy
- 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
| |
Collapse
|
41
|
Li Y, Fin A, McCoy L, Tor Y. Polymerase‐Mediated Site‐Specific Incorporation of a Synthetic Fluorescent Isomorphic G Surrogate into RNA. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609327] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Yao Li
- 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
| | - Lisa McCoy
- 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
| |
Collapse
|
42
|
Zhang XH, Xu YZ. NMR studies on 4-thio-5-furan-modified and 4-thio-5-thiophene-modified nucleosides. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2016; 54:887-892. [PMID: 27529164 DOI: 10.1002/mrc.4501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/03/2016] [Accepted: 08/12/2016] [Indexed: 06/06/2023]
Abstract
Systematic NMR characterization of 4-thio-5-furan-pyrimidine nucleosides or 4-thio-5-thiophene-pyrimidine nucleosides (ribonucleosides and 2'-deoxynucleosides) was performed. All proton and carbon signals of 4-thio-5-thiophene-ribouridine and related analogues were unambiguously assigned. The orientations of the base (4-thiouridine or its deoxy analogue) relative to the ring (furan or thiophene) are explored by a NMR approach and further supported by X-ray crystallographic studies. The procedures presented here would be applicable to other modified nucleosides and nucleotides. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Xiao-Hui Zhang
- College of Environment and Chemical Engineering, Dalian University, Dalian, 116622, China.
| | - Yao-Zhong Xu
- Department of Life, Health and Chemical Sciences, Open University, Walton Hall, Milton Keynes, MK7 6AA, UK.
| |
Collapse
|
43
|
Chawla M, Poater A, Oliva R, Cavallo L. Structural and energetic characterization of the emissive RNA alphabet based on the isothiazolo[4,3-d]pyrimidine heterocycle core. Phys Chem Chem Phys 2016; 18:18045-53. [PMID: 27328414 DOI: 10.1039/c6cp03268k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We present theoretical characterization of fluorescent non-natural nucleobases, (tz)A, (tz)G, (tz)C, and (tz)U, derived from the isothiazolo[4,3-d]pyrimidine heterocycle. Consistent with the experimental evidence, our calculations show that the non-natural bases have minimal impact on the geometry and stability of the classical Watson-Crick base pairs, allowing them to accurately mimic natural bases in a RNA duplex, in terms of H-bonding. In contrast, our calculations indicate that H-bonded base pairs involving the Hoogsteen edge are destabilized relative to their natural counterparts. Analysis of the photophysical properties of the non-natural bases allowed us to correlate their absorption/emission peaks to the strong impact of the modification on the energy of the lowest unoccupied molecular orbital, LUMO, which is stabilized by roughly 1.0-1.2 eV relative to the natural analogues, while the highest occupied molecular orbital, HOMO, is not substantially affected. As a result, the HOMO-LUMO gap is reduced from 5.3-5.5 eV in the natural bases to 4.0-4.4 eV in the modified ones, with a consequent bathochromic shift in the absorption and emission spectra.
Collapse
Affiliation(s)
- Mohit Chawla
- King Abdullah University of Science and Technology (KAUST), Physical Sciences and Engineering Division, KAUST Catalysis Center, Thuwal 23955-6900, Saudi Arabia.
| | | | | | | |
Collapse
|
44
|
Wang M, Zhang Y, Yue X, Yao S, Bondar MV, Belfield KD. A Deoxyuridine-Based Far-Red Emitting Viscosity Sensor. Molecules 2016; 21:molecules21060709. [PMID: 27248991 PMCID: PMC6273067 DOI: 10.3390/molecules21060709] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/20/2016] [Accepted: 05/24/2016] [Indexed: 12/03/2022] Open
Abstract
A novel deoxyuridine (dU) benzothiazolium (BZ) derivative, referred to as dU-BZ, is reported that was synthesized via Sonogashira coupling reaction methodology. The deoxyuridine building block was introduced to enhance hydrophilicity, while an alkynylated benzothiazolium dye was incorporated for long wavelength absorption to reduce potential phototoxicity that is characteristic of using UV light to excite common fluorphores, better discriminate from native autofluorescence, and potentially facilitate deep tissue imaging. An impressive 30-fold enhancement of fluorescence intensity of dU-BZ was achieved upon increasing viscosity. Fluorescence quantum yields in 99% glycerol/1% methanol (v/v) solution as a function of temperature (293–343 K), together with viscosity-dependent fluorescence lifetimes and radiative and non-radiative rate constants in glycerol/methanol solutions (ranging from 4.8 to 950 cP) were determined. Both fluorescence quantum yields and lifetimes increased with increased viscosity, consistent with results predicted by theory. This suggests that the newly-designed compound, dU-BZ, is capable of functioning as a probe of local microviscosity, an aspect examined by in vitro bioimaging experiments.
Collapse
Affiliation(s)
- Mengyuan Wang
- Department of Chemistry, University of Central Florida, P.O. Box 162366, Orlando, FL 32816, USA.
| | - Yuanwei Zhang
- Department of Chemistry, University of Central Florida, P.O. Box 162366, Orlando, FL 32816, USA.
| | - Xiling Yue
- Department of Chemistry, University of Central Florida, P.O. Box 162366, Orlando, FL 32816, USA.
| | - Sheng Yao
- Department of Chemistry, University of Central Florida, P.O. Box 162366, Orlando, FL 32816, USA.
| | - Mykhailo V Bondar
- Institute of Physics, National Academy of Sciences of Ukraine, Prospect Nauki, 46, Kiev-28 03028, Ukraine.
| | - Kevin D Belfield
- School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
- College of Science and Liberal Arts, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA.
| |
Collapse
|
45
|
Sawant AA, Mukherjee PP, Jangid RK, Galande S, Srivatsan SG. A clickable UTP analog for the posttranscriptional chemical labeling and imaging of RNA. Org Biomol Chem 2016; 14:5832-42. [PMID: 27173127 DOI: 10.1039/c6ob00576d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of robust tools and practical RNA labeling strategies that would facilitate the biophysical analysis of RNA in both cell-free and cellular systems will have profound implications in the discovery of new RNA diagnostic tools and therapeutic strategies. In this context, we describe the development of a new alkyne-modified UTP analog, 5-(1,7-octadinyl)uridine triphosphate (ODUTP), which serves as an efficient substrate for the introduction of a clickable alkyne label into RNA transcripts by bacteriophage T7 RNA polymerase and mammalian cellular RNA polymerases. The ODU-labeled RNA is effectively used by reverse transcriptase to produce cDNA, a property which could be utilized in expanding the chemical space of a RNA library in the aptamer selection scheme. Further, the alkyne label on RNA provides a convenient tool for the posttranscriptional chemical functionalization with a variety of biophysical tags (fluorescent, affinity, amino acid and sugar) by using alkyne-azide cycloaddition reaction. Importantly, the ability of endogenous RNA polymerases to specifically incorporate ODUTP into cellular RNA transcripts enabled the visualization of newly transcribing RNA in cells by microscopy using click reactions. In addition to a clickable alkyne group, ODU contains a Raman scattering label (internal disubstituted alkyne), which exhibits characteristic Raman shifts that fall in the Raman-silent region of cells. Our results indicate that an ODU label could potentially facilitate two-channel visualization of RNA in cells by using click chemistry and Raman spectroscopy. Taken together, ODU represents a multipurpose ribonucleoside tool, which is expected to provide new avenues to study RNA in cell-free and cellular systems.
Collapse
Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India.
| | | | | | | | | |
Collapse
|
46
|
Pany SPP, Bommisetti P, Diveshkumar KV, Pradeepkumar PI. Benzothiazole hydrazones of furylbenzamides preferentially stabilize c-MYC and c-KIT1 promoter G-quadruplex DNAs. Org Biomol Chem 2016; 14:5779-93. [DOI: 10.1039/c6ob00138f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The stabilization of G-quadruplex DNA structures by using small molecule ligands having simple structural scaffolds has the potential to be harnessed for developing next generation anticancer agents.
Collapse
Affiliation(s)
| | - Praneeth Bommisetti
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - K. V. Diveshkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| | - P. I. Pradeepkumar
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
| |
Collapse
|
47
|
Ren H, An H, Hatala PJ, Stevens WC, Tao J, He B. Versatile synthesis and biological evaluation of novel 3'-fluorinated purine nucleosides. Beilstein J Org Chem 2015; 11:2509-20. [PMID: 26734098 PMCID: PMC4685831 DOI: 10.3762/bjoc.11.272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 11/26/2015] [Indexed: 01/03/2023] Open
Abstract
A unified synthetic strategy accessing novel 3'-fluorinated purine nucleoside derivatives and their biological evaluation were achieved. Novel 3'-fluorinated analogues were constructed from a common 3'-deoxy-3'-fluororibofuranose intermediate. Employing Suzuki and Stille cross-coupling reactions, fifteen 3'-fluororibose purine nucleosides 1-15 and eight 3'-fluororibose 2-chloro/2-aminopurine nucleosides 16-23 with various substituents at position 6 of the purine ring were efficiently synthesized. Furthermore, 3'-fluorine analogs of natural products nebularine and 6-methylpurine riboside were constructed via our convergent synthetic strategy. Synthesized nucleosides were tested against HT116 (colon cancer) and 143B (osteosarcoma cancer) tumor cell lines. We have demonstrated 3'-fluorine purine nucleoside analogues display potent tumor cell growth inhibition activity at sub- or low micromolar concentration.
Collapse
Affiliation(s)
- Hang Ren
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
- Granlen, Inc., 7864 Paseo Tulipero, Carlsbad, CA 92009, USA
| | - Haoyun An
- Granlen, Inc., 7864 Paseo Tulipero, Carlsbad, CA 92009, USA
| | - Paul J Hatala
- Granlen, Inc., 7864 Paseo Tulipero, Carlsbad, CA 92009, USA
| | | | - Jingchao Tao
- College of Chemistry and Molecular Engineering, Zhengzhou University, 100 Science Avenue, Zhengzhou 450001, China
| | - Baicheng He
- Molecular Oncology Laboratory, The University of Chicago Medical Center, Chicago, Illinois 60637, USA
| |
Collapse
|
48
|
Holstein JM, Rentmeister A. Current covalent modification methods for detecting RNA in fixed and living cells. Methods 2015; 98:18-25. [PMID: 26615954 DOI: 10.1016/j.ymeth.2015.11.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/20/2015] [Accepted: 11/22/2015] [Indexed: 12/13/2022] Open
Abstract
Labeling RNAs is of particular interest for elucidating localization, transport, and regulation of specific transcripts, ideally in living cells. Numerous methods have been developed ranging from hybridizing probes to genetically encoded reporters and chemo-enzymatic approaches. This review focuses on covalent labeling approaches that rely on the introduction of a small reactive group into the nascent or completed transcript followed by bioorthogonal click chemistry. State of the approaches for labeling RNA in fixed and living cells will be presented and emerging strategies with great potential for application in the complex cellular environment will be discussed.
Collapse
Affiliation(s)
- Josephin M Holstein
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster, Institute of Biochemistry, 48149 Muenster, Germany; Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM), University of Muenster, 48149 Muenster, Germany.
| |
Collapse
|
49
|
Kore AR, Yang B, Thiyagarajan SS, Srinivasan B. Synthesis and Substrate Evaluation of (E)-5-[(3-Selenophene-2-Carboxamido)Prop-1-en-1-yl]-Uridine-5'-O-Triphosphate for RNA Polymerase. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:866-76. [PMID: 26430834 DOI: 10.1080/15257770.2015.1081941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Design, synthesis and T7 RNA polymerase substrate evaluation of (E)-5-[(3-selenophene-2-carboxamido)prop-1-en-1-yl]-uridine-5'-O-triphosphate is reported. The title compound is shown to be a good substrate for RNA polymerase by RNA labeling through in vitro transcription. pTRI-plasmid DNA with β-actin gene sequence (∼300 base pairs) with T7 promoter was used as a template for the in vitro transcription. Transcribed product is characterized for incorporation by gel assay and for integrity, full length and size by bioanalyzer. The title compound will be very useful in biophysical techniques to obtain information on dynamics and recognition properties in real time as well as 3D structure of nucleic acids.
Collapse
Affiliation(s)
- Anilkumar R Kore
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
| | - Bo Yang
- a Life Sciences Solutions Group, Thermo Fisher Scientific , Austin , TX , USA
| | | | | |
Collapse
|
50
|
Sawant AA, Tanpure AA, Mukherjee PP, Athavale S, Kelkar A, Galande S, Srivatsan SG. A versatile toolbox for posttranscriptional chemical labeling and imaging of RNA. Nucleic Acids Res 2015; 44:e16. [PMID: 26384420 PMCID: PMC4737177 DOI: 10.1093/nar/gkv903] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 08/31/2015] [Indexed: 12/21/2022] Open
Abstract
Cellular RNA labeling strategies based on bioorthogonal chemical reactions are much less developed in comparison to glycan, protein and DNA due to its inherent instability and lack of effective methods to introduce bioorthogonal reactive functionalities (e.g. azide) into RNA. Here we report the development of a simple and modular posttranscriptional chemical labeling and imaging technique for RNA by using a novel toolbox comprised of azide-modified UTP analogs. These analogs facilitate the enzymatic incorporation of azide groups into RNA, which can be posttranscriptionally labeled with a variety of probes by click and Staudinger reactions. Importantly, we show for the first time the specific incorporation of azide groups into cellular RNA by endogenous RNA polymerases, which enabled the imaging of newly transcribing RNA in fixed and in live cells by click reactions. This labeling method is practical and provides a new platform to study RNA in vitro and in cells.
Collapse
Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Progya P Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Soumitra Athavale
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Ashwin Kelkar
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Sanjeev Galande
- Center of Excellence in Epigenetics, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India National Centre for Cell Science, Ganeshkhind, Pune 411007, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| |
Collapse
|