1
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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.
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Affiliation(s)
- Yitzhak Tor
- Department of Chemistry and
Biochemistry, University of California,
San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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2
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Břehová P, Řezníčková E, Škach K, Jorda R, Dejmek M, Vojáčková V, Šála M, Kovalová M, Dračínský M, Dolníková A, Strmeň T, Kinnertová M, Chalupský K, Dvořáková A, Gucký T, Mertlíková Kaiserová H, Klener P, Nencka R, Kryštof V. Inhibition of FLT3-ITD Kinase in Acute Myeloid Leukemia by New Imidazo[1,2- b]pyridazine Derivatives Identified by Scaffold Hopping. J Med Chem 2023; 66:11133-11157. [PMID: 37535845 PMCID: PMC10461230 DOI: 10.1021/acs.jmedchem.3c00575] [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: 03/31/2023] [Indexed: 08/05/2023]
Abstract
FLT3 kinase is a potential drug target in acute myeloid leukemia (AML). Patients with FLT3 mutations typically have higher relapse rates and worse outcomes than patients without FLT3 mutations. In this study, we investigated the suitability of various heterocycles as central cores of FLT3 inhibitors, including thieno[3,2-d]pyrimidine, pyrazolo[1,5-a]pyrimidine, imidazo[4,5-b]pyridine, pyrido[4,3-d]pyrimidine, and imidazo[1,2-b]pyridazine. Our assays revealed a series of imidazo[1,2-b]pyridazines with high potency against FLT3. Compound 34f showed nanomolar inhibitory activity against recombinant FLT3-ITD and FLT3-D835Y (IC50 values 4 and 1 nM, respectively) as well as in the FLT3-ITD-positive AML cell lines MV4-11, MOLM-13, and MOLM-13 expressing the FLT3-ITD-D835Y mutant (GI50 values of 7, 9, and 4 nM, respectively). In contrast, FLT3-independent cell lines were much less sensitive. In vitro experiments confirmed suppression of FLT3 downstream signaling pathways. Finally, the treatment of MV4-11 xenograft-bearing mice with 34f at doses of 5 and 10 mg/kg markedly blocked tumor growth without any adverse effects.
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Affiliation(s)
- Petra Břehová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Eva Řezníčková
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Kryštof Škach
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Radek Jorda
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Milan Dejmek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Veronika Vojáčková
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Michal Šála
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Markéta Kovalová
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Martin Dračínský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Alexandra Dolníková
- Institute
of Pathological Physiology, First Faculty of Medicine, Charles University, 12108 Prague, Czech Republic
| | - Timotej Strmeň
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Monika Kinnertová
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Karel Chalupský
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Alexandra Dvořáková
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Tomáš Gucký
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
| | - Helena Mertlíková Kaiserová
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Pavel Klener
- Institute
of Pathological Physiology, First Faculty of Medicine, Charles University, 12108 Prague, Czech Republic
| | - Radim Nencka
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 16000 Prague, Czech Republic
| | - Vladimír Kryštof
- Department
of Experimental Biology, Faculty of Science, Palacký University Olomouc, Šlechtitelů 27, 78371 Olomouc, Czech
Republic
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University Olomouc, Hněvotínská 5, 77900 Olomouc, Czech Republic
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3
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Papis M, Loro C, Penso M, Broggini G, Foschi F. Synthesis of Morpholino Nucleosides Starting From Enantiopure Glycidol. Org Chem Front 2022. [DOI: 10.1039/d2qo00400c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A protocol for the synthesis of modified morpholino monomers was performed in few steps through the condensation between 6-hydroxymethyl-morpholine acetal and nucleobases under Lewis acid conditions. The key common precursor...
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4
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Dziuba D, Didier P, Ciaco S, Barth A, Seidel CAM, Mély Y. Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues. Chem Soc Rev 2021; 50:7062-7107. [PMID: 33956014 DOI: 10.1039/d1cs00194a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.
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Affiliation(s)
- Dmytro Dziuba
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Pascal Didier
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
| | - Stefano Ciaco
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France. and Department of Biotechnology, Chemistry and Pharmacy, University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Anders Barth
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Claus A M Seidel
- Institut für Physikalische Chemie, Lehrstuhl für Molekulare Physikalische Chemie, Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Yves Mély
- Laboratoire de Bioimagerie et Pathologies, UMR 7021, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch, France.
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5
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Abdel Hamid AM, Hamed EO. Synthesis and fluorescent properties of some Furan‐tagged Thieno[2,3‐
d
]pyrimidines and Thieno[2,3‐
d
:4,5‐
d
']dipyrimidines. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Atef M. Abdel Hamid
- Department of Chemistry, Faculty of Science Zagazig University Zagazig Egypt
| | - Eman O. Hamed
- Department of Chemistry, Faculty of Science Zagazig University Zagazig Egypt
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6
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Saito Y, Hudson RH. Base-modified fluorescent purine nucleosides and nucleotides for use in oligonucleotide probes. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2018. [DOI: 10.1016/j.jphotochemrev.2018.07.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Design of a fused triazolyl 2-quinolinone unnatural nucleoside via tandem CuAAC-Ullmann coupling reaction and study of photophysical property. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.03.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Abstract
The response of nucleobases to UV radiation depends on structure in subtle ways, as revealed by gas-phase experiments.
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Affiliation(s)
- Samuel Boldissar
- Department of Chemistry and Biochemistry University of California Santa Barbara
- USA
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9
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Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 211] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
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10
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Zhou J, Zheng Y, Roembke BT, Robinson S, Opoku-Temeng C, Sayre DA, Sintim HO. Fluorescent analogs of cyclic and linear dinucleotides as phosphodiesterase and oligoribonuclease activity probes. RSC Adv 2017. [DOI: 10.1039/c6ra25394f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2-Aminopurine or etheno adenosine cyclic dinucleotide probes can report the activity of cyclic dinucleotide PDEs or oligoribonucleases.
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Affiliation(s)
- Jie Zhou
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
| | - Yue Zheng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - Benjamin T. Roembke
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Sarah M. Robinson
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Clement Opoku-Temeng
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry and Biochemistry
| | - David A. Sayre
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Herman O. Sintim
- Purdue Institute for Drug Discovery
- Purdue University
- West Lafayette
- USA
- Department of Chemistry
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11
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El-Sayed R, Shaldom A, Mazrouee LA. Synthesis and Evaluation of Polyfunctionally Substituted Heterocyclic Compounds Derived from 2-Cyano-N-(5-pentadecyl-1,3,4-thiadiazol-2-yl)acetamide. SYNTHETIC COMMUN 2015. [DOI: 10.1080/00397911.2014.984852] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Refat El-Sayed
- Chemistry Department, College of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Chemistry Department, Faculty of Science, Benha University, Benha, Egypt
| | - Amani Shaldom
- Chemistry Department, College of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Layla Al Mazrouee
- Chemistry Department, College of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
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12
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Park S, Otomo H, Zheng L, Sugiyama H. Highly emissive deoxyguanosine analogue capable of direct visualization of B-Z transition. Chem Commun (Camb) 2014; 50:1573-5. [PMID: 24382561 DOI: 10.1039/c3cc48297a] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A 2-aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside, (th)dG, was synthesized and incorporated readily into oligonucleotides as a versatile fluorescent guanine analogue. We demonstrate that (th)dG enables the visual detection of Z-DNA successfully based on different π-stacking of B- and Z-DNA.
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Affiliation(s)
- Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
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13
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Temburnikar KW, Zimmermann SC, Kim NT, Ross CR, Gelbmann C, Salomon CE, Wilson GM, Balzarini J, Seley-Radtke KL. Antiproliferative activities of halogenated thieno[3,2-d]pyrimidines. Bioorg Med Chem 2014; 22:2113-22. [PMID: 24631358 PMCID: PMC4565497 DOI: 10.1016/j.bmc.2014.02.033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/10/2014] [Accepted: 02/18/2014] [Indexed: 12/17/2022]
Abstract
The in vitro evaluation of thieno[3,2-d]pyrimidines identified halogenated compounds 1 and 2 with antiproliferative activity against three different cancer cell lines. A structure activity relationship study indicated the necessity of the chlorine at the C4-position for biological activity. The two most active compounds 1 and 2 were found to induce apoptosis in the leukemia L1210 cell line. Additionally, the compounds were screened against a variety of other microbial targets and as a result, selective activity against several fungi was also observed. The synthesis and preliminary biological results are reported herein.
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Affiliation(s)
- Kartik W Temburnikar
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Sarah C Zimmermann
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Nathaniel T Kim
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Christina R Ross
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Christopher Gelbmann
- Center for Drug Design, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Christine E Salomon
- Center for Drug Design, University of Minnesota, 516 Delaware St. SE, Minneapolis, MN 55455, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene Street, Baltimore, MD 21201, USA
| | - Jan Balzarini
- Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
| | - Katherine L Seley-Radtke
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA.
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14
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Pesnot T, Tedaldi LM, Jambrina PG, Rosta E, Wagner GK. Exploring the role of the 5-substituent for the intrinsic fluorescence of 5-aryl and 5-heteroaryl uracil nucleotides: a systematic study. Org Biomol Chem 2014; 11:6357-71. [PMID: 23945704 DOI: 10.1039/c3ob40485d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Derivatives of UMP (uridine monophosphate) with a fluorogenic substituent in position 5 represent a small but unique class of fluorophores, which has found important applications in chemical biology and biomolecular chemistry. In this study, we have synthesised a series of derivatives of the uracil nucleotides UMP, UDP and UTP with different aromatic and heteroaromatic substituents in position 5, in order to systematically investigate the influence of the 5-substituent on fluorescence emission. We have determined relevant photophysical parameters for all derivatives in this series, including quantum yields for the best fluorophores. The strongest fluorescence emission was observed with a 5-formylthien-2-yl substituent in position 5 of the uracil base, while the corresponding 3-formylthien-2-yl-substituted regioisomer was significantly less fluorescent. The 5-(5-formylthien-2-yl) uracil fluorophore was studied further in solvents of different polarity and proticity. In conjunction with results from a conformational analysis based on NMR data and computational experiments, these findings provide insights into the steric and electronic factors that govern fluorescence emission in this class of fluorophores. In particular, they highlight the interplay between fluorescence emission and conformation in this series. Finally, we carried out ligand-binding experiments with the 5-(5-formylthien-2-yl) uracil fluorophore and a UDP-sugar-dependent glycosyltransferase, demonstrating its utility for biological applications. The results from our photophysical and biological studies suggest, for the first time, a structural explanation for the fluorescence quenching effect that is observed upon binding of these fluorophores to a target protein.
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Affiliation(s)
- Thomas Pesnot
- School of Pharmacy, University of East Anglia, Norwich, UK
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15
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Otomo H, Park S, Yamamoto S, Sugiyama H. Amplification of fluorescent DNA through enzymatic incorporation of a highly emissive deoxyguanosine analogue. RSC Adv 2014. [DOI: 10.1039/c4ra05678g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A highly emissive thio-analogue of deoxyguanosine triphosphate was synthesized and enzymatically incorporated into DNA. The straightforward amplification of fluorescent DNA by natural polymerases was demonstrated.
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Affiliation(s)
- Haruka Otomo
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
| | - Soyoung Park
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
| | - Seigi Yamamoto
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS)
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16
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Sinkeldam RW, McCoy LS, Shin D, Tor Y. Enzymatic interconversion of isomorphic fluorescent nucleosides: adenosine deaminase transforms an adenosine analogue into an inosine analogue. Angew Chem Int Ed Engl 2013; 52:14026-30. [PMID: 24288262 PMCID: PMC3947497 DOI: 10.1002/anie.201307064] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 10/06/2013] [Indexed: 12/24/2022]
Abstract
Adenosine deaminase, a major enzyme involved in purine metabolism, converts an isomorphic fluorescent analogue of adenosine (thA) to an isomorphic inosine analogue (thI), which possesses distinct spectral features, allowing one to monitor the enzyme-catalyzed reaction and its inhibition in real time. The utility of this sensitive fluorescently-monitored transformation for the high throughput detection and analysis of ADA inhibitors is demonstrated.
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Affiliation(s)
| | | | | | - Yitzhak Tor
- Chemistry and Biochemistry University of California, San Diego 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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17
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Sinkeldam RW, McCoy LS, Shin D, Tor Y. Enzymatic Interconversion of Isomorphic Fluorescent Nucleosides: Adenosine Deaminase Transforms an Adenosine Analogue into an Inosine Analogue. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307064] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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18
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Mata G, Luedtke NW. Stereoselective N-Glycosylation of 2-Deoxythioribosides for Fluorescent Nucleoside Synthesis. J Org Chem 2012; 77:9006-17. [DOI: 10.1021/jo3014929] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Guillaume Mata
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland
| | - Nathan W. Luedtke
- Institute of Organic Chemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich,
Switzerland
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19
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Heffron TP, Salphati L, Alicke B, Cheong J, Dotson J, Edgar K, Goldsmith R, Gould SE, Lee LB, Lesnick JD, Lewis C, Ndubaku C, Nonomiya J, Olivero AG, Pang J, Plise EG, Sideris S, Trapp S, Wallin J, Wang L, Zhang X. The Design and Identification of Brain Penetrant Inhibitors of Phosphoinositide 3-Kinase α. J Med Chem 2012; 55:8007-20. [DOI: 10.1021/jm300867c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Timothy P. Heffron
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Laurent Salphati
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Bruno Alicke
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Jonathan Cheong
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Jennafer Dotson
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Kyle Edgar
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Richard Goldsmith
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Stephen E. Gould
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Leslie B. Lee
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - John D. Lesnick
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Cristina Lewis
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Chudi Ndubaku
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Jim Nonomiya
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Alan G. Olivero
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Jodie Pang
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Emile G. Plise
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Steve Sideris
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Sean Trapp
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Jeffrey Wallin
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Lan Wang
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
| | - Xiaolin Zhang
- Genentech, Inc., 1 DNA Way, South San Francisco,
California 94080, United States
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20
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Sinkeldam RW, Hopkins PA, Tor Y. Modified 6-aza uridines: highly emissive pH-sensitive fluorescent nucleosides. Chemphyschem 2012; 13:3350-6. [PMID: 22777983 DOI: 10.1002/cphc.201200375] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 06/19/2012] [Indexed: 12/12/2022]
Abstract
Optimized facile syntheses and highly desirable spectroscopic properties of two isomorphic fluorescent pyrimidines, comprising a 1,2,4-triazine motif conjugated to a thiophene (1 a) or a furan (1 b), are described. Although structurally related to their 5-modified uridine counterparts, these modified 6-aza-uridines reveal dramatically improved fluorescence properties and a remarkable sensitivity to polarity and pH changes. The thiophene derivative 1 a has an absorption maximum around 335 nm, which upon excitation yields visible emission with a polarity-sensitive maximum and fluorescence quantum yield ranging from 415 nm (Φ=0.8) to 455 nm (Φ=0.2) in dioxane and water, respectively. Nucleoside 1 a also displays susceptibility to acidity. Correlating emission intensity and solution pH yields a pK(a) value of 6.7-6.9, reasonably close to physiological pH values. The results illustrate that highly sought-after fluorescence features (brightness and responsiveness) are not necessarily the trait of large fluorophores alone, but can be observed with probes that meet stringent isomorphic design criteria.
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Affiliation(s)
- Renatus W Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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21
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Abstract
A fluorescent ribonucleoside alphabet consisting of highly emissive purine ((th)A, (th)G) and pyrimidine ((th)U, (th)C) analogues, all derived from thieno[3,4-d]pyrimidine as the heterocyclic nucleus, is described. Structural and biophysical analyses demonstrated that the emissive analogues are faithful isomorphic nucleoside surrogates. Photophysical analysis established that the nucleosides offer highly desirable qualities, including visible emission, high quantum yield, and responsiveness to environmental perturbations, traits entirely lacking in their native counterparts.
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Affiliation(s)
- Dongwon Shin
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, United States
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22
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Novel synthesis and antitumor evaluation of polyfunctionally substituted heterocyclic compounds derived from 2-cyano-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-acetamide. Molecules 2010; 16:52-73. [PMID: 21187817 PMCID: PMC6259152 DOI: 10.3390/molecules16010052] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 12/20/2010] [Accepted: 12/22/2010] [Indexed: 11/26/2022] Open
Abstract
The reaction of 2-amino-3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophene with ethyl cyanoacetate gave 2-cyano-N-(3-cyano-4,5,6,7-tetrahydrobenzo[b]thiophen-2-yl)-acetamide. The latter was used to synthesize different heterocyclic derivatives comprising thiophene, thiazole, pyrazole, pyridine, pyrimidine, and coumarin rings. The mechanistic and synthetic pathways depended on regioselective attack and/or cyclization by the cyanoacetamido moiety in the key precursor on various chemical reagents. The competition of the reaction pathways including dipolar cyclization, dinucleophilic-bielectrophilic attack, β-attack, Gewald-type attack, and condensation reactions led to the diversity of the synthesized products. The antitumor activities of the synthesized products were studied and evaluated. Most of the compounds revealed high inhibitory effects when screened in vitro for their antiproliferative activity. Three human cancer cell lines, namely, breast adenocarcinoma (MCF-7), non-small cell lung cancer (NCI-H460) and CNS cancer (SF-268) were used in the screening tests. The simplicity of the synthetic procedures which mainly involved one-pot reactions under mild reaction conditions, the convenience of yield production and the diversity of the reactive sites in the produced systems play a valuable role for further heterocyclic transformations and further biological investigations.
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23
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Greco NJ, Sinkeldam RW, Tor Y. An emissive C analog distinguishes between G, 8-oxoG, and T. Org Lett 2010; 11:1115-8. [PMID: 19196162 DOI: 10.1021/ol802656n] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A minimally disruptive fluorescent dC analog provides a rapid and non-destructive method for in vitro detection of G, 8-oxoG, and T, the downstream transverse mutation product.
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Affiliation(s)
- Nicholas J Greco
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0358, USA
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24
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Abstract
The use of fluorescent nucleic acid base analogues is becoming increasingly important in the fields of biology, biochemistry and biophysical chemistry as well as in the field of DNA nanotechnology. The advantage of being able to incorporate a fluorescent probe molecule close to the site of examination in the nucleic acid-containing system of interest with merely a minimal perturbation to the natural structure makes fluorescent base analogues highly attractive. In recent years, there has been a growing interest in developing novel candidates in this group of fluorophores for utilization in various investigations. This review describes the different classes of fluorophores that can be used for studying nucleic acid-containing systems, with an emphasis on choosing the right kind of probe for the system under investigation. It describes the characteristics of the large group of base analogues that has an emission that is sensitive to the surrounding microenvironment and gives examples of investigations in which this group of molecules has been used so far. Furthermore, the characterization and use of fluorescent base analogues that are virtually insensitive to changes in their microenvironment are described in detail. This group of base analogues can be used in several fluorescence investigations of nucleic acids, especially in fluorescence anisotropy and fluorescence resonance energy transfer (FRET) measurements. Finally, the development and characterization of the first nucleic base analogue FRET pair, tC(O)-tC(nitro), and its possible future uses are discussed.
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25
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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26
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Abstract
The enzymatic incorporation of a series of emissive pyrimidine analogues into RNA oligonucleotides is explored. T7 RNA polymerase is challenged with accepting three non-natural, yet related, triphosphates as substrates and incorporating them into diverse RNA transcripts. The three ribonucleoside triphosphates differ only in the modification of their uracil nucleus and include a thieno[3,2-d]pyrimidine nucleoside, a thieno[3,4-d]pyrimidine derivative, and a uridine containing a thiophene ring conjugated at its 5-position. All thiophene-containing uridine triphosphates (UTPs) get incorporated into RNA oligonucleotides at positions that are remote to the promoter, although the yields of the transcripts vary compared with the transcript obtained with only native triphosphates. Among the three derivatives, the 5-modified UTP is found to be the most "polymerase-friendly" and is well accommodated by T7 RNA polymerase. Although the fused thiophene analogues cannot be incorporated next to the promoter region, the 5-modified non-natural UTP gets incorporated near the promoter (albeit in relatively low yields) and even in multiple copies. Labeling experiments shed light on the mediocre incorporation of the fused analogues, suggesting the enzyme frequently pauses at the incorporation position. When incorporation does take place, the enzyme fails to elongate the modified oligonucleotide and yields aborted transcripts. Taken together, these results highlight the versatility and robustness, as well as the scope and limitation, of T7 RNA polymerase in accepting and incorporating reporter nucleotides into modified RNA transcripts.
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Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
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27
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Abstract
RNA molecules play essential roles in biological processes and are evolving as important targets for therapeutic intervention. Small molecules that specifically bind unique RNA sites and prevent the formation of functional RNA folds or RNA-protein complexes can modulate cell functions and can become of therapeutic potential. To explore such recognition events and to fabricate discovery assays, effective biophysical tools need to be advanced. When carefully designed, new fluorescent nucleosides can serve an unparalleled role in such studies. Our criteria for "ideal" fluorescent nucleoside analogs include: (a) high structural similarity to the native nucleobases to faithfully mimic their size and shape, as well as hybridization and recognition properties; (b) red-shifted absorption bands; (c) red-shifted emission band (preferably in the visible); (d) a reasonable emission quantum efficiency; and, importantly, (e) sensitivity of their photophysical parameters to changes in the microenvironment. Our program, aimed at the development of new emissive isomorphic nucleoside analogs, has yielded several useful nucleobases. Selected analogs were implemented in fluorescence-based assays. This overview presents the motivation for this work by introducing RNA-ligand interactions and discusses the design and synthesis of fluorescent isosteric nucleobase analogs and their utilization for the fabrication of "real-time" fluorescence-based biophysical assays.
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28
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Butler RS, Cohn P, Tenzel P, Abboud KA, Castellano RK. Synthesis, Photophysical Behavior, and Electronic Structure of Push−Pull Purines. J Am Chem Soc 2008; 131:623-33. [DOI: 10.1021/ja806348z] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Roslyn S. Butler
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Pamela Cohn
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Phillip Tenzel
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Khalil A. Abboud
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
| | - Ronald K. Castellano
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200
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29
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Zhao Y, Knee JL, Baranger AM. Characterization of two adenosine analogs as fluorescence probes in RNA. Bioorg Chem 2008; 36:271-7. [PMID: 18707751 PMCID: PMC2661016 DOI: 10.1016/j.bioorg.2008.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Revised: 06/10/2008] [Accepted: 06/12/2008] [Indexed: 11/22/2022]
Abstract
The fluorescence properties of two adenosine analogs, 2-(3-phenylpropyl)adenosine [A-3CPh] and 2-(4-phenylbutyl)adenosine [A-4CPh], are reported. As monomers, the quantum yields and the mean lifetimes are 0.011 and 6.22 ns for A-3CPh and 0.007 and 7.13 ns for A-4CPh, respectively. Surprisingly, the quantum yields of the two probes are enhanced 11- to 82-fold upon incorporation into RNA, while the mean lifetimes decrease 23-40%. The data suggest that a subpopulation of molecules is responsible for the fluorescence characteristics and that the distribution of emitting and non-emitting structures is altered upon incorporation of the probes into RNA. Thus, although both adenosine analogs have low quantum yields as monomers, their fluorescence signals are significantly enhanced in RNA. Thermodenaturation experiments and CD spectroscopy indicate that incorporation of the adenosine analogs into three different RNAs does not alter their global structure or stability. Therefore, these probes should be useful for probing events occurring close to the site of modification.
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Affiliation(s)
- Ying Zhao
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
| | - Joseph L. Knee
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
| | - Anne M. Baranger
- Department of Chemistry, Wesleyan University, Middletown, CT 06459
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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30
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Srivatsan SG, Weizman H, Tor Y. A highly fluorescent nucleoside analog based on thieno[3,4-d]pyrimidine senses mismatched pairing. Org Biomol Chem 2008; 6:1334-8. [PMID: 18385838 PMCID: PMC5263222 DOI: 10.1039/b801054d] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A highly emissive nucleobase analog, based on a thieno[3,4-d]pyrimidine core, is enzymatically incorporated into RNA oilgonucleotides that function as base discriminating fluorescent probes.
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Affiliation(s)
- Seergazhi G Srivatsan
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA
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31
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Venkatesan N, Seo YJ, Kim BH. Quencher-free molecular beacons: a new strategy in fluorescence based nucleic acid analysis. Chem Soc Rev 2008; 37:648-63. [PMID: 18362974 DOI: 10.1039/b705468h] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Molecular beacons (MBs) have been used as viable fluorescent probes in nucleic acid analysis. Many researchers around the world continue to modify the MBs to suit their needs. As a result, a number of nucleic acid probing systems with close resemblance to the MBs are being reported from time to time. Quencher-free molecular beacons (QF-MBs) are a significant modification of the conventional MB; in QF-MBs the quencher part has been eliminated. Despite the absence of the quencher, the QF-MBs can identify specific target DNA. They can also be used in SNP typing and in real-time PCR analysis for quantification of DNAs. The design, factors behind functioning and applications of different types of QF-MBs and closely related quencher-free nucleic acid probing systems (QF-NAPs) have been described in this tutorial review.
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Affiliation(s)
- Natarajan Venkatesan
- Laboratory for Modified Nucleic Acid Systems, Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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