1
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Abstract
A new fluorescent ribonucleoside alphabet (mth N) consisting of pyrimidine and purine analogues, all derived from methylthieno[3,4-d]pyrimidine as the heterocyclic core, is described. Large bathochromic shifts and high microenvironmental susceptibility of their emission relative to previous alphabets derived from thieno[3,4-d]pyrimidine (th N) and isothiazole[4,3-d]pyrimidine (tz N) scaffolds are observed. Subjecting the purine analogues to adenosine deaminase, guanine deaminase and T7 RNA polymerase indicate that, while varying, all but one enzyme tolerate the corresponding mth N/mth NTP substrates. The robust emission quantum yields, high photophysical responsiveness and enzymatic accommodation suggest that the mth N alphabet is a biophysically viable tool and can be used to probe the tolerance of nucleoside/tide-processing enzymes to structural perturbations of their substrates.
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Affiliation(s)
- Paul T Ludford
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Shenghua Yang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Marcela S Bucardo
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0358, USA
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2
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Determination of two-photon absorption in nucleobase analogues: a QR-DFT perspective. Photochem Photobiol Sci 2022; 21:529-543. [PMID: 35179700 DOI: 10.1007/s43630-022-00182-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/27/2022] [Indexed: 10/19/2022]
Abstract
With the prevalence of fluorescence spectroscopy in biological systems, and the benefits of two-photon absorption techniques, presented here is an assessment of the two-photon accessibility of modern fluorescent nucleobase analogues utilising quadratic response DFT. Due to the complex environment experienced by these nucleobases, the two-photon spectra of each analogue has been assessed in the presence of both [Formula: see text]-stacked and hydrogen-bonding interactions involving the canonical nucleobases. Findings suggest that the [Formula: see text]-stacking environment provides a more significant effect on the spectra of the analogues studies than a hydrogen-bonding environment; analogue structures presenting high two-photon cross-section values for one or more states coincide with polycyclic extensions to preserved canonical base structure, as observed in the qA family of analogues, while analogue structures more closely resembling the structure of the base in question present a much more muted spectra in comparison. Results from this investigation have also allowed for the derivation of a number of design rules for the development of potential, two-photon specific, analogues for future use in both imaging and potential photochemical activation.
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3
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Kishimoto Y, Fujii A, Nakagawa O, Obika S. Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative. Org Biomol Chem 2021; 19:8063-8074. [PMID: 34494641 DOI: 10.1039/d1ob01462e] [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: 11/21/2022]
Abstract
We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).
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Affiliation(s)
- Yuki Kishimoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Akane Fujii
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Osamu Nakagawa
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, 180 Nishihamahoji, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Sciences and Technology Agency (JST), 7 Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
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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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Wee WA, Yum JH, Hirashima S, Sugiyama H, Park S. Synthesis and application of a 19F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs. RSC Chem Biol 2021; 2:876-882. [PMID: 34458815 PMCID: PMC8382138 DOI: 10.1039/d1cb00020a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 03/04/2021] [Indexed: 11/21/2022] Open
Abstract
Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (FPdC) that displays an unprecedented quantum yield and highly sensitive 19F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19F NMR spectroscopic DNA analysis. FPdC and FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19F chemical shift in response to i-motif formation. The utility of FPdC was exemplified through reversible fluorescence switching of an FPdC-containing i-motif oligonucleotide in the presence of Ag(i) and cysteine.
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Affiliation(s)
- Wen Ann Wee
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Ji Hye Yum
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Shingo Hirashima
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University Yoshida-ushinomiyacho, Sakyo-ku Kyoto 606-8501 Japan
| | - Soyoung Park
- Department of Chemistry, Graduate School of Science, Kyoto University Kitashirakawa-oiwakecho, Sakyo-ku Kyoto 606-8502 Japan
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6
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Füchtbauer AF, Wranne MS, Sarangamath S, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Lighting Up DNA with the Environment-Sensitive Bright Adenine Analogue qAN4. Chempluschem 2021; 85:319-326. [PMID: 32045137 DOI: 10.1002/cplu.201900712] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 01/24/2020] [Indexed: 12/20/2022]
Abstract
The fluorescent adenine analogue qAN4 was recently shown to possess promising photophysical properties, including a high brightness as a monomer. Here we report the synthesis of the phosphoramidite of qAN4 and its successful incorporation into DNA oligonucleotides using standard solid-phase synthesis. Circular dichroism and thermal melting studies indicate that the qAN4-modification has a stabilizing effect on the B-form of DNA. Moreover, qAN4 base-pairs selectively with thymine with mismatch penalties similar to those of mismatches of adenine. The low energy absorption band of qAN4 inside DNA has its peak around 358 nm and the emission in duplex DNA is partly quenched and blue-shifted (ca. 410 nm), compared to the monomeric form. The spectral properties of the fluorophore also show sensitivity to pH; a property that may find biological applications. Quantum yields in single-stranded DNA range from 1-29 % and in duplex DNA from 1-7 %. In combination with the absorptive properties, this gives an average brightness inside duplex DNA of 275 M-1 cm-1 , more than five times higher than the most used environment-sensitive fluorescent base analogue, 2-aminopurine. Finally, we show that qAN4 can be used to advantage as a donor for interbase FRET applications in combination with adenine analogue qAnitro as an acceptor.
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Affiliation(s)
- Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden.,Cardiovascular Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom.,Chemistry Branch Department of Science and Mathematics Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, United Kingdom
| | - Henrik Gradén
- Cardiovascular Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, SE-431 83, Mölndal, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96, Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96, Gothenburg, Sweden
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7
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Wypijewska Del Nogal A, Füchtbauer AF, Bood M, Nilsson JR, Wranne MS, Sarangamath S, Pfeiffer P, Rajan VS, El-Sagheer AH, Dahlén A, Brown T, Grøtli M, Wilhelmsson LM. Getting DNA and RNA out of the dark with 2CNqA: a bright adenine analogue and interbase FRET donor. Nucleic Acids Res 2020; 48:7640-7652. [PMID: 32558908 PMCID: PMC7641321 DOI: 10.1093/nar/gkaa525] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/15/2020] [Accepted: 06/09/2020] [Indexed: 12/16/2022] Open
Abstract
With the central role of nucleic acids there is a need for development of fluorophores that facilitate the visualization of processes involving nucleic acids without perturbing their natural properties and behaviour. Here, we incorporate a new analogue of adenine, 2CNqA, into both DNA and RNA, and evaluate its nucleobase-mimicking and internal fluorophore capacities. We find that 2CNqA displays excellent photophysical properties in both nucleic acids, is highly specific for thymine/uracil, and maintains and slightly stabilises the canonical conformations of DNA and RNA duplexes. Moreover, the 2CNqA fluorophore has a quantum yield in single-stranded and duplex DNA ranging from 10% to 44% and 22% to 32%, respectively, and a slightly lower one (average 12%) inside duplex RNA. In combination with a comparatively strong molar absorptivity for this class of compounds, the resulting brightness of 2CNqA inside double-stranded DNA is the highest reported for a fluorescent base analogue. The high, relatively sequence-independent quantum yield in duplexes makes 2CNqA promising as a nucleic acid label and as an interbase Förster resonance energy transfer (FRET) donor. Finally, we report its excellent spectral overlap with the interbase FRET acceptors qAnitro and tCnitro, and demonstrate that these FRET pairs enable conformation studies of DNA and RNA.
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Affiliation(s)
- Anna Wypijewska Del Nogal
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden.,Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden.,Medicinal Chemistry, Research and EarlyDevelopment, Cardiovascular, Renal and Metabolism (CVRM), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| | - Jesper R Nilsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Pauline Pfeiffer
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Vinoth Sundar Rajan
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Anders Dahlén
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Pepparedsleden 1, Mölndal, SE-431 83, Sweden
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg SE-412 96, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
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8
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Flexibility and Preorganization of Fluorescent Nucleobase-Pyrene Conjugates Control DNA and RNA Recognition. Molecules 2020; 25:molecules25092188. [PMID: 32392853 PMCID: PMC7248712 DOI: 10.3390/molecules25092188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/23/2020] [Accepted: 05/03/2020] [Indexed: 11/17/2022] Open
Abstract
We synthesized a new amino acid-fluorescent nucleobase derivative (qAN1-AA) and from it two new fluorescent nucleobase–fluorophore (pyrene) conjugates, whereby only the analogue with the longer and more flexible linker (qAN1-pyr2) self-folded into intramolecularly stacked qAN1/pyrene conformation, yielding characteristic, 100 nm-red-shifted emission (λmax = 500 nm). On the contrary, the shorter and more rigid linker resulted in non-stacked conformation (qAN1-pyr1), characterized by the emission of free pyrene at λmax = 400 nm. Both fluorescent nucleobase–fluorophore (pyrene) conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite fluorescence response (due to pre-organization), whereas the amino acid-fluorescent base derivative (qAN1-AA) was inactive. However, only intramolecularly self-folded qAN1-pyr2 showed strong fluorescence selectivity toward poly U (Watson–Crick complementary to qAN1 nucleobase) and poly A (reverse Hoogsteen complementary to qAN1 nucleobase), while an opposite emission change was observed for non-complementary poly G and poly C. Non-folded analogue (qAN1-pyr1) showed no ss-RNA selectivity, demonstrating the importance of nucleobase-fluorophore pre-organization.
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9
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Lee V. Application of copper(i) salt and fluoride promoted Stille coupling reactions in the synthesis of bioactive molecules. Org Biomol Chem 2020; 17:9095-9123. [PMID: 31596305 DOI: 10.1039/c9ob01602c] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The Stille coupling between organostannanes and organohalides is an effective catalytic method for organic synthesis. Despite the ample amount of published results in this area, finding the optimal conditions for this transformation is often not straightforward. It was observed that this reaction could be accelerated with improved efficiency by the addition of a Cu(i) salt and fluoride. This review summarises the application of this simple protocol in the synthesis of natural products, their analogues and other biologically active molecules, from 2004 to 2018.
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Affiliation(s)
- Victor Lee
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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10
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New Size‐Expanded Fluorescent Thymine Analogue: Synthesis, Characterization, and Application. Chemistry 2019; 25:9913-9919. [DOI: 10.1002/chem.201900843] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Indexed: 01/25/2023]
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11
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Matarazzo A, Brow J, Hudson RH. Synthesis and photophysical evaluation of new fluorescent 7-arylethynyl-7-deazaadenosine analogs. CAN J CHEM 2018. [DOI: 10.1139/cjc-2018-0303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Three new fluorescent 7-deaza-2′-deoxyadenosine analogs were synthesized via the Sonogashira cross-coupling reaction of 7-iodo-7-deaza-2′-deoxyadenosine with 1-ethynylpyrene, 2-ethynyl-6-methoxynaphthalene, and 9-ethynylphenanthrene. The spectral properties of these analogs were evaluated in dioxane, EtOH, and H2O to determine their potential for use as environmentally sensitive fluorescent probes. All three analogs displayed large solvatofluorochromicity in H2O, relative to their emission wavelengths in dioxane or EtOH. Moreover, all three analogs exhibited microenvironmental sensitivity of their fluorescence emission intensity, being moderate to high quantum yields in dioxane and EtOH and significantly lower in H2O. Various attempts to perform domino cross-coupling and annuation reactions on 7-deaza-7-alkynyladenine derivatives to form a new fused tricyclic adenine analog were unsuccessful.
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Affiliation(s)
- Augusto Matarazzo
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Justin Brow
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Robert H.E. Hudson
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
- Department of Chemistry, The University of Western Ontario, London, ON N6A 5B7, Canada
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12
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13
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Lawson CP, Füchtbauer AF, Wranne MS, Giraud T, Floyd T, Dumat B, Andersen NK, H El-Sagheer A, Brown T, Gradén H, Wilhelmsson LM, Grøtli M. Synthesis, oligonucleotide incorporation and fluorescence properties in DNA of a bicyclic thymine analogue. Sci Rep 2018; 8:13970. [PMID: 30228309 PMCID: PMC6143597 DOI: 10.1038/s41598-018-31897-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/23/2018] [Indexed: 12/26/2022] Open
Abstract
Fluorescent base analogues (FBAs) have emerged as a powerful class of molecular reporters of location and environment for nucleic acids. In our overall mission to develop bright and useful FBAs for all natural nucleobases, herein we describe the synthesis and thorough characterization of bicyclic thymidine (bT), both as a monomer and when incorporated into DNA. We have developed a robust synthetic route for the preparation of the bT DNA monomer and the corresponding protected phosphoramidite for solid-phase DNA synthesis. The bT deoxyribonucleoside has a brightness value of 790 M−1cm−1 in water, which is comparable or higher than most fluorescent thymine analogues reported. When incorporated into DNA, bT pairs selectively with adenine without perturbing the B-form structure, keeping the melting thermodynamics of the B-form duplex DNA virtually unchanged. As for most fluorescent base analogues, the emission of bT is reduced inside DNA (4.5- and 13-fold in single- and double-stranded DNA, respectively). Overall, these properties make bT an interesting thymine analogue for studying DNA and an excellent starting point for the development of brighter bT derivatives.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Tristan Giraud
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Thomas Floyd
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Nicolai K Andersen
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK.,Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez, 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Henrik Gradén
- Cardiovascular, Renal and Metabolic Diseases IMED Biotech Unit, AstraZeneca Gothenburg, Pepparedsleden 1, Molndal, SE-431 83, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden.
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296, Gothenburg, Sweden.
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14
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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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15
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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]
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16
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Bood M, Füchtbauer AF, Wranne MS, Ro JJ, Sarangamath S, El-Sagheer AH, Rupert DLM, Fisher RS, Magennis SW, Jones AC, Höök F, Brown T, Kim BH, Dahlén A, Wilhelmsson LM, Grøtli M. Pentacyclic adenine: a versatile and exceptionally bright fluorescent DNA base analogue. Chem Sci 2018; 9:3494-3502. [PMID: 29780479 PMCID: PMC5934695 DOI: 10.1039/c7sc05448c] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 03/01/2018] [Indexed: 12/16/2022] Open
Abstract
A highly fluorescent, non-perturbing, pentacyclic adenine analog was designed, synthesized, incorporated into DNA and photophysical evaluated.
Emissive base analogs are powerful tools for probing nucleic acids at the molecular level. Herein we describe the development and thorough characterization of pentacyclic adenine (pA), a versatile base analog with exceptional fluorescence properties. When incorporated into DNA, pA pairs selectively with thymine without perturbing the B-form structure and is among the brightest nucleobase analogs reported so far. Together with the recently established base analog acceptor qAnitro, pA allows accurate distance and orientation determination via Förster resonance energy transfer (FRET) measurements. The high brightness at emission wavelengths above 400 nm also makes it suitable for fluorescence microscopy, as demonstrated by imaging of single liposomal constructs coated with cholesterol-anchored pA–dsDNA, using total internal reflection fluorescence microscopy. Finally, pA is also highly promising for two-photon excitation at 780 nm, with a brightness (5.3 GM) that is unprecedented for a base analog.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
| | - Anders F Füchtbauer
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Jong Jin Ro
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Afaf H El-Sagheer
- Chemistry Branch , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Déborah L M Rupert
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Rachel S Fisher
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Steven W Magennis
- WestCHEM , School of Chemistry , University of Glasgow , Glasgow , G12 8QQ , UK
| | - Anita C Jones
- School of Chemistry , University of Edinburgh , The King's Buildings , Edinburgh EH9 3JJ , UK
| | - Fredrik Höök
- Division of Biological Physics , Department of Physics , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden
| | - Tom Brown
- Department of Chemistry , Chemistry Research Laboratory , University of Oxford , Oxford , OX1 3TA , UK
| | - Byeang Hyean Kim
- Department of Chemistry , Division of Advanced Materials Science , Pohang University of Science and Technology (POSTECH) , Pohang 37673 , South Korea
| | - Anders Dahlén
- AstraZeneca R&D , Innovative Medicines , Cardiovascular & Metabolic Diseases (CVMD) , Pepparedsleden 1, SE-431 83 Mölndal , Gothenburg , Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry , Chalmers University of Technology , SE-412 96 Gothenburg , Sweden .
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology , University of Gothenburg , SE-412 96 Gothenburg , Sweden .
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17
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Bood M, Sarangamath S, Wranne MS, Grøtli M, Wilhelmsson LM. Fluorescent nucleobase analogues for base-base FRET in nucleic acids: synthesis, photophysics and applications. Beilstein J Org Chem 2018; 14:114-129. [PMID: 29441135 PMCID: PMC5789401 DOI: 10.3762/bjoc.14.7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.
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Affiliation(s)
- Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - Sangamesh Sarangamath
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Moa S Wranne
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, SE-412 96 Gothenburg, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering, Chemistry and Biochemistry, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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18
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Wranne MS, Füchtbauer AF, Dumat B, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Toward Complete Sequence Flexibility of Nucleic Acid Base Analogue FRET. J Am Chem Soc 2017; 139:9271-9280. [PMID: 28613885 DOI: 10.1021/jacs.7b04517] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Förster resonance energy transfer (FRET) using fluorescent base analogues is a powerful means of obtaining high-resolution nucleic acid structure and dynamics information that favorably complements techniques such as NMR and X-ray crystallography. Here, we expand the base-base FRET repertoire with an adenine analogue FRET-pair. Phosphoramidite-protected quadracyclic 2'-deoxyadenosine analogues qAN1 (donor) and qAnitro (acceptor) were synthesized and incorporated into DNA by a generic, reliable, and high-yielding route, and both constitute excellent adenine analogues. The donor, qAN1, has quantum yields reaching 21% and 11% in single- and double-strands, respectively. To the best of our knowledge, this results in the highest average brightness of an adenine analogue inside DNA. Its potent emissive features overlap well with the absorption of qAnitro and thus enable accurate FRET-measurements over more than one turn of B-DNA. As we have shown previously for our cytosine analogue FRET-pair, FRET between qAN1 and qAnitro positioned at different base separations inside DNA results in efficiencies that are highly dependent on both distance and orientation. This facilitates significantly enhanced resolution in FRET structure determinations, demonstrated here in a study of conformational changes of DNA upon binding of the minor groove binder netropsin. Finally, we note that the donor and acceptor of our cytosine FRET-pair, tCO and tCnitro, can be conveniently combined with the acceptor and donor of our current adenine pair, respectively. Consequently, our base analogues can now measure base-base FRET between 3 of the 10 possible base combinations and, through base-complementarity, between all sequence positions in a duplex.
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Affiliation(s)
- Moa S Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Anders Foller Füchtbauer
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden.,Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Afaf H El-Sagheer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom.,Chemistry Branch, Faculty of Petroleum and Mining Engineering, Suez University , Suez 43721, Egypt
| | - Tom Brown
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford , Oxford OX1 3TA, United Kingdom
| | - Henrik Gradén
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development, AstraZeneca , Mölndal S-43183, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg , Gothenburg S-41296, Sweden
| | - L Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology , Gothenburg S-41296, Sweden
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19
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Kochman MA, Pola M, Miller RJD. Theoretical Study of the Photophysics of 8-Vinylguanine, an Isomorphic Fluorescent Analogue of Guanine. J Phys Chem A 2016; 120:6200-15. [DOI: 10.1021/acs.jpca.6b04723] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Michał A. Kochman
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Martina Pola
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Institut
für Theoretische Physik, Universität Hamburg, Jungiusstraße
9, 20355 Hamburg, Germany
| | - R. J. Dwayne Miller
- Max Planck Institute for the Structure and Dynamics of Matter and Hamburg Centre for Ultrafast Imaging, Bldg. 99 (CFEL), Luruper Chaussee 149, 22761 Hamburg, Germany
- Department
of Chemistry and Physics, University of Toronto, 80 St. George
Street, Toronto, Ontario M5S 3H6, Canada
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20
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Freeman NS, Moore CE, Wilhelmsson LM, Tor Y. Chromophoric Nucleoside Analogues: Synthesis and Characterization of 6-Aminouracil-Based Nucleodyes. J Org Chem 2016; 81:4530-9. [PMID: 27128151 PMCID: PMC5493935 DOI: 10.1021/acs.joc.6b00310] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nucleodyes, visibly colored chromophoric nucleoside analogues, are reported. Design criteria are outlined and the syntheses of cytidine and uridine azo dye analogues derived from 6-aminouracil are described. Structural analysis shows that the nucleodyes are sound structural analogues of their native nucleoside counterparts, and photophysical studies demonstrate that the nucleodyes are sensitive to microenvironmental changes. Quantum chemical calculations are presented as a valuable complementary tool for the design of strongly absorbing nucleodyes, which overlap with the emission of known fluorophores. Förster critical distance (R0) calculations determine that the nucleodyes make good FRET pairs with both 2-aminopurine (2AP) and pyrrolocytosine (PyC). Additionally, unique tautomerization features exhibited by 5-(4-nitrophenylazo)-6-oxocytidine (8) are visualized by an extraordinary crystal structure.
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Affiliation(s)
- Noam S. Freeman
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - Curtis E. Moore
- Department of Chemistry and Biochemistry, University of
California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United
States
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry
and Biochemistry, Chalmers University of Technology, Gothenburg 41296, Sweden
| | - 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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21
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Tokugawa M, Masaki Y, Canggadibrata JC, Kaneko K, Shiozawa T, Kanamori T, Grøtli M, Wilhelmsson LM, Sekine M, Seio K. 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein. Chem Commun (Camb) 2016; 52:3809-12. [DOI: 10.1039/c5cc09700b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (BFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN).
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Affiliation(s)
- Munefumi Tokugawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | | | - Kazuhei Kaneko
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Shiozawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- S-41296 Gothenburg
- Sweden
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry
- Chalmers University of Technology
- S-41296 Gothenburg
- Sweden
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
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22
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Abstract
An evolved fluorescent ribonucleoside alphabet comprising isomorphic purine ((tz)A, (tz)G) and pyrimidine ((tz)U, (tz)C) analogues, all derived from isothiazolo[4,3-d]pyrimidine as a common heterocyclic core, is described. Structural and biochemical analyses illustrate that the nucleosides, particularly the C-nucleosidic purine analogues, are faithful isomorphic and isofunctional surrogates of their natural counterparts and show improved features when compared to an RNA alphabet derived from thieno[3,4-d]-pyrimidine. The restoration of the nitrogen in a position equivalent to the purines' N7 leads to "isofunctional" behavior, as illustrated by the ability of adenosine deaminase to deaminate (tz)A as effectively as adenosine, the native substrate.
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Affiliation(s)
- Alexander R Rovira
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0358, United States
| | - Andrea Fin
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0358, United States
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093-0358, United States
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23
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Foller Larsen A, Dumat B, Wranne MS, Lawson CP, Preus S, Bood M, Gradén H, Marcus Wilhelmsson L, Grøtli M. Development of bright fluorescent quadracyclic adenine analogues: TDDFT-calculation supported rational design. Sci Rep 2015; 5:12653. [PMID: 26227585 PMCID: PMC4530663 DOI: 10.1038/srep12653] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 07/06/2015] [Indexed: 02/01/2023] Open
Abstract
Fluorescent base analogues (FBAs) comprise a family of increasingly important molecules for the investigation of nucleic acid structure and dynamics. We recently reported the quantum chemical calculation supported development of four microenvironment sensitive analogues of the quadracyclic adenine (qA) scaffold, the qANs, with highly promising absorptive and fluorescence properties that were very well predicted by TDDFT calculations. Herein, we report on the efficient synthesis, experimental and theoretical characterization of nine novel quadracyclic adenine derivatives. The brightest derivative, 2-CNqA, displays a 13-fold increased brightness (εΦF = 4500) compared with the parent compound qA and has the additional benefit of being a virtually microenvironment-insensitive fluorophore, making it a suitable candidate for nucleic acid incorporation and use in quantitative FRET and anisotropy experiments. TDDFT calculations, conducted on the nine novel qAs a posteriori, successfully describe the relative fluorescence quantum yield and brightness of all qA derivatives. This observation suggests that the TDDFT-based rational design strategy may be employed for the development of bright fluorophores built up from a common scaffold to reduce the otherwise costly and time-consuming screening process usually required to obtain useful and bright FBAs.
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Affiliation(s)
- Anders Foller Larsen
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Blaise Dumat
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Moa S. Wranne
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Christopher P. Lawson
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | - Søren Preus
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, DK-8000, Denmark
| | - Mattias Bood
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
| | | | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry, Chalmers University of Technology, S-41296 Gothenburg, Sweden
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology, University of Gothenburg, S-41296 Gothenburg, Sweden
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24
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Lawson CP, Dierckx A, Miannay FA, Wellner E, Wilhelmsson LM, Grøtli M. Synthesis and photophysical characterisation of new fluorescent triazole adenine analogues. Org Biomol Chem 2015; 12:5158-67. [PMID: 24912077 DOI: 10.1039/c4ob00904e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorescent nucleic acid base analogues are powerful probes of DNA structure. Here we describe the synthesis and photo-physical characterisation of a series of 2-(4-amino-5-(1H-1,2,3-triazol-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl) and 2-(4-amino-3-(1H-1,2,3-triazol-4-yl)-1H-pyrazolo[3,4-d]pyrimidin-1-yl) analogues via Sonogashira cross-coupling and [3 + 2]-cycloaddition reactions as the key steps in the synthesis. Compounds with a nitrogen atom in position 8 showed an approximately ten-fold increase in quantum yield and decreased Stokes shift compared to analogues with a carbon atom in position 8. Furthermore, the analogues containing nitrogen in the 8-position showed a more red-shifted and structured absorption as opposed to those which have a carbon incorporated in the same position. Compared to the previously characterised C8-triazole modified adenine, the emissive potential was significantly lower (tenfold or more) for this new family of triazoles-adenine compounds. However, three of the compounds have photophysical properties which will make them interesting to monitor inside DNA.
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Affiliation(s)
- Christopher P Lawson
- Department of Chemistry, Medicinal Chemistry, University of Gothenburg, S-41296 Gothenburg, Sweden.
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25
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26
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Gophane DB, Sigurdsson ST. TEMPO-derived spin labels linked to the nucleobases adenine and cytosine for probing local structural perturbations in DNA by EPR spectroscopy. Beilstein J Org Chem 2015; 11:219-27. [PMID: 25815073 PMCID: PMC4362019 DOI: 10.3762/bjoc.11.24] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 01/15/2015] [Indexed: 02/04/2023] Open
Abstract
Three 2´-deoxynucleosides containing semi-flexible spin labels, namely (T)A, (U)A and (U)C, were prepared and incorporated into deoxyoligonucleotides using the phosphoramidite method. All three nucleosides contain 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO) connected to the exocyclic amino group; (T)A directly and (U)A as well as (U)C through a urea linkage. (T)A and (U)C showed a minor destabilization of a DNA duplex, as registered by a small decrease in the melting temperature, while (U)A destabilized the duplex by more than 10 °C. Circular dichroism (CD) measurements indicated that all three labels were accommodated in B-DNA duplex. The mobility of the spin label (T)A varied with different base-pairing partners in duplex DNA, with the (T)A•T pair being the least mobile. Furthermore, (T)A showed decreased mobility under acidic conditions for the sequences (T)A•C and (T)A•G, to the extent that the EPR spectrum of the latter became nearly superimposable to that of (T)A•T. The reduced mobility of the (T)A•C and (T)A•G mismatches at pH 5 is consistent with the formation of (T)AH(+)•C and (T)AH(+)•G, in which protonation of N1 of A allows the formation of an additional hydrogen bond to N3 of C and N7 of G, respectively, with G in a syn-conformation. The urea-based spin labels (U)A and (U)C were more mobile than (T)A, but still showed a minor variation in their EPR spectra when paired with A, G, C or T in a DNA duplex. (U)A and (U)C had similar mobility order for the different base pairs, with the lowest mobility when paired with C and the highest when paired with T.
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Affiliation(s)
- Dnyaneshwar B Gophane
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
| | - Snorri Th Sigurdsson
- University of Iceland, Department of Chemistry, Science Institute, Dunhaga 3, 107 Reykjavik, Iceland
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27
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Dumat B, Bood M, Wranne MS, Lawson CP, Larsen AF, Preus S, Streling J, Gradén H, Wellner E, Grøtli M, Wilhelmsson LM. Second-generation fluorescent quadracyclic adenine analogues: environment-responsive probes with enhanced brightness. Chemistry 2015; 21:4039-48. [PMID: 25641628 DOI: 10.1002/chem.201405759] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 01/10/2023]
Abstract
Fluorescent base analogues comprise a group of increasingly important molecules for the investigation of nucleic acid structure, dynamics, and interactions with other molecules. Herein, we report on the quantum chemical calculation aided design, synthesis, and characterization of four new putative quadracyclic adenine analogues. The compounds were efficiently synthesized from a common intermediate through a two-step pathway with the Suzuki-Miyaura coupling as the key step. Two of the compounds, qAN1 and qAN4, display brightnesses (εΦF) of 1700 and 2300, respectively, in water and behave as wavelength-ratiometric pH probes under acidic conditions. The other two, qAN2 and qAN3, display lower brightnesses but exhibit polarity-sensitive dual-band emissions that could prove useful to investigate DNA structural changes induced by DNA-protein or -drug interactions. The four qANs are very promising microenvironment-sensitive fluorescent adenine analogues that display considerable brightness for such compounds.
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Affiliation(s)
- Blaise Dumat
- Department of Chemical and Chemical Engineering/, Chemistry and Biochemistry, Chalmers University of Technology, 41296 Gothenburg (Sweden)
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28
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Tanpure AA, Srivatsan SG. Synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue based on the Lucifer chromophore. Chembiochem 2014; 15:1309-16. [PMID: 24861713 DOI: 10.1002/cbic.201402052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/10/2022]
Abstract
The majority of fluorescent nucleoside analogues used in nucleic acid studies have excitation maxima in the UV region and show very low fluorescence within oligonucleotides (ONs); hence, they cannot be utilised with certain fluorescence methods and for cell-based analysis. Here, we describe the synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue, derived by attaching a Lucifer chromophore (1,8-naphthalimide core) at the 5-position of uracil. The emissive nucleoside displays excitation and emission maxima in the visible region and exhibits high quantum yield. Importantly, when incorporated into ON duplexes it retains appreciable fluorescence efficiency and is sensitive to the neighbouring base environment. Notably, the nucleoside signals the presence of purine repeats in ON duplexes with an enhancement in fluorescence intensity, a property rarely displayed by other nucleoside analogues.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008 (India)
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29
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Lefoix M, Mathis G, Kleinmann T, Truffert JC, Asseline U. Pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside as deoxyadenosine analogue: synthesis, pairing, and resistance to hydrolysis. J Org Chem 2014; 79:3221-7. [PMID: 24649913 DOI: 10.1021/jo5000253] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthesis of a pyrazolo[1,5-a]-1,3,5-triazine C-nucleoside (dA(PT)), designed to form two hydrogen bonds with a complementary dT residue, is reported. Oligonucleotides including this dA nucleoside analogue possess base-pairing properties similar to those of the parent oligonucleotide. This dA nucleoside analogue is more resistant to acid-catalyzed hydrolysis than dA.
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Affiliation(s)
- Myriam Lefoix
- NucleoSyn. Pépinières d'entreprises - Centre Innovation 16, Rue Léonard de Vinci 45074 Orléans Cedex 2, France
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30
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Liu H, Song Q, Yang Y, Li Y, Wang H. Theoretical study on absorption and emission spectra of adenine analogues. J Mol Model 2014; 20:2100. [PMID: 24633764 DOI: 10.1007/s00894-014-2100-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Accepted: 12/01/2013] [Indexed: 11/27/2022]
Abstract
Fluorescent nucleoside analogues have attracted much attention in studying the structure and dynamics of nucleic acids in recent years. In the present work, we use theoretical calculations to investigate the structural and optical properties of four adenine analogues (termed as A1, A2, A3, and A4), and also consider the effects of aqueous solution and base pairing. The results show that the fluorescent adenine analogues can pair with thymine to form stable H-bonded WC base pairs. The excited geometries of both adenine analogues and WC base pairs are similar to the ground geometries. The absorption and emission maxima of adenine analogues are greatly red shifted compared with nature adenine, the oscillator strengths of A1 and A2 are stronger than A3 and A4 in both absorption and emission spectra. The calculated low-energy peaks in the absorption spectra are in good agreement with the experimental data. In general, the aqueous solution and base pairing can slightly red-shift both the absorption and emission maxima, and can increase the oscillator strengths of absorption spectra, but significantly decrease the oscillator strengths of A3 in emission spectra.
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Affiliation(s)
- Hongxia Liu
- School of Chemical and Material Engineering, Jiangnan University, Wuxi, Jiangsu, 214122, People's Republic of China
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31
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32
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Rodgers BJ, Elsharif NA, Vashisht N, Mingus MM, Mulvahill MA, Stengel G, Kuchta RD, Purse BW. Functionalized tricyclic cytosine analogues provide nucleoside fluorophores with improved photophysical properties and a range of solvent sensitivities. Chemistry 2013; 20:2010-5. [PMID: 24311229 DOI: 10.1002/chem.201303410] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/11/2022]
Abstract
Tricyclic cytosines (tC and tC(O) frameworks) have emerged as a unique class of fluorescent nucleobase analogues that minimally perturb the structure of B-form DNA and that are not quenched in duplex nucleic acids. Systematic derivatization of these frameworks is a likely approach to improve on and diversify photophysical properties, but has not so far been examined. Synthetic methods were refined to improve on tolerance for electron-donating and electron-withdrawing groups, resulting in a series of eight new, fluorescent cytidine analogues. Photophysical studies show that substitution of the framework results in a pattern of effects largely consistent across tC and tC(O) and provides nucleoside fluorophores that are brighter than either parent. Moreover, a range of solvent sensitivities is observed, offering promise that this family of probes can be extended to new applications that require reporting on the local environment.
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Affiliation(s)
- Brittney J Rodgers
- Department of Chemistry and Biochemistry, University of Denver, 2199 S. University Blvd., Denver, CO 80208 (USA)
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Tanpure AA, Pawar MG, Srivatsan SG. Fluorescent Nucleoside Analogs: Probes for Investigating Nucleic Acid Structure and Function. Isr J Chem 2013. [DOI: 10.1002/ijch.201300010] [Citation(s) in RCA: 101] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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