1
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Chowdhury M, Hudson RHE. Exploring Nucleobase Modifications in Oligonucleotide Analogues for Use as Environmentally Responsive Fluorophores and Beyond. CHEM REC 2023; 23:e202200218. [PMID: 36344432 DOI: 10.1002/tcr.202200218] [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: 09/06/2022] [Revised: 10/07/2022] [Indexed: 11/09/2022]
Abstract
Over the past two decades, it has become abundantly clear that nucleic acid biochemistry, especially with respect to RNA, is more convoluted and complex than previously appreciated. Indeed, the application and exploitation of nucleic acids beyond their predestined role as the medium for storage and transmission of genetic information to the treatment and study of diseases has been achieved. In other areas of endeavor, utilization of nucleic acids as a probe molecule requires that they possess a reporter group. The reporter group of choice is often a luminophore because fluorescence spectroscopy has emerged as an indispensable tool to probe the structural and functional properties of modified nucleic acids. The scope of this review spans research done in the Hudson lab at The University of Western Ontario and is focused on modified pyrimidine nucleobases and their applications as environmentally sensitive fluorophores, base discriminating fluorophores, and in service of antisense applications as well as tantalizing new results as G-quadruplex destabilizing agents. While this review is a focused personal account, particularly influential work of colleagues in the chemistry community will be highlighted. The intention is not to make a comprehensive review, citations to the existing excellent reviews are given, any omission of the wonderful and impactful work being done by others globally is not intentional. Thus, this review will briefly introduce the context of our work, summarize what has been accomplished and finish with the prospects of future developments.
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Affiliation(s)
- Mria Chowdhury
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
| | - Robert H E Hudson
- Department of Chemistry, The University of Western Ontario, London, Ontario, Canada, N6A 5B7
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2
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Bag SS, Gogoi H, Sinha S. Synthesis and studies on the photophysical/biophysical properties of triazolylfluorene-labeled 2′-deoxyuridines. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Karimi A, Börner R, Mata G, Luedtke NW. A Highly Fluorescent Nucleobase Molecular Rotor. J Am Chem Soc 2020; 142:14422-14426. [PMID: 32786749 DOI: 10.1021/jacs.0c05180] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescent base analogs (FBAs) are powerful probes of nucleic acids' structures and dynamics. However, previously reported FBAs exhibit relatively low brightness and therefore limited sensitivity of detection. Here we report the hitherto brightest FBA that has ideal molecular rotor properties for detecting local dynamic motions associated with base pair mismatches. The new trans-stilbene annulated uracil derivative "tsT" exhibits bright fluorescence emissions in various solvents (ε × Φ = 3400-29 700 cm-1 M-1) and is highly sensitive to mechanical motions in duplex DNA (ε × Φ = 150-4250 cm-1 M-1). tsT is thereby a "smart" thymidine analog, exhibiting a 28-fold brighter fluorescence intensity when base paired with A as compared to T or C. Time-correlated single photon counting revealed that the fluorescence lifetime of tsT (τ = 4-11 ns) was shorter than its anisotropy decay in well-matched duplex DNA (θ = 20 ns), yet longer than the dynamic motions of base pair mismatches (0.1-10 ns). These properties enable unprecedented sensitivity in detecting local dynamics of nucleic acids.
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Affiliation(s)
- Ashkan Karimi
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada
| | - Richard Börner
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Laserinstitut Hochschule Mittweida, University of Applied Sciences, 09648 Mittweida, Germany
| | - Guillaume Mata
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Nathan W Luedtke
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Chemistry, McGill University, H3A-0B8 Montreal, Canada.,Department of Pharmacology and Therapeutics, McGill University, H3A-1A3 Montreal, Canada
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4
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Michel BY, Dziuba D, Benhida R, Demchenko AP, Burger A. Probing of Nucleic Acid Structures, Dynamics, and Interactions With Environment-Sensitive Fluorescent Labels. Front Chem 2020; 8:112. [PMID: 32181238 PMCID: PMC7059644 DOI: 10.3389/fchem.2020.00112] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fluorescence labeling and probing are fundamental techniques for nucleic acid analysis and quantification. However, new fluorescent probes and approaches are urgently needed in order to accurately determine structural and conformational dynamics of DNA and RNA at the level of single nucleobases/base pairs, and to probe the interactions between nucleic acids with proteins. This review describes the means by which to achieve these goals using nucleobase replacement or modification with advanced fluorescent dyes that respond by the changing of their fluorescence parameters to their local environment (altered polarity, hydration, flipping dynamics, and formation/breaking of hydrogen bonds).
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Affiliation(s)
- Benoît Y. Michel
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
| | - Dmytro Dziuba
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Laboratoire de Bioimagerie et Pathologies, UMR 7021 CNRS, Faculté de Pharmacie, Université de Strasbourg, Illkirch, France
| | - Rachid Benhida
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
- Mohamed VI Polytechnic University, UM6P, Ben Guerir, Morocco
| | - Alexander P. Demchenko
- Laboratory of Nanobiotechnologies, Palladin Institute of Biochemistry, Kyiv, Ukraine
- Institute of Physical, Technical and Computer Science, Yuriy Fedkovych National University, Chernivtsi, Ukraine
| | - Alain Burger
- Université Côte d'Azur, CNRS, Institut de Chimie de Nice, UMR 7272 – Parc Valrose, Nice, France
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5
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Lee SY, Hong SW, Yeo H, Hwang GT. The linkers in fluorene-labeled 2′-deoxyuridines affect fluorescence discriminating phenomena upon duplex formation. RSC Adv 2020; 10:18853-18859. [PMID: 35518342 PMCID: PMC9053879 DOI: 10.1039/d0ra01651a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 05/08/2020] [Indexed: 11/29/2022] Open
Abstract
Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers—UF (without linker), UFL (with ethynyl linker), and UDF (with diethynyl linker)—have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the fluorescence emission properties upon duplex formation with fully matched and single-base-mismatched targets. Here, we describe the influence of the linkers on the emission behavior, the intramolecular electron transfer between the fluorene moiety and the uracil base after photoexcitation, and the structural stability upon duplex formation. The probe containing the UFL residue (with an ethynyl linker) and cytosine residues as flanking bases exhibited the greatest fluorescence turn-on selective behavior toward the perfectly matched target. Three fluorene-labeled 2′-deoxyuridines that differ in terms of their linkers have been introduced at the central positions of oligodeoxynucleotides to examine the effects that their linkers have on the emission properties upon duplex formations.![]()
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Affiliation(s)
- So Young Lee
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Seung Woo Hong
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Hyeonuk Yeo
- Department of Chemistry Education
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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6
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Hwang GT. Single-Labeled Oligonucleotides Showing Fluorescence Changes Upon Hybridization with Target Nucleic Acids. Molecules 2018; 23:E124. [PMID: 29316733 PMCID: PMC6017082 DOI: 10.3390/molecules23010124] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/05/2018] [Accepted: 01/08/2018] [Indexed: 12/12/2022] Open
Abstract
Sequence-specific detection of nucleic acids has been intensively studied in the field of molecular diagnostics. In particular, the detection and analysis of single-nucleotide polymorphisms (SNPs) is crucial for the identification of disease-causing genes and diagnosis of diseases. Sequence-specific hybridization probes, such as molecular beacons bearing the fluorophore and quencher at both ends of the stem, have been developed to enable DNA mutation detection. Interestingly, DNA mutations can be detected using fluorescently labeled oligonucleotide probes with only one fluorophore. This review summarizes recent research on single-labeled oligonucleotide probes that exhibit fluorescence changes after encountering target nucleic acids, such as guanine-quenching probes, cyanine-containing probes, probes containing a fluorophore-labeled base, and microenvironment-sensitive probes.
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Affiliation(s)
- Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 41566, Korea.
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7
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Hong SW, Hwang GT. Photophysical Study of 2-Fluorenyl-1,2,3-Triazole-labeled 2′-Deoxyuridine and Its Oligonucleotide. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Seung Woo Hong
- Department of Chemistry; Kyungpook National University; Daegu 41566 Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry; Kyungpook National University; Daegu 41566 Republic of Korea
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8
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Park Y, Nim-Anussornkul D, Vilaivan T, Morii T, Kim BH. Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon. Bioorg Med Chem Lett 2017; 28:77-80. [PMID: 29248297 DOI: 10.1016/j.bmcl.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 11/23/2017] [Accepted: 12/05/2017] [Indexed: 01/02/2023]
Abstract
We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex.
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Affiliation(s)
- Yoojin Park
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | | | - Tirayut Vilaivan
- Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea.
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9
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Lee JW, Son YS, Hwang JY, Park Y, Hwang GT. pH-Responsive quencher-free molecular beacon systems containing 2′-deoxyuridine units labeled with fluorene derivatives. Org Biomol Chem 2017; 15:7165-7172. [DOI: 10.1039/c7ob01703k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
pH-Responsive oligodeoxynucleotides only exhibited dramatic increases in fluorescence upon duplex formation with their fully matched target DNAs.
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Affiliation(s)
- Ji Won Lee
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Ye-Seul Son
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Jun Yeon Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
| | - Yoojin Park
- Department of Chemistry
- Division of Advanced Materials Science
- Pohang University of Science and Technology
- Pohang 37673
- Republic of Korea
| | - Gil Tae Hwang
- Department of Chemistry
- Kyungpook National University
- Daegu 41566
- Republic of Korea
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10
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Fluorescent Oligonucleotides Containing a 2-Ethynylfluorene- or 2-Ethynylfluorenone-labeled 2′-Deoxyguanosine Unit: Fluorescence Changes upon Duplex Formation. B KOREAN CHEM SOC 2016. [DOI: 10.1002/bkcs.10856] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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11
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Morihiro K, Hasegawa O, Mori S, Tsunoda S, Obika S. C5-azobenzene-functionalized locked nucleic acid uridine: isomerization properties, hybridization ability, and enzymatic stability. Org Biomol Chem 2016; 13:5209-14. [PMID: 25853508 DOI: 10.1039/c5ob00477b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Oligonucleotides (ONs) modified with a locked nucleic acid (LNA) are widely used in the fields of therapeutics, diagnosis, and nanotechnology. There have been significant efforts towards developing LNA analogues bearing modified bridges to improve their hybridization ability, nuclease resistance, and pharmacokinetic profiles. Moreover, nucleobase modifications of LNA are useful strategies for the functionalization of ONs. Modifications of the C5-position of pyrimidine nucleobases are particularly interesting because they enable predictable positioning of functional groups in the major groove of the duplex. Here we report the synthesis of C5-azobenzene-functionalized LNA uridine (LNA-U(Az)) and properties of LNA-U(Az)-modified ONs, including isomerization properties, hybridization ability, and enzyme stability. LNA-U(Az) in ON is photo-isomerized effectively and reversibly by irradiation at 365 nm (trans to cis) and 450 nm (cis to trans). LNA-U(Az)-modified ONs show RNA-selective hybridization ability despite the large hydrophobic azobenzene moiety extending into the major groove of the duplex. The enzymatic stability of LNA-U(Az)-modified ONs is higher than that of natural and LNA-modified ONs with or without photo-irradiation. Our results indicate that LNA-U(Az) holds promise for RNA targeting and photo-switchable technologies.
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Affiliation(s)
- K Morihiro
- National Institute of Biomedical Innovation (NIBIO), 7-6-8 Saito-Asagi, Ibaraki, Osaka 567-0085, Japan.
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12
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Park JW, Park Y, Kim BH. Quencher-free molecular aptamer beacons (QF-MABs) for detection of ATP. Bioorg Med Chem Lett 2015; 25:4597-600. [PMID: 26320623 DOI: 10.1016/j.bmcl.2015.08.052] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/18/2015] [Accepted: 08/20/2015] [Indexed: 12/11/2022]
Abstract
We have constructed a simple and efficient system-based on quencher-free molecular aptamer beacons (QF-MABs)-for probing ATP. In the absence of ATP, the fluorescence of a pyrene fluorophore on the loop position (15 nucleotides from the 5' end) of the optimal QF-MAB was quenched by the neighboring nucleobases; in its presence, fluorescence was recovered, due to a conformational change in the secondary structure of the QF-MAB.
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Affiliation(s)
- Jung Woo Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
| | - Yoojin Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
| | - Byeang Hyean Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea.
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13
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Chowdhury JA, Moriguchi T, Shinozuka K. Pseudo-Dumbbell-Type Molecular Beacon Probes Bearing Modified Deoxyuridine Derivatives and a Silylated Pyrene as a Fluorophore. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20140372] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jakir Ahmed Chowdhury
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
| | - Tomohisa Moriguchi
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
| | - Kazuo Shinozuka
- Division of Molecular Science, Graduate School of Science and Technology, Gunma University
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14
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Barthes NPF, Karpenko IA, Dziuba D, Spadafora M, Auffret J, Demchenko AP, Mély Y, Benhida R, Michel BY, Burger A. Development of environmentally sensitive fluorescent and dual emissive deoxyuridine analogues. RSC Adv 2015. [DOI: 10.1039/c5ra02709h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We designed and developed fluorescent deoxyuridine analogues with strong sensitivity to hydration for the major groove labelling of DNA.
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Affiliation(s)
- N. P. F. Barthes
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - I. A. Karpenko
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - D. Dziuba
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - M. Spadafora
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - J. Auffret
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | | | - Y. Mély
- Laboratoire de Biophotonique et Pharmacologie
- UMR 7213
- Faculté de Pharmacie
- Université de Strasbourg
- CNRS
| | - R. Benhida
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - B. Y. Michel
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
| | - A. Burger
- Institut de Chimie de Nice
- UMR 7272
- Université de Nice Sophia Antipolis
- CNRS
- 06108 Nice Cedex 2
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15
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Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Org Biomol Chem 2014; 11:5605-14. [PMID: 23846401 DOI: 10.1039/c3ob41222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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16
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Dziuba D, Karpenko IA, Barthes NPF, Michel BY, Klymchenko AS, Benhida R, Demchenko AP, Mély Y, Burger A. Rational Design of a Solvatochromic Fluorescent Uracil Analogue with a Dual-Band Ratiometric Response Based on 3-Hydroxychromone. Chemistry 2014; 20:1998-2009. [DOI: 10.1002/chem.201303399] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Indexed: 12/24/2022]
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17
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Kim MJ, Seo Y, Hwang GT. Synthesis and photophysical properties of 2′-deoxyguanosine derivatives labeled with fluorene and fluorenone units: toward excimer probes. RSC Adv 2014. [DOI: 10.1039/c3ra47383j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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18
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Boonlua C, Ditmangklo B, Reenabthue N, Suparpprom C, Poomsuk N, Siriwong K, Vilaivan T. Pyrene-labeled pyrrolidinyl peptide nucleic acid as a hybridization-responsive DNA probe: comparison between internal and terminal labeling. RSC Adv 2014. [DOI: 10.1039/c3ra47997h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Internally pyrene-labeled pyrrolidinyl PNA yields much larger fluorescence increase than terminally labeled PNA upon hybridization with complementary DNA.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Boonsong Ditmangklo
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
| | - Nisanath Reenabthue
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry
- Faculty of Science
- Naresuan University
- Phitsanulok 65000, Thailand
| | - Nattawee Poomsuk
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Unit
- Department of Chemistry
- Faculty of Science
- Khon Kaen University
- Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit
- Department of Chemistry
- Faculty of Science
- Chulalongkorn University
- Bangkok 10330, Thailand
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19
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A quencher-free molecular beacon design based on pyrene excimer fluorescence using pyrene-labeled UNA (unlocked nucleic acid). Bioorg Med Chem 2013; 21:6186-90. [DOI: 10.1016/j.bmc.2013.04.062] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 04/08/2013] [Accepted: 04/16/2013] [Indexed: 11/18/2022]
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20
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Lee J, Cho HY, Hwang GT. Highly efficient quencher-free molecular beacon systems containing 2-ethynyldibenzofuran- and 2-ethynyldibenzothiophene-labeled 2'-deoxyuridine units. Chembiochem 2013; 14:1353-62. [PMID: 23824637 DOI: 10.1002/cbic.201300240] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Indexed: 12/21/2022]
Abstract
We have prepared two fluorescent DNA probes--UDBF and UDBT, containing 2-ethynyldibenzofuran and 2-ethynyldibenzothiophene moieties, respectively, covalently attached to the base dU--and incorporated them in the central positions of oligodeoxynucleotides (ODNs) so as to develop new types of quencher-free linear beacon probes and investigate the effect of functionalization of the fluorene scaffold on the photophysical properties of the fluorescent ODNs. The ODNs containing adenine flanking bases (FBs) displayed a selective fluorescence "turn-off" response to mismatched targets with guanine bases; this suggests that these probes could be used as base-discriminating fluorescent nucleotides. On the other hand, we observed a "turn-on" response to matched targets when the UDBF and UDBT units of ODNs containing pyrimidine-based FBs were positioned opposite the four natural nucleobases. In particular, an ODN incorporating UDBT and cytosine FBs has potential use in single-nucleotide polymorphism typing.
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Affiliation(s)
- Jiwon Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 1370 Sankyuk-dong, Buk-gu, Daegu 702-701, South Korea
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21
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Cho HY, Woo SK, Hwang GT. Synthesis and photophysical study of 2'-deoxyuridines labeled with fluorene derivatives. Molecules 2012; 17:12061-71. [PMID: 23085656 PMCID: PMC6268453 DOI: 10.3390/molecules171012061] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/03/2012] [Accepted: 10/10/2012] [Indexed: 12/17/2022] Open
Abstract
We examined microenvironment-sensitive fluorescent 2′-deoxyuridines labeled with fluorene derivatives that exhibited solvent-dependent photophysical properties. The high sensitivity of the fluorescence shift and the nucleoside intensity dependence on solvent polarity provided information useful for estimating the polarity of the environment surrounding the fluorescent nucleoside.
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Affiliation(s)
- Hyun Yi Cho
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 702-701, Korea;
| | - Sang Keun Woo
- Molecular Imaging Research Center, Korea Institute of Radiological and Medical Sciences, 75 Nowon-gil, Seoul 139-706, Korea
- Authors to whom correspondence should be addressed; (S.K.W.); (G.T.H.); Tel.: +82-2-970-1659 (S.K.W.); Fax: +82-2-970-1341 (S.K.W.); Tel.: +82-53-950-5331 (G.T.H.); Fax: +82-53-950-6330 (G.T.H.)
| | - Gil Tae Hwang
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, Daegu 702-701, Korea;
- Authors to whom correspondence should be addressed; (S.K.W.); (G.T.H.); Tel.: +82-2-970-1659 (S.K.W.); Fax: +82-2-970-1341 (S.K.W.); Tel.: +82-53-950-5331 (G.T.H.); Fax: +82-53-950-6330 (G.T.H.)
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Quencher-free molecular beacon tethering 7-hydroxycoumarin detects targets through protonation/deprotonation. Bioorg Med Chem 2012; 20:4310-5. [DOI: 10.1016/j.bmc.2012.05.052] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2012] [Revised: 05/23/2012] [Accepted: 05/23/2012] [Indexed: 12/11/2022]
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Ryu JH, Heo JY, Bang EK, Hwang GT, Kim BH. Quencher-free linear beacon systems containing 2-ethynylfluorenone-labeled 2′-deoxyuridine units. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.10.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Guo J, Wang T, Yang R. Construction of logic gates with the fluorene-based small molecule/DNA probes. MOLECULAR BIOSYSTEMS 2012; 8:2347-50. [DOI: 10.1039/c2mb25129a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2′-deoxyuridines. Bioorg Med Chem 2012; 20:480-6. [DOI: 10.1016/j.bmc.2011.10.041] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/10/2011] [Accepted: 10/14/2011] [Indexed: 11/19/2022]
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26
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Riedl J, Pohl R, Rulíšek L, Hocek M. Synthesis and photophysical properties of biaryl-substituted nucleos(t)ides. Polymerase synthesis of DNA probes bearing solvatochromic and pH-sensitive dual fluorescent and 19F NMR labels. J Org Chem 2011; 77:1026-44. [PMID: 22148188 DOI: 10.1021/jo202321g] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The design of four new fluorinated biaryl fluorescent labels and their attachment to nucleosides and nucleoside triphosphates (dNTPs) by the aqueous cross-coupling reactions of biarylboronates is reported. The modified dNTPs were good substrates for KOD XL polymerase and were enzymatically incorporated into DNA probes. The photophysical properties of the biaryl-modified nucleosides, dNTPs, and DNA were studied systematically. The different substitution pattern of the biaryls was used for tuning of emission maxima in the broad range of 366-565 nm. Using methods of computational chemistry the emission maxima were reproduced with a satisfactory degree of accuracy, and it was shown that the large solvatochromic shifts observed for the studied probes are proportional to the differences in dipole moments of the ground (S(0)) and excited (S(1)) states that add on top of smaller shifts predicted already for these systems in vacuo. Thus, we present a set of compounds that may serve as multipurpose base-discriminating fluorophores for sensing of hairpins, deletions, and mismatches by the change of emission maxima and intensities of fluorescence and that can be also conviently studied by (19)F NMR spectroscopy. In addition, aminobenzoxazolyl-fluorophenyl-labeled nucleotides and DNA also exert dual pH-sensitive and solvatochromic fluorescence, which may imply diverse applications.
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Affiliation(s)
- Jan Riedl
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences & IOCB Research Center, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic
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Seo YJ, Hwang GT. Quencher-free Linear Beacon Systems with Dual Fluorene-labeled Deoxyuridines. B KOREAN CHEM SOC 2011. [DOI: 10.5012/bkcs.2011.32.11.4129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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28
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Boonlua C, Vilaivan C, Wagenknecht HA, Vilaivan T. 5-(Pyren-1-yl)uracil as a base-discriminating fluorescent nucleobase in pyrrolidinyl peptide nucleic acids. Chem Asian J 2011; 6:3251-9. [PMID: 21976408 DOI: 10.1002/asia.201100490] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Indexed: 12/15/2022]
Abstract
A pyrene-labeled uridine (U(Py)) monomer for a pyrrolidinyl peptide nucleic acid with an alternating proline/2-aminocyclopentanecarboxylic acid backbone (acpcPNA) was synthesized and incorporated into the PNA. The U(Py) base in acpcPNA could specifically recognize the base A in its complementary DNA strand as determined by thermal denaturation (T(m)) experiments. The fluorescence of the U(Py)-containing single-stranded acpcPNA was very weak in aqueous buffer. In the presence of a complementary DNA target, the fluorescence was enhanced significantly (2.7-41.9 folds, depending on sequences). The fluorescence enhancement was specific to the pairing between U(Py) and dA, making the U(Py)-modified acpcPNA useful as a hybridization-responsive fluorescence probe for DNA-sequence determination.
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Affiliation(s)
- Chalothorn Boonlua
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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Park SM, Nam SJ, Jeong HS, Kim WJ, Kim BH. The effects of the 4-(4-Methylpiperazine)phenyl group on nucleosides and oligonucleotides: cellular delivery, detection, and stability. Chem Asian J 2010; 6:487-92. [PMID: 21254426 DOI: 10.1002/asia.201000574] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Indexed: 11/11/2022]
Abstract
As drug candidates, one promising way to improve the cellular delivery efficacy of oligonucleotides is to introduce a cationic group. By introducing a cationic moiety into the oligonucleotide structure, they become capable of approaching the cell surface and also of crossing the cellular membrane. In an effort to develop cell-permeable oligonucleotides, we examined the piperazinephenyl-bearing 2'-deoxyuridine ((PP)U), which can be not only cationic but also fluorescent as a cationic monomer for cationic oligonucleotides. Several modified DNA oligonucleotides with different numbers of (PP)U building blocks were synthesized and evaluated for the effect on thermal stability and conformation by the introduction of (PP)U. The cellular delivery of modified oligonucleotides was different depending on the number of (PP)U building blocks. Furthermore, these (PP)U-modified oligonucleotides had sufficient fluorescence that we were able to identify the delivery results without the use of conventional fluorescent tags. They were predominantly localized in the cell cytoplasm. In addition, they were stable enough after 3 hours in the presence of nuclease. These results showed that a piperazinephenyl moiety that is conjugated with nucleobase is able to deliver and detect the oligonucleotides, which suggests that this concept of 'dual-function oligonucleotides' might be utilized in diagnostics, therapeutics, and as a convenient biological tool for probing the activity of oligonucleotides inside cells.
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Affiliation(s)
- Sun Min Park
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology (POSTECH), Pohang, 790-784, Republic of Korea
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Yi JW, Park J, Singh NJ, Lee IJ, Kim KS, Kim BH. Quencher-free molecular beacon: Enhancement of the signal-to-background ratio with graphene oxide. Bioorg Med Chem Lett 2010; 21:704-6. [PMID: 21194937 DOI: 10.1016/j.bmcl.2010.12.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 11/29/2010] [Accepted: 12/01/2010] [Indexed: 01/13/2023]
Abstract
We report the highly improved version of quencher-free molecular beacon (QF-MB) system by using graphene oxide (GO) as an external quencher. This QF-MB/GO system provided a higher S/B ratio (31.0) relative to that (2.2) of the same system in the absence of GO, while retaining a high selectivity for fully matched over single-base-mismatched targets.
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Affiliation(s)
- Jeong Wu Yi
- Laboratory for Modified Nucleic Acid Systems, Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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31
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Xie Y, Maxson T, Tor Y. Fluorescent nucleoside analogue displays enhanced emission upon pairing with guanine. Org Biomol Chem 2010; 8:5053-5. [PMID: 20862439 PMCID: PMC3032630 DOI: 10.1039/c0ob00413h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A fluorescent nucleobase analogue, 7-aminoquinazoline-2,4-(1H,3H)-dione, is incorporated into a DNA oligonucleotide and senses mismatched pairing by displaying G-specific fluorescence enhancement.
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Affiliation(s)
- Yun Xie
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Tucker Maxson
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San
Diego, La Jolla, CA, 92093-0358, USA. ; Fax:
+1 858 534 0202; Tel: +1 858 534 6401
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Østergaard ME, Cheguru P, Papasani MR, Hill RA, Hrdlicka PJ. Glowing Locked Nucleic Acids: Brightly Fluorescent Probes for Detection of Nucleic Acids in Cells. J Am Chem Soc 2010; 132:14221-8. [DOI: 10.1021/ja1057295] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Pallavi Cheguru
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Madhusudhan R. Papasani
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Rodney A. Hill
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, Department of Animal Veterinary Science, University of Idaho, Moscow, Idaho 83844-2330, and Biological Applications of Nanotechnology (BANTech) Center, University of Idaho, Moscow, Idaho 83844
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Orner B. The first Asian Chemical Biology conference meets at Seoul National University. ACS Chem Biol 2010; 5:725-7. [PMID: 20722456 DOI: 10.1021/cb100206k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brendan Orner
- Nanyang Technological University, Singapore, Singapore.
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Lee YA, Hwang GT. A Linear Beacon System Featuring an Internal Deoxyguanine Quencher Allows Highly Selective Detection of Single Base Mismatches. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.7.2011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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35
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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: 665] [Impact Index Per Article: 47.5] [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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Ueno Y, Komatsuzaki S, Takasu K, Kawai S, Kitamura Y, Kitade Y. Synthesis and Properties of Oligonucleotides Containing Novel Fluorescent Biaryl Units. European J Org Chem 2009. [DOI: 10.1002/ejoc.200900567] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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37
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Bang EK, Kim BH. Synthesis of hairpin siRNA using 18β-glycyrrhetinic acid derivative as a loop motif. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2009.03.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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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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Seo YJ, Lee IJ, Kim BH. Detection of structure-switching in G-quadruplexes using end-stacking ability. Bioorg Med Chem Lett 2008; 18:3910-3. [PMID: 18585032 DOI: 10.1016/j.bmcl.2008.06.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2008] [Revised: 06/04/2008] [Accepted: 06/11/2008] [Indexed: 10/21/2022]
Abstract
G-quadruplex-forming ODNs containing nonpolar aromatic fluorophore moiety, A(PY) at the dangling ends undergo pi-stacking on surface of G-quadruplex, and the fluorescence change can be used to distinguish the structure-switching between the mixed parallel/antiparallel structure and antiparallel structure.
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Affiliation(s)
- Young Jun Seo
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea
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40
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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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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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