1
|
Ito Y, Tanaka H, Murakami A, Fuchi Y, Hari Y. Synthesis of fluorescent 5-heteroarylpyrimidine-containing oligonucleotides via post-synthetic trifluoromethyl conversion. Org Biomol Chem 2024; 22:3510-3517. [PMID: 38619422 DOI: 10.1039/d4ob00402g] [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: 04/16/2024]
Abstract
Post-synthetic conversion of the trifluoromethyl group to a heteroaryl group at the C5 position of the pyrimidine base in DNA oligonucleotides was achieved. Specifically, the oligonucleotides containing 5-trifluoromethylpyrimidine bases were treated with o-phenylenediamines and o-aminothiophenols as nucleophiles to afford the corresponding 5-(benzimidazol-2-yl)- and 5-(benzothiazol-2-yl)-pyrimidine-modified bases. Furthermore, evaluation of the fluorescence properties of the obtained oligonucleotides revealed that among them the oligonucleotide containing 5-(5-methylbenzimidazol-2-yl)cytosine exhibited the highest fluorescence intensity. These results indicated that post-synthetic trifluoromethyl conversion, which is practical and operationally simple, is a powerful tool for exploring functional oligonucleotides.
Collapse
Affiliation(s)
- Yuta Ito
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Hisato Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Ayana Murakami
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yasufumi Fuchi
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| | - Yoshiyuki Hari
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Nishihama, Yamashiro-cho, Tokushima 770-8514, Japan.
| |
Collapse
|
2
|
Kumagai T, Kinoshita B, Hirashima S, Sugiyama H, Park S. Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions. ACS Sens 2023; 8:923-932. [PMID: 36740828 DOI: 10.1021/acssensors.2c02617] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (ThexT) and its 2'-O-methyluridine analogue (2'-OMe-ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ThexT and 2'-OMe-ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.
Collapse
Affiliation(s)
- Tomotaka Kumagai
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Ban Kinoshita
- 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
- Immunology Frontier Research Center, Osaka University, Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
3
|
Eyberg J, Ringenberg M, Richert C. Caging of a Strongly Pairing Fluorescent Thymidine Analog with Soft Nucleophiles. Chemistry 2023; 29:e202203289. [PMID: 36395348 PMCID: PMC10107337 DOI: 10.1002/chem.202203289] [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: 10/20/2022] [Revised: 11/15/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022]
Abstract
Controlling the pairing strength of nucleobases in DNA through reactions with compounds found inside the cell is a formidable challenge. Here we report how a thiazolyl substituent turns a strongly pairing ethynylpyridone C-nucleoside into a reactive residue in oligonucleotides. The thiazolyl-bearing pyridone reacts with soft nucleophiles, such as glutathione, but not with hard nucleophiles like hydroxide or carbonate. The addition products pair much more weakly with adenine in a complementary strand than the starting material, and also change their fluorescence. This makes oligonucleotides containing the new deoxynucleoside interesting for controlled release. Due to its reactivity toward N, P, S, and Se-nucleophiles, and the visual signal accompanying chemical conversion, the fluorescent nucleotide reported here may also have applications in chemical biology, sensing and diagnostics.
Collapse
Affiliation(s)
- Juri Eyberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Mark Ringenberg
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clemens Richert
- Institute of Organic Chemistry, University of Stuttgart, 70569, Stuttgart, Germany
| |
Collapse
|
4
|
Ghosh P, Kropp HM, Betz K, Ludmann S, Diederichs K, Marx A, Srivatsan SG. Microenvironment-Sensitive Fluorescent Nucleotide Probes from Benzofuran, Benzothiophene, and Selenophene as Substrates for DNA Polymerases. J Am Chem Soc 2022; 144:10556-10569. [PMID: 35666775 DOI: 10.1021/jacs.2c03454] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA polymerases can process a wide variety of structurally diverse nucleotide substrates, but the molecular basis by which the analogs are processed is not completely understood. Here, we demonstrate the utility of environment-sensitive heterocycle-modified fluorescent nucleotide substrates in probing the incorporation mechanism of DNA polymerases in real time and at the atomic level. The nucleotide analogs containing a selenophene, benzofuran, or benzothiophene moiety at the C5 position of 2'-deoxyuridine are incorporated into oligonucleotides (ONs) with varying efficiency, which depends on the size of the heterocycle modification and the DNA polymerase sequence family used. KlenTaq (A family DNA polymerase) is sensitive to the size of the modification as it incorporates only one heterobicycle-modified nucleotide into the growing polymer, whereas it efficiently incorporates the selenophene-modified nucleotide analog at multiple positions. Notably, in the single nucleotide incorporation assay, irrespective of the heterocycle size, it exclusively adds a single nucleotide at the 3'-end of a primer, which enabled devising a simple two-step site-specific ON labeling technique. KOD and Vent(exo-) DNA polymerases, belonging to the B family, tolerate all the three modified nucleotides and produce ONs with multiple labels. Importantly, the benzofuran-modified nucleotide (BFdUTP) serves as an excellent reporter by providing real-time fluorescence readouts to monitor enzyme activity and estimate the binding events in the catalytic cycle. Further, a direct comparison of the incorporation profiles, fluorescence data, and crystal structure of a ternary complex of KlenTaq DNA polymerase with BFdUTP poised for catalysis provides a detailed understanding of the mechanism of incorporation of heterocycle-modified nucleotides.
Collapse
Affiliation(s)
- Pulak Ghosh
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| | - Heike M Kropp
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Karin Betz
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Samra Ludmann
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Kay Diederichs
- Department of Biology and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry and Konstanz Research School Chemical Biology, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr. Homi Bhabha Road, Pune 411008, India
| |
Collapse
|
5
|
Kumar S, Kumar S, Maity J, Kumar B, Bali Mehta S, Prasad AK. Synthesis and photophysical properties of 5-(3′′-alkyl/aryl-amino-1′′-azaindolizin-2′′-yl)-2′-deoxyuridines. NEW J CHEM 2021. [DOI: 10.1039/d1nj02423j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Groebke–Blackburn–Bienayame (GBB) reaction has been used for the efficient synthesis of novel fluorescent 5-azaindolizino-2′-deoxyuridines starting from commercially available thymidine following two strategies.
Collapse
Affiliation(s)
- Sandeep Kumar
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
| | - Sumit Kumar
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
| | - Jyotirmoy Maity
- Department of Chemistry, St. Stephen's College, University of Delhi, Delhi, India
| | - Banty Kumar
- Department of Chemistry, Rajdhani College, University of Delhi, Delhi, India
| | | | - Ashok K. Prasad
- Department of Chemistry, Bioorganic Laboratory, University of Delhi, Delhi 110007, India
| |
Collapse
|
6
|
George JT, Srivatsan SG. Responsive fluorescent nucleotides serve as efficient substrates to probe terminal uridylyl transferase. Chem Commun (Camb) 2020; 56:12319-12322. [PMID: 32939524 PMCID: PMC7611084 DOI: 10.1039/d0cc05092j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We repurposed a terminal uridylyl transferase enzyme to site-specifically label RNA with microenvironment sensing fluorescent nucleotide mimics, which in turn provided direct read-outs to estimate the binding affinities of the enzyme to RNA and nucleotide substrates. This enzyme-probe system provides insights into the catalytic cycle, and can facilitate the development of discovery platforms to identify robust enzyme inhibitors.
Collapse
Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India.
| | | |
Collapse
|
7
|
Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
Collapse
Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
| |
Collapse
|
8
|
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.![]()
Collapse
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
| |
Collapse
|
9
|
Depaix A, Kowalska J. NAD Analogs in Aid of Chemical Biology and Medicinal Chemistry. Molecules 2019; 24:molecules24224187. [PMID: 31752261 PMCID: PMC6891637 DOI: 10.3390/molecules24224187] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/06/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD) serves as an essential redox co-factor and mediator of multiple biological processes. Besides its well-established role in electron transfer reactions, NAD serves as a substrate for other biotransformations, which, at the molecular level, can be classified as protein post-translational modifications (protein deacylation, mono-, and polyADP-ribosylation) and formation of signaling molecules (e.g., cyclic ADP ribose). These biochemical reactions control many crucial biological processes, such as cellular signaling and recognition, DNA repair and epigenetic modifications, stress response, immune response, aging and senescence, and many others. However, the links between the biological effects and underlying molecular processes are often poorly understood. Moreover, NAD has recently been found to tag the 5′-ends of some cellular RNAs, but the function of these NAD-capped RNAs remains largely unrevealed. Synthetic NAD analogs are invaluable molecular tools to detect, monitor, structurally investigate, and modulate activity of NAD-related enzymes and biological processes in order to aid their deeper understanding. Here, we review the recent advances in the design and development of NAD analogs as probes for various cellular NAD-related enzymes, enzymatic inhibitors with anticancer or antimicrobial therapeutic potential, and other NAD-related chemical biology tools. We focus on research papers published within the last 10 years.
Collapse
|
10
|
Krishna MS, Toh DFK, Meng Z, Ong AAL, Wang Z, Lu Y, Xia K, Prabakaran M, Chen G. Sequence- And Structure-Specific Probing of RNAs by Short Nucleobase-Modified dsRNA-Binding PNAs Incorporating a Fluorescent Light-up Uracil Analog. Anal Chem 2019; 91:5331-5338. [PMID: 30873827 DOI: 10.1021/acs.analchem.9b00280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNAs are emerging as important biomarkers and therapeutic targets. The strategy of directly targeting double-stranded RNA (dsRNA) by triplex-formation is relatively underexplored mainly due to the weak binding at physiological conditions for the traditional triplex-forming oligonucleotides (TFOs). Compared to DNA and RNA, peptide nucleic acids (PNAs) are chemically stable and have a neutral peptide-like backbone, and thus, they show significantly enhanced binding to natural nucleic acids. We have successfully developed nucleobase-modified dsRNA-binding PNAs (dbPNAs) to facilitate structure-specific and selective recognition of dsRNA over single-stranded RNA (ssRNA) and dsDNA regions at near-physiological conditions. The triplex formation strategy facilitates the targeting of not only the sequence but also the secondary structure of RNA. Here, we report the development of novel dbPNA-based fluorescent light-up probes through the incorporation of A-U pair-recognizing 5-benzothiophene uracil (btU). The incorporation of btU into dbPNAs does not affect the binding affinity toward dsRNAs significantly, in most cases, as evidenced by our nondenaturing gel shift assay data. The blue fluorescence emission intensity of btU-modified dbPNAs is sequence- and structure-specifically enhanced by dsRNAs, including the influenza viral RNA panhandle duplex and HIV-1-1 ribosomal frameshift-inducing RNA hairpin, but not ssRNAs or DNAs, at 200 mM NaCl, pH 7.5. Thus, dbPNAs incorporating btU-modified and other further modified fluorescent nucleobases will be useful biochemical tools for probing and detecting RNA structures, interactions, and functions.
Collapse
Affiliation(s)
- Manchugondanahalli S Krishna
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Desiree-Faye Kaixin Toh
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Zhenyu Meng
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Alan Ann Lerk Ong
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Zhenzhang Wang
- Temasek Life Science Laboratory , 1 Research Link, National University of Singapore , 117604 , Singapore
| | - Yunpeng Lu
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Kelin Xia
- Division of Mathematical Sciences, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| | - Mookkan Prabakaran
- Temasek Life Science Laboratory , 1 Research Link, National University of Singapore , 117604 , Singapore
| | - Gang Chen
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences , Nanyang Technological University , 21 Nanyang Link , 637371 , Singapore
| |
Collapse
|
11
|
Le BH, Seo YJ. Transcription of Unnatural Fluorescent Nucleotides and their Application with Graphene Oxide for the Simple and Direct Detection of miRNA. B KOREAN CHEM SOC 2018. [DOI: 10.1002/bkcs.11549] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju 561-756 South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences; Chonbuk National University; Jeonju 561-756 South Korea
- Department of Chemistry; Chonbuk National University; Jeonju 561-756 South Korea
| |
Collapse
|
12
|
Ejlersen M, Lou C, Sanghvi YS, Tor Y, Wengel J. Modification of oligodeoxynucleotides by on-column Suzuki cross-coupling reactions. Chem Commun (Camb) 2018; 54:8003-8006. [PMID: 29967912 DOI: 10.1039/c8cc01360h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The on-column functionalization of oligodeoxynucleotides via base-free Suzuki cross-coupling reactions is reported herein. These cross-coupling reactions were carried out with various boronic acids and either full-length modified oligonucleotides containing one or more 2'-deoxy-5-iodouridine (5IdU) monomer(s) or on oligonucleotide fragments immediately after incorporation of 5IdU. Five different functionalities were coupled to oligonucleotides containing one or three attachment points.
Collapse
Affiliation(s)
- Maria Ejlersen
- Biomolecular Nanoscale Engineering Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.
| | | | | | | | | |
Collapse
|
13
|
Suzol S, Howlader AH, Wen Z, Ren Y, Laverde EE, Garcia C, Liu Y, Wnuk SF. Pyrimidine Nucleosides with a Reactive (β-Chlorovinyl)sulfone or (β-Keto)sulfone Group at the C5 Position, Their Reactions with Nucleophiles and Electrophiles, and Their Polymerase-Catalyzed Incorporation into DNA. ACS OMEGA 2018; 3:4276-4288. [PMID: 29732453 PMCID: PMC5928487 DOI: 10.1021/acsomega.8b00584] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 04/05/2018] [Indexed: 05/28/2023]
Abstract
Transition-metal-catalyzed chlorosulfonylation of 5-ethynylpyrimidine nucleosides provided (E)-5-(β-chlorovinyl)sulfones A, which undergo nucleophilic substitution with amines or thiols affording B. The treatment of vinyl sulfones A with ammonia followed by acid-catalyzed hydrolysis of the intermediary β-sulfonylvinylamines gave 5-(β-keto)sulfones C. The latter reacts with electrophiles, yielding α-carbon-alkylated or -sulfanylated analogues D. The 5'-triphosphates of A and C were incorporated into double-stranded DNA, using open and one-nucleotide gap substrates, by human or Escherichia coli DNA-polymerase-catalyzed reactions.
Collapse
Affiliation(s)
- Sazzad
H. Suzol
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - A. Hasan Howlader
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Zhiwei Wen
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yaou Ren
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Eduardo E. Laverde
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Carol Garcia
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Yuan Liu
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| | - Stanislaw F. Wnuk
- Department
of Chemistry and Biochemistry and Biomolecular Sciences Institute, Florida International University, Miami, Florida 33199, United States
| |
Collapse
|
14
|
Jia X, Zhao J, Xu S, Zhang F, Sun J, Lu R. Luminescent Organogels Generated from Nucleosides Functionalized with Carbazole: Synthesis and Probing for F-. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701728] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xiaoyu Jia
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| | - Jinyu Zhao
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| | - Shenzheng Xu
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| | - Fushuang Zhang
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| | - Jingbo Sun
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| | - Ran Lu
- State Key Laboratory of Supramolecular Structure and Materials; College of Chemistry; Jilin University; 130012 Changchun P. R. China
| |
Collapse
|
15
|
Le BH, Seo YJ. Direct incorporation and extension of a fluorescent nucleotide through rolling circle DNA amplification for the detection of microRNA 24-3P. Bioorg Med Chem Lett 2018; 28:2035-2038. [PMID: 29709251 DOI: 10.1016/j.bmcl.2018.04.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/16/2018] [Accepted: 04/24/2018] [Indexed: 12/27/2022]
Abstract
We designed and synthesized several fluorescent nucleotides from thiophene, anthracene and pyrene, which have different sizes, and screened their incorporation and extension capability during the rolling circle amplification of DNA. The thiophene-based fluorescent nucleotide (dUthioTP) could highly incorporate and extended into the rolling circle DNA product, while other fluorescent nucleotides (dUanthTP, and dUpyrTP) could not. This dUthioTP fluorescent nucleotide could be used for the detection of miRNA 24-3P, which is related PRRSV. This direct labeling system during rolling circle DNA amplification exhibited an increased fluorescence signal showing gel formation for the detection of miRNA 24-3P. This direct labeling system is a very simple and cost-efficient method for the detection miRNA 24-3P and also exhibited highly sensitive and selective detection properties.
Collapse
Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Research Center of Bioactive Materials Chonbuk National University, Jeonju 561-756, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 561-756, South Korea.
| |
Collapse
|
16
|
Sabale PM, Ambi UB, Srivatsan SG. A Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. Chembiochem 2018; 19:826-835. [PMID: 29396904 PMCID: PMC5972818 DOI: 10.1002/cbic.201700661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.
Collapse
Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
17
|
Fluorescent nucleobases as tools for studying DNA and RNA. Nat Chem 2017; 9:1043-1055. [PMID: 29064490 DOI: 10.1038/nchem.2859] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023]
Abstract
Understanding the diversity of dynamic structures and functions of DNA and RNA in biology requires tools that can selectively and intimately probe these biomolecules. Synthetic fluorescent nucleobases that can be incorporated into nucleic acids alongside their natural counterparts have emerged as a powerful class of molecular reporters of location and environment. They are enabling new basic insights into DNA and RNA, and are facilitating a broad range of new technologies with chemical, biological and biomedical applications. In this Review, we will present a brief history of the development of fluorescent nucleobases and explore their utility as tools for addressing questions in biophysics, biochemistry and biology of nucleic acids. We provide chemical insights into the two main classes of these compounds: canonical and non-canonical nucleobases. A point-by-point discussion of the advantages and disadvantages of both types of fluorescent nucleobases is made, along with a perspective into the future challenges and outlook for this burgeoning field.
Collapse
|
18
|
Manna S, Panse CH, Sontakke VA, Sangamesh S, Srivatsan SG. Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes. Chembiochem 2017; 18:1604-1615. [PMID: 28569423 PMCID: PMC5724660 DOI: 10.1002/cbic.201700283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 01/03/2023]
Abstract
The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential.
Collapse
Affiliation(s)
- Sudeshna Manna
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Cornelia H. Panse
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Vyankat A. Sontakke
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Sarangamath Sangamesh
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Seergazhi G. Srivatsan
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| |
Collapse
|
19
|
Synthesis of two 6-aza-uridines modified by benzoheterocycle as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2017. [DOI: 10.1016/j.tetlet.2017.05.087] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
20
|
Le BH, Koo JC, Joo HN, Seo YJ. Diverse size approach to incorporate and extend highly fluorescent unnatural nucleotides into DNA. Bioorg Med Chem 2017; 25:3591-3596. [PMID: 28501432 DOI: 10.1016/j.bmc.2017.03.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 03/17/2017] [Accepted: 03/21/2017] [Indexed: 11/28/2022]
Abstract
We have prepared a series of size-diverse unnatural nucleotides containing fluorescent (dApyrTP, dUpyrTP, dUantTP, dUthiTP) and quencher (dUazoTP) units, as well as nucleotides presenting small functional groups (dAethTP, dAoctTP, dUethTP, dUiodTP), all based on deoxyadenosine and deoxyuridine, and examined their suitability for use in enzymatic incorporation and extension into DNA. We observed a size-dependence of the incorporation and extension capability (following the order dUiodTP=dUethTP=dUthiTP>dUazoTP>dUpyrTP>dUantTP) during primer extension. This result was supported by circular dichroism (CD) spectra, which revealed a trend in the different B-form DNA structures depending on the size of the unit at the 5-position of the deoxyuridine (dUiodTP>dUethTP>dUthiTP>dUpyrTP), obtained from the PCR products. Interestingly, dUthiTP could be incorporated and extended into long DNA strands during primer extension and even PCR amplification, with CD spectroscopy confirming a stable secondary B-form duplex DNA structure. We observed full-length extension products even when combining dUthiTP with a template containing 24 continuous dA units during the primer extension. Thus, we believe that dUthiTP is a promising fluorescent nucleotide for a diverse range of biological applications requiring multiple incorporation and extension directly without disruption of B-form DNA structures.
Collapse
Affiliation(s)
- Binh Huy Le
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju 54896, South Korea
| | - Ja Choon Koo
- Division of Science Education and Institute of Fusion Science, Chonbuk National University, Jeonju 54896, South Korea
| | - Han Na Joo
- Department of Chemistry, Chonbuk National University, Jeonju 54896, South Korea
| | - Young Jun Seo
- Department of Bioactive Material Sciences, Chonbuk National University, Jeonju 54896, South Korea; Department of Chemistry, Chonbuk National University, Jeonju 54896, South Korea.
| |
Collapse
|
21
|
Wen Z, Suzol SH, Peng J, Liang Y, Snoeck R, Andrei G, Liekens S, Wnuk SF. Antiviral and Cytostatic Evaluation of 5-(1-Halo-2-sulfonylvinyl)- and 5-(2-Furyl)uracil Nucleosides. Arch Pharm (Weinheim) 2017; 350. [DOI: 10.1002/ardp.201700023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 02/23/2017] [Accepted: 02/27/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Zhiwei Wen
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Sazzad H. Suzol
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Jufang Peng
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Yong Liang
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| | - Robert Snoeck
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Graciela Andrei
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Sandra Liekens
- Rega Institute for Medical Research; KU Leuven; Leuven Belgium
| | - Stanislaw F. Wnuk
- Department of Chemistry and Biochemistry; Florida International University; Miami FL USA
| |
Collapse
|
22
|
Okamura I, Park S, Hiraga R, Yamamoto S, Sugiyama H. Synthesis, Photophysical Properties, and Enzymatic Incorporation of an Emissive Thymidine Analogue. CHEM LETT 2017. [DOI: 10.1246/cl.161024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
23
|
Nguyen JC, Dzowo YK, Wolfbrandt C, Townsend J, Kukatin S, Wang H, Resendiz MJE. Synthesis, Thermal Stability, Biophysical Properties, and Molecular Modeling of Oligonucleotides of RNA Containing 2'-O-2-Thiophenylmethyl Groups. J Org Chem 2016; 81:8947-8958. [PMID: 27584708 DOI: 10.1021/acs.joc.6b01615] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Dodecamers of RNA [CUACGGAAUCAU] were functionalized with C2'-O-2-thiophenylmethyl groups to obtain oligonucleotides 10-14 and 17. The modified nucleotides were incorporated into RNA strands via solid-phase synthesis. The biophysical properties of these ONs were used to quantify the effects of this modification on RNA:RNA and RNA:DNA duplexes. A combination of UV-vis and circular dichroism were used to determine thermal stabilities of all strands, which hybridized into A-form geometries. Destabilization of the double stranded RNA was measured as a function of number of consecutive modifications, reflected in decreased thermal denaturation values (ΔTm, ca. 2.5-11.5 °C). Van't Hoff plots on a duplex containing one modification (10:15) displayed a ca. ΔΔG° of +4 kcal/mol with respect to its canonical analogue. Interestingly, hybridization of two modified strands (13:17, containing a total of eight modifications) resulted in increased stability and a distinct secondary structure, reflected in its CD spectrum. Molecular modeling based on DFT calculations shed light on the nature of this stability, with induced changes in the torsional angle δ (C5'-C4'-C3'-O3) and phosphate-phosphate distances that are in agreement with a compacted structure. The described synthetic methodology and structural information will be useful in the design of thermodynamically stable structures containing chemically reactive modifications.
Collapse
Affiliation(s)
- Joseph C Nguyen
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Yannick Kokouvi Dzowo
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Carly Wolfbrandt
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Justin Townsend
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Stanislav Kukatin
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Haobin Wang
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| | - Marino J E Resendiz
- Department of Chemistry, University of Colorado Denver , Science Building 1151 Arapahoe Street, Denver, Colorado 80204, United States
| |
Collapse
|
24
|
Sabale PM, Srivatsan SG. Responsive Fluorescent PNA Analogue as a Tool for Detecting G-quadruplex Motifs of Oncogenes and Activity of Toxic Ribosome-Inactivating Proteins. Chembiochem 2016; 17:1665-73. [PMID: 27271025 DOI: 10.1002/cbic.201600192] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Indexed: 12/13/2022]
Abstract
Fluorescent oligomers that are resistant to enzymatic degradation and report their binding to target oligonucleotides (ONs) by changes in fluorescence properties are highly useful in developing nucleic-acid-based diagnostic tools and therapeutic strategies. Here, we describe the synthesis and photophysical characterization of fluorescent peptide nucleic acid (PNA) building blocks made of microenvironment-sensitive 5-(benzofuran-2-yl)- and 5-(benzothiophen-2-yl)-uracil cores. The emissive monomers, when incorporated into PNA oligomers and hybridized to complementary ONs, are minimally perturbing and are highly sensitive to their neighboring base environment. In particular, benzothiophene-modified PNA reports the hybridization process with significant enhancement in fluorescence intensity, even when placed in the vicinity of guanine residues, which often quench fluorescence. This feature was used in the turn-on detection of G-quadruplex-forming promoter DNA sequences of human proto-oncogenes (c-myc and c-kit). Furthermore, the ability of benzothiophene-modified PNA oligomer to report the presence of an abasic site in RNA enabled us to develop a simple fluorescence hybridization assay to detect and estimate the depurination activity of ribosome-inactivating protein toxins. Our results demonstrate that this approach with responsive PNA probes will provide new opportunities to develop robust tools to study nucleic acids.
Collapse
Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India.
| |
Collapse
|
25
|
2-aminopurine as a fluorescent probe of DNA conformation and the DNA–enzyme interface. Q Rev Biophys 2015; 48:244-79. [DOI: 10.1017/s0033583514000158] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNearly 50 years since its potential as a fluorescent base analogue was first recognized, 2-aminopurine (2AP) continues to be the most widely used fluorescent probe of DNA structure and the perturbation of that structure by interaction with enzymes and other molecules. In this review, we begin by considering the origin of the dramatic and intriguing difference in photophysical properties between 2AP and its structural isomer, adenine; although 2AP differs from the natural base only in the position of the exocyclic amine group, its fluorescence intensity is one thousand times greater. We then discuss the mechanism of interbase quenching of 2AP fluorescence in DNA, which is the basis of its use as a conformational probe but remains imperfectly understood. There are hundreds of examples in the literature of the use of changes in the fluorescence intensity of 2AP as the basis of assays of conformational change; however, in this review we will consider in detail only a few intensity-based studies. Our primary aim is to highlight the use of time-resolved fluorescence measurements, and the interpretation of fluorescence decay parameters, to explore the structure and dynamics of DNA. We discuss the salient features of the fluorescence decay of 2AP when incorporated in DNA and review the use of decay measurements in studying duplexes, single strands and other structures. We survey the use of 2AP as a probe of DNA-enzyme interaction and enzyme-induced distortion, focusing particularly on its use to study base flipping and the enhanced mechanistic insights that can be gained by a detailed analysis of the decay parameters, rather than merely monitoring changes in fluorescence intensity. Finally we reflect on the merits and shortcomings of 2AP and the prospects for its wider adoption as a fluorescence-decay-based probe.
Collapse
|
26
|
Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
Collapse
Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Zhang LM, Guo LE, Li XM, Shi YG, Wu GF, Xie XG, Zhou Y, Zhao QH, Zhang JF. 1,8-Naphthalimide-based colorimetric and fluorescent sensor for recognition of GMP, TMP, and UMP and its application in in vivo imaging. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.09.074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
28
|
Isaac K, Stemper J, Retailleau P, Betzer JF, Marinetti A. Chiral Synthetic Equivalents of 2-Cyanoethyl Tetraisopropylphosphorodiamidite: Application to the Synthesis and Resolution of Chiral Phosphoric Acids. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402203] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
29
|
Liang Y, Gloudeman J, Wnuk SF. Palladium-catalyzed direct arylation of 5-halouracils and 5-halouracil nucleosides with arenes and heteroarenes promoted by TBAF. J Org Chem 2014; 79:4094-103. [PMID: 24724921 PMCID: PMC4011569 DOI: 10.1021/jo500602p] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
The
1-N-benzyl-5-iodo(or bromo)uracil undergoes
Pd-catalyzed [Pd2(dba)3] direct arylation with
benzene and other simple arenes in the presence of TBAF in DMF without
the necessity of adding any ligands or additives to give 5-arylated
uracil analogues. The TBAF-promoted coupling also occurs efficiently
with electron rich heteroarenes at 100 °C (1 h) even with only
small excess of heteroarenes. The protocol avoids usage of the arylboronic
acid or stannane precursors for the synthesis of 5-(2-furyl, or 2-thienyl,
or 2-pyrrolyl)uracil nucleosides, which are used as important RNA
and DNA fluorescent probes. The fact that 1-N-benzyl-3-N-methyl-5-iodouracil did not undergo the TBAF-promoted
couplings with arenes or heteroarenes suggests that the C4-alkoxide
(enol form of uracil) facilitates coupling by participation in the
intramolecular processes of hydrogen abstraction from arenes. TBAF-promoted
arylation was extended into the other enolizable heterocyclic systems
such as 3-bromo-2-pyridone. The π-excessive heteroarenes also
coupled with 5-halouracils in the presence of Pd(OAc)2/Cs2CO3/PivOH combination in DMF (100 °C, 2 h)
to yield 5-arylated uracils.
Collapse
Affiliation(s)
- Yong Liang
- Department of Chemistry and Biochemistry, Florida International University , Miami, Florida 33199, United States
| | | | | |
Collapse
|