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Jestřábová I, Poštová Slavětínská L, Hocek M. Arylethynyl- or Alkynyl-Linked Pyrimidine and 7-Deazapurine 2'-Deoxyribonucleoside 3'-Phosphoramidites for Chemical Synthesis of Hypermodified Hydrophobic Oligonucleotides. ACS OMEGA 2023; 8:39447-39453. [PMID: 37901526 PMCID: PMC10601081 DOI: 10.1021/acsomega.3c05202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
Abstract
We designed and synthesized a set of 2'-deoxyribonucleoside 3'-phosphoramidites derived from 5-phenylethynyluracil, 5-(pentyn-1-yl)cytosine, 7-(indol-3-yl)ethynyl-7-deazaadenine, and 7-isopropylethynyl-7-deazaguanine. These nucleoside phosphoramidites were successfully used for automated solid-phase synthesis of oligonucleotides containing one or several modifications, including fully modified sequences where every nucleobase was displaying a modification, and their hybridization was studied. The phosphoramidite building blocks have potential for synthesis of hypermodified aptamers and other functional nucleic acid-based polymers, which sequence-specifically display amino acid-like hydrophobic substituents.
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Affiliation(s)
- Ivana Jestřábová
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Lenka Poštová Slavětínská
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry, Czech
Academy of Sciences, Flemingovo nam. 2, CZ-16000 Prague 6, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, CZ-12843 Prague 2, Czech Republic
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2
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Nonoshita D, Kashihara W, Tanabe K, Isozaki T, Xu YZ, Suzuki T. Excited States of Thio-2'-deoxyuridine Bearing an Extended π-Conjugated System: 3',5'-Di- O-acetyl-5-phenylethynyl-4-thio-2'-deoxyuridine. J Phys Chem A 2021; 125:597-606. [PMID: 33307688 DOI: 10.1021/acs.jpca.0c09343] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A new thio-2'-deoxyuridine with an extended π-conjugated group was successfully synthesized: 3',5'-di-O-acetyl-5-phenylethynyl-4-thio-2'-deoxyuridine. The thio-2'-deoxyuridine derivative has a large red-shifted absorption band in the UVA region and also shows fluorescence, a rare photo-property among thionucleobases/thionucleosides. The triplet-triplet absorption spectrum and the rate constants (the intrinsic decay rate constant of the triplet state, the self-quenching rate constant, and the quenching rate constant of the triplet state by an oxygen molecule) of the thio-2'-deoxyuridine were obtained by transient absorption spectroscopy. The quantum yield of intersystem crossing and the quantum yield of singlet molecular oxygen formation (ϕΔ) under an oxygen atmosphere were also determined. The ϕΔ value of the new thio-2'-deoxyuridine was found to be substantially higher than all reported values of other thio-2'-deoxyribonucleosides in low oxygen concentrations similar to cancer cell environments. The fluorescence quantum yield depended on the excitation wavelength, revealing certain photochemical reactions in the higher excited singlet states. However, when excited into the higher excited state with non-resonant two-photon absorption, the ϕΔ of the thio-2'-deoxyuridine derivative was found to remain sufficiently large. These findings should be very useful for the development of thio-2'-deoxyribonucleoside-based pharmaceuticals as DNA-specific photosensitizers for photochemotherapy.
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Affiliation(s)
- Daiki Nonoshita
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Wataru Kashihara
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Kazuhito Tanabe
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Tasuku Isozaki
- Division of Natural Sciences, College of Arts and Sciences, J. F. Oberlin University, Tokiwa-machi, Machida 194-0294, Tokyo, Japan
| | - Yao Zhong Xu
- School of Life, Health and Chemical Sciences, The Open University, Keynes MK7 6AA, U.K
| | - Tadashi Suzuki
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
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3
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Müller S, Fritz Y, Wagenknecht H. Control of Energy Transfer Between Pyrene- and Perylene-Nucleosides by the Sequence of DNA-Templated Supramolecular Assemblies. ChemistryOpen 2020; 9:389-392. [PMID: 32257746 PMCID: PMC7110160 DOI: 10.1002/open.201900346] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/09/2020] [Indexed: 12/18/2022] Open
Abstract
DNA was used as supramolecular scaffold to order chromophores and control their optical properties. Ethynylpyrene as energy donor was attached to 2'-desoxy-2-aminoadenosine that binds selectively to thymidines (T) in the template. Ethynylperylene as acceptor was attached to 2'-desoxyuridine that is complementary to 2'-desoxyadenosine (A). This donor-acceptor pair was assembled along single-stranded DNA templates of different A-T sequences to investigate the sequence control of the energy transfer between the chromophores. The fluorescence intensities increase in the mixed assemblies along the DNA templates from A10T10 over (AATT)5 to (AT)10, although these templates provide equal numbers of potential binding sites for the two different nucleoside chromophore conjugates and exhibit similar absorbances. This shows that the sequence selective assembly of the two building blocks along DNA templates is programmable and alters the fluorescence readout. Such sequence-controlled supramolecular chemistry represents the key element for future functional π-systems in materials for light harvesting of solar energy.
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Affiliation(s)
- Sara Müller
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Yannic Fritz
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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4
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Hofsäβ R, Ensslen P, Wagenknecht HA. Control of helical chirality in supramolecular chromophore-DNA architectures. Chem Commun (Camb) 2019; 55:1330-1333. [PMID: 30638231 DOI: 10.1039/c8cc08887j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Four different d- and l-configured chromophore-2'-deoxyuridine conjugates were applied to elucidate the helical chirality of their non-covalent assemblies along the d- and l-configured DNA templates by optical spectroscopy. There is no configuration-selective recognition between these nucleosides and the DNA templates. The helicity of the DNA assemblies is either controlled by the configuration of the DNA template or by the nucleoside configuration.
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Affiliation(s)
- Robert Hofsäβ
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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5
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Hofsäß R, Sinn S, Biedermann F, Wagenknecht HA. Programmable and Sequence-Selective Supramolecular Assembly of Two Different Chromophores along DNA Templates. Chemistry 2018; 24:16257-16261. [DOI: 10.1002/chem.201804314] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Robert Hofsäß
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan Sinn
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Frank Biedermann
- Institute of Nanotechnology; Karlsruhe Institute of Technology (KIT); Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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6
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Substitution of Metallocenes with [2.2]Paracyclophane to Enable Confocal Microscopy Imaging in Living Cells. Eur J Inorg Chem 2016. [DOI: 10.1002/ejic.201600281] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. A DNA-Fullerene Conjugate as a Template for Supramolecular Chromophore Assemblies: Towards DNA-Based Solar Cells. Angew Chem Int Ed Engl 2015; 55:1904-8. [DOI: 10.1002/anie.201509332] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/23/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Germany
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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8
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Ensslen P, Gärtner S, Glaser K, Colsmann A, Wagenknecht HA. Ein DNA-Fulleren-Konjugat als Templat für supramolekulare Chromophorstapel: Auf dem Weg zu DNA-basierten Solarzellen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201509332] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Philipp Ensslen
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
| | - Stefan Gärtner
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Konstantin Glaser
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Alexander Colsmann
- Lichttechnisches Institut; Karlsruher Institut für Technologie (KIT); Engesserstrasse 13 76131 Karlsruhe Deutschland
| | - Hans-Achim Wagenknecht
- Institut für Organische Chemie; Karlsruher Institut für Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Deutschland
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9
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Ensslen P, Wagenknecht HA. One-Dimensional Multichromophor Arrays Based on DNA: From Self-Assembly to Light-Harvesting. Acc Chem Res 2015; 48:2724-33. [PMID: 26411920 DOI: 10.1021/acs.accounts.5b00314] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Light-harvesting complexes collect light energy and deliver it by a cascade of energy and electron transfer processes to the reaction center where charge separation leads to storage as chemical energy. The design of artificial light-harvesting assemblies faces enormous challenges because several antenna chromophores need to be kept in close proximity but self-quenching needs to be avoided. Double stranded DNA as a supramolecular scaffold plays a promising role due to its characteristic structural properties. Automated DNA synthesis allows incorporation of artificial chromophore-modified building blocks, and sequence design allows precise control of the distances and orientations between the chromophores. The helical twist between the chromophores, which is induced by the DNA framework, controls energy and electron transfer and thereby reduces the self-quenching that is typically observed in chromophore aggregates. This Account summarizes covalently multichromophore-modified DNA and describes how such multichromophore arrays were achieved by Watson-Crick-specific and DNA-templated self-assembly. The covalent DNA systems were prepared by incorporation of chromophores as DNA base substitutions (either as C-nucleosides or with acyclic linkers as substitutes for the 2'-deoxyribofuranoside) and as DNA base modifications. Studies with DNA base substitutions revealed that distances but more importantly relative orientations of the chromophores govern the energy transfer efficiencies and thereby the light-harvesting properties. With DNA base substitutions, duplex stabilization was faced and could be overcome, for instance, by zipper-like placement of the chromophores in both strands. For both principal structural approaches, DNA-based light-harvesting antenna could be realized. The major disadvantages, however, for covalent multichromophore DNA conjugates are the poor yields of synthesis and the solubility issues for oligonucleotides with more than 5-10 chromophore modifications in a row. A logical alternative approach is to leave out the phosphodiester bridges between the chromophores and let chromophore-nucleoside conjugates self-assemble specifically along single stranded DNA as template. The self-organization of chromophores along the DNA template based on canonical base pairing would be advantageous because sequence selective base pairing could provide a structural basis for programmed complexity within the chromophore assembly. The self-assembly is governed by two interactions. The chromophore-nucleoside conjugates as guest molecules are recognized via hydrogen bonds to the corresponding counter bases in the single stranded DNA template. Moreover, the π-π interactions between the stacked chromophores stabilize these self-assembled constructs with increasing length. Longer DNA templates are more attractive for self-assembled antenna. The helicity in the stack of porphyrins as guest molecules assembled on the DNA template can be switched by environmental changes, such as pH variations. DNA-templated stacks of ethynyl pyrene and nile red exhibit left-handed chirality, which stands in contrast to similar covalent multichromophore-DNA conjugates with enforced right-handed helicity. With ethynyl nile red, it is possible to occupy every available binding site on the templates. Mixed assemblies of ethynyl pyrene and nile red show energy transfer and thereby provide a proof-of-principle that simple light-harvesting antennae can be obtained in a noncovalent and self-assembled fashion. With respect to the next important step, chemical storage of the absorbed light energy, future research has to focus on the coupling of sophisticated DNA-based light-harvesting antenna to reaction centers.
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Affiliation(s)
- Philipp Ensslen
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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10
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Stadler JM, Stafforst T. Pyrene chromophores for the photoreversal of psoralen interstrand crosslinks. Org Biomol Chem 2015; 12:5260-6. [PMID: 24922335 DOI: 10.1039/c4ob00603h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Applying psoralen interstrand crosslinks for the photoactivation of nucleic acids is a new concept. To find chromophores that can efficiently stimulate crosslink repair we screened several pyrenes and appended them to peptide nucleic acids for their site-selective addressing. Even though pyrenes conjugated to uracil revealed desirable spectroscopic properties they were not effective in crosslink reversal. In contrast, bare pyrenes are well suitable for crosslink repair with 350 nm light showing an uncaging efficiency similar to classical photocaging groups.
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Affiliation(s)
- Jens M Stadler
- Interfaculty Institute of Biochemistry, Auf der Morgenstelle 15. and University of Tübingen, 72076 Tübingen, Germany.
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11
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Tasaki S, Momotake A, Kanna Y, Sato T, Nishimura Y, Arai T. Producing a dual-fluorescent molecule by tuning the energetics of excited-state intramolecular proton transfer. Photochem Photobiol Sci 2015. [PMID: 26219627 DOI: 10.1039/c5pp00088b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We report herein the selective preparation of normal, tautomeric, and dual-fluorescent molecules with a common ESIPT core.
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Affiliation(s)
- Satomi Tasaki
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Atsuya Momotake
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoko Kanna
- Faculty of Science
- University of the Ryukyus
- Nishihara
- Japan
| | - Tomoo Sato
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Yoshinobu Nishimura
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
| | - Tatsuo Arai
- Graduate School of Pure and Applied Sciences
- University of Tsukuba
- Tsukuba
- Japan
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12
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Ensslen P, Fritz Y, Wagenknecht HA. Mixed non-covalent assemblies of ethynyl nile red and ethynyl pyrene along oligonucleotide templates. Org Biomol Chem 2014; 13:487-92. [PMID: 25374296 DOI: 10.1039/c4ob01860e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Ethynyl pyrene and ethynyl nile red as modifications at the 5-position of 2'-deoxyuridines self-assemble non-covalently and specifically along oligo-2'-deoxyadenosines as templates. Oligo-2'-deoxyadenosines of the lengths (dA)10-(dA)20 are able to retain nearly exactly as many ethynyl nile red units in solution as binding sites are available on these templates. In contrast, in the presence of oligo-2'-thymidines the ethynyl nile red moieties are similarly insoluble to those in the absence of any oligonucleotide and yield an aggregate. The mixed assemblies of both chromophores are highly ordered, show left-handed chirality and yield dual fluorescence. The strong excitonic coupling indicates assemblies with a high degree of order. These results show that DNA represents an important supramolecular scaffold for the templated, helical and non-covalent arrangement not only for one type of chromophore but also for mixtures of two different chromophores.
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Affiliation(s)
- Philipp Ensslen
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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13
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Kumar P, Baral B, Anderson BA, Guenther DC, Østergaard ME, Sharma PK, Hrdlicka PJ. C5-alkynyl-functionalized α-L-LNA: synthesis, thermal denaturation experiments and enzymatic stability. J Org Chem 2014; 79:5062-73. [PMID: 24797769 PMCID: PMC4049248 DOI: 10.1021/jo5006153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 12/23/2022]
Abstract
Major efforts are currently being devoted to improving the binding affinity, target specificity, and enzymatic stability of oligonucleotides used for nucleic acid targeting applications in molecular biology, biotechnology, and medicinal chemistry. One of the most popular strategies toward this end has been to introduce additional modifications to the sugar ring of affinity-inducing conformationally restricted nucleotide building blocks such as locked nucleic acid (LNA). In the preceding article in this issue, we introduced a different strategy toward this end, i.e., C5-functionalization of LNA uridines. In the present article, we extend this strategy to α-L-LNA: i.e., one of the most interesting diastereomers of LNA. α-L-LNA uridine monomers that are conjugated to small C5-alkynyl substituents induce significant improvements in target affinity, binding specificity, and enzymatic stability relative to conventional α-L-LNA. The results from the back-to-back articles therefore suggest that C5-functionalization of pyrimidines is a general and synthetically straightforward approach to modulate biophysical properties of oligonucleotides modified with LNA or other conformationally restricted monomers.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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Kumar P, Østergaard ME, Baral B, Anderson BA, Guenther DC, Kaura M, Raible DJ, Sharma PK, Hrdlicka PJ. Synthesis and biophysical properties of C5-functionalized LNA (locked nucleic acid). J Org Chem 2014; 79:5047-61. [PMID: 24825249 PMCID: PMC4049237 DOI: 10.1021/jo500614a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2014] [Indexed: 01/07/2023]
Abstract
Oligonucleotides modified with conformationally restricted nucleotides such as locked nucleic acid (LNA) monomers are used extensively in molecular biology and medicinal chemistry to modulate gene expression at the RNA level. Major efforts have been devoted to the design of LNA derivatives that induce even higher binding affinity and specificity, greater enzymatic stability, and more desirable pharmacokinetic profiles. Most of this work has focused on modifications of LNA's oxymethylene bridge. Here, we describe an alternative approach for modulation of the properties of LNA: i.e., through functionalization of LNA nucleobases. Twelve structurally diverse C5-functionalized LNA uridine (U) phosphoramidites were synthesized and incorporated into oligodeoxyribonucleotides (ONs), which were then characterized with respect to thermal denaturation, enzymatic stability, and fluorescence properties. ONs modified with monomers that are conjugated to small alkynes display significantly improved target affinity, binding specificity, and protection against 3'-exonucleases relative to regular LNA. In contrast, ONs modified with monomers that are conjugated to bulky hydrophobic alkynes display lower target affinity yet much greater 3'-exonuclease resistance. ONs modified with C5-fluorophore-functionalized LNA-U monomers enable fluorescent discrimination of targets with single nucleotide polymorphisms (SNPs). In concert, these properties render C5-functionalized LNA as a promising class of building blocks for RNA-targeting applications and nucleic acid diagnostics.
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Affiliation(s)
- Pawan Kumar
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Michael E. Østergaard
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Bharat Baral
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Brooke A. Anderson
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Dale C. Guenther
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Mamta Kaura
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Daniel J. Raible
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
| | - Pawan K. Sharma
- Department of Chemistry, Kurukshetra University, Kurukshetra 136119, India
| | - Patrick J. Hrdlicka
- Department of Chemistry, University of Idaho, Moscow, Idaho 83844-2343, United States
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15
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Synthesis and characterization of a fluorescent adenosine derivative for detection of intermolecular RNA G-quadruplexes. Tetrahedron Lett 2014. [DOI: 10.1016/j.tetlet.2014.01.048] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Abstract
Formation of the so far elusive chrysene excimer in solution is achieved by using DNA as a supramolecular scaffold.
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Affiliation(s)
- Oleg Khorev
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Caroline D. Bösch
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Markus Probst
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry and Biochemistry
- University of Bern
- CH-3012 Bern, Switzerland
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17
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Pyrene and bis-pyrene DNA nucleobase conjugates: excimer and monomer fluorescence of linear and dendronized cytosine and 7-deazaguanine click adducts. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.03.054] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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18
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Kaura M, Kumar P, Hrdlicka PJ. Synthesis and hybridization properties of oligonucleotides modified with 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridines. Org Biomol Chem 2013; 10:8575-8. [PMID: 23042241 DOI: 10.1039/c2ob26717a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Oligonucleotides modified with consecutive incorporations of 5-(1-aryl-1,2,3-triazol-4-yl)-2'-deoxyuridine monomers display strong thermal affinity and binding specificity toward RNA targets, due to formation of chromophore arrays in the major groove.
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Affiliation(s)
- Mamta Kaura
- Department of Chemistry, University of Idaho, PO Box 442343, Moscow, ID 83844-2343, USA
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19
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Sezi S, Wagenknecht HA. DNA-templated formation of fluorescent self-assembly of ethynyl pyrenes. Chem Commun (Camb) 2013; 49:9257-9. [DOI: 10.1039/c3cc44733b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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20
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Tanaka M, Oguma K, Saito Y, Saito I. Enhancement of fluorescence quenching and exciplex formation in DNA major groove by double incorporation of modified fluorescent deoxyuridines. Bioorg Med Chem Lett 2012; 22:4103-5. [PMID: 22578464 DOI: 10.1016/j.bmcl.2012.04.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/07/2012] [Accepted: 04/13/2012] [Indexed: 12/30/2022]
Abstract
5-(1-Naphthalenylethynyl)-2'-deoxyuridine ((N)U) and 5-[(4-cyano-1-naphthalenyl)ethynyl]-2'-deoxyuridine ((CN)U) were synthesized and incorporated into oligodeoxynucleotides. Fluorescence emissions of modified duplexes containing double (N)U were efficiently quenched depending upon the sequence pattern of the naphthalenes in DNA major groove, as compared to the duplex possessing single (N)U. When one of the naphthalene moieties has a cyano substituent, the exciplex emission from the chromophores in DNA major groove was observed at longer wavelength.
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Affiliation(s)
- Makiko Tanaka
- Department of Chemical Biology and Applied Chemistry, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan
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21
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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22
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Tanaka M, Kozakai R, Saito Y, Saito I. Stabilization of DNA duplex by 2-substituted adenine as a minor groove modifier. Bioorg Med Chem Lett 2011; 21:7021-4. [DOI: 10.1016/j.bmcl.2011.09.104] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 09/24/2011] [Accepted: 09/27/2011] [Indexed: 01/07/2023]
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23
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Østergaard ME, Hrdlicka PJ. Pyrene-functionalized oligonucleotides and locked nucleic acids (LNAs): tools for fundamental research, diagnostics, and nanotechnology. Chem Soc Rev 2011; 40:5771-88. [PMID: 21487621 PMCID: PMC3644995 DOI: 10.1039/c1cs15014f] [Citation(s) in RCA: 202] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Pyrene-functionalized oligonucleotides (PFOs) are increasingly explored as tools in fundamental research, diagnostics and nanotechnology. Their popularity is linked to the ability of pyrenes to function as polarity-sensitive and quenchable fluorophores, excimer-generating units, aromatic stacking moieties and nucleic acid duplex intercalators. These characteristics have enabled development of PFOs for detection of complementary DNA/RNA targets, discrimination of single nucleotide polymorphisms (SNPs), and generation of π-arrays on nucleic acid scaffolds. This critical review will highlight the physical properties and applications of PFOs that are likely to provide high degree of positional control of the chromophore in nucleic acid complexes. Particular emphasis will be placed on pyrene-functionalized Locked Nucleic Acids (LNAs) since these materials display interesting properties such as fluorescence quantum yields approaching unity and recognition of mixed-sequence double stranded DNA (144 references).
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24
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Dick B. Circular Dichroism of a Finite Number of Identical Chromophores in a Helical Arrangement. Chemphyschem 2011; 12:1578-87. [DOI: 10.1002/cphc.201000949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2010] [Indexed: 11/11/2022]
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25
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Brewer A, Siligardi G, Neylon C, Stulz E. Introducing structural flexibility into porphyrin-DNA zipper arrays. Org Biomol Chem 2010; 9:777-82. [PMID: 21103551 DOI: 10.1039/c0ob00535e] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).
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Affiliation(s)
- Ashley Brewer
- School of Chemistry, University of Southampton, Highfield, Southampton, UK SO17 1BJ
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26
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Omumi A, Beach DG, Baker M, Gabryelski W, Manderville RA. Postsynthetic guanine arylation of DNA by Suzuki-Miyaura cross-coupling. J Am Chem Soc 2010; 133:42-50. [PMID: 21067186 DOI: 10.1021/ja106158b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Direct radical addition reactions at the C(8)-site of 2'-deoxyguanosine (dG) can afford C(8)-Ar-dG adducts that are produced by carcinogenic arylhydrazines, polycyclic aromatic hydrocarbons, and certain phenolic toxins. Such modified nucleobases are also highly fluorescent for sensing applications and possess useful electron transfer properties. The site-specific synthesis of oligonucleotides containing the C(8)-Ar-G adduct can be problematic. These lesions are sensitive to acids and oxidants that are commonly used in solid-phase DNA synthesis and are too bulky to be accepted as substrates for enzymatic synthesis by DNA polymerases. Using the Suzuki-Miyaura cross-coupling reaction, we have synthesized a number of C(8)-Ar-G-modified oligonucleotides (dimers, trimers, decamers, and a 15-mer) using a range of arylboronic acids. Good to excellent yields were obtained, and the reaction is insensitive to the nature of the bases flanking the convertible 8-Br-G nucleobase, as both pyrimidines and purines are tolerated. The impact of the C(8)-Ar-G lesion was also characterized by electrospray ionization tandem mass spectrometry, UV melting temperature analysis, circular dichroism, and fluorescence spectroscopy. The C(8)-Ar-G-modified oligonucleotides are expected to be useful substrates for diagnostic applications and understanding the biological impact of the C(8)-Ar-G lesion.
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Affiliation(s)
- Alireza Omumi
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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27
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Bandy TJ, Brewer A, Burns JR, Marth G, Nguyen T, Stulz E. DNA as supramolecular scaffold for functional molecules: progress in DNA nanotechnology. Chem Soc Rev 2010; 40:138-48. [PMID: 20694258 DOI: 10.1039/b820255a] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.
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Affiliation(s)
- Thomas J Bandy
- University of Southampton, School of Chemistry, Highfield, Southampton SO17 1BJ, UK
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28
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Varghese R, Wagenknecht HA. Non-covalent Versus Covalent Control of Self-Assembly and Chirality of Nile Red-modified Nucleoside and DNA. Chemistry 2010; 16:9040-6. [DOI: 10.1002/chem.201001136] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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29
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Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev 2010; 110:2579-619. [PMID: 20205430 PMCID: PMC2868948 DOI: 10.1021/cr900301e] [Citation(s) in RCA: 658] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Renatus W. Sinkeldam
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
| | | | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California, San Diego 9500 Gilman Drive, La Jolla, California 92093-0358
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30
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Jeong HS, Park M, Yi JW, Joo T, Kim BH. Structural diversity induced by pyrene intercalators in homogeneous oligodeoxyguanylates. MOLECULAR BIOSYSTEMS 2010; 6:951-3. [PMID: 20485740 DOI: 10.1039/b926677a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Homogeneous oligodeoxyguanylates incorporating small-molecule intercalator pyrene moieties in a 1,5 relationship form various structures of dimer, trimer, tetramer and internal hairpin form that are yellowish in color because of the intermolecular interactions between the pyrene units.
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Affiliation(s)
- Hyun Seok Jeong
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, Korea
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31
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Hainke S, Seitz O. Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed Engl 2010; 48:8250-3. [PMID: 19790219 DOI: 10.1002/anie.200903194] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Hainke
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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32
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Affiliation(s)
- Thomas Rühl
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
| | - Eugen Stulz
- a School of Chemistry , University of Southampton , Highfield, Southampton, SO17 1EW, UK
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33
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Schwartz E, Le Gac S, Cornelissen JJLM, Nolte RJM, Rowan AE. Macromolecular multi-chromophoric scaffolding. Chem Soc Rev 2010; 39:1576-99. [DOI: 10.1039/b922160c] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Hainke S, Seitz O. Binaphthyl-DNA: Stapelung und Fluoreszenz eines nichtplanaren aromatischen Basensurrogates in DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Fluorescence quenching properties of multiple pyrene-modified RNAs. Bioorg Med Chem 2009; 17:4996-5000. [DOI: 10.1016/j.bmc.2009.05.074] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2009] [Revised: 05/28/2009] [Accepted: 05/29/2009] [Indexed: 11/21/2022]
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36
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Abstract
The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
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Affiliation(s)
- Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
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37
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Zhou H, Ma X, Wang J, Zhang L. Pyrene acetylide nucleotides in GNA: probing duplex formation and sensing of copper(II) ions. Org Biomol Chem 2009; 7:2297-302. [PMID: 19462038 DOI: 10.1039/b900167k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and evaluation of GNA duplexes containing fluorescent pyrene and pyrene acetylide nucleotides is reported. Interestingly, only the pyrene acetylides, but not the related plain pyrene nucleotides, form strong excimers upon stacking in glycol nucleic acid (GNA) duplexes. The ability of the large pyrene acetylide nucleotide to be accommodated in GNA duplexes opposite an abasic site was investigated by molecular modeling. The interstrand pyrene acetylide excimer formation was used to monitor GNA duplex formation and was applied to the design of a copper(II)-selective "turn-on" fluorescence sensor.
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Affiliation(s)
- Hui Zhou
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Strasse, D-35032, Marburg, Germany
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38
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Varghese R, Wagenknecht HA. DNA as a supramolecular framework for the helical arrangements of chromophores: towards photoactive DNA-based nanomaterials. Chem Commun (Camb) 2009:2615-24. [PMID: 19532903 DOI: 10.1039/b821728a] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nucleic acids have been emerging as supramolecular structural scaffolds for the helical organization of chromophores in the creation of functional nanomaterials mainly because of the their unique structural features and synthetic accessibility. A large number of chromophores have been successfully incorporated into DNA or RNA as C-nucleosides, as base surrogates or as modified sugars using solid phase phosphoramidite chemistry. Moreover, multiple incorporations yield the helical organization of the chromophores inside or outside the DNA or RNA double helix depending upon the conjugation of the chromophores. Significant photophysical interactions are observed in the chromophore stacks resulting in unique optical properties that are significantly different from the monomer properties. In this feature article, multichromophore labelled nucleic acids are reviewed with special emphasis on the self-assembly induced modulation of the optical properties.
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Affiliation(s)
- Reji Varghese
- University of Regensburg, Institute for Organic Chemistry, D-93053 Regensburg, Germany
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39
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Wagenknecht HA. Helicale Anordnung von Porphyrinen entlang der DNA: auf dem Weg zu DNA-Nanoarchitekturen. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900327] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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40
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Wagenknecht HA. Helical Arrangement of Porphyrins along DNA: Towards Photoactive DNA-Based Nanoarchitectures. Angew Chem Int Ed Engl 2009; 48:2838-41. [DOI: 10.1002/anie.200900327] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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41
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Filichev V, Astakhova I, Malakhov A, Korshun V, Pedersen E. 1-, 2-, and 4-Ethynylpyrenes in the Structure of Twisted Intercalating Nucleic Acids: Structure, Thermal Stability, and Fluorescence Relationship. Chemistry 2008; 14:9968-80. [DOI: 10.1002/chem.200800380] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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42
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Baumstark D, Wagenknecht HA. Fluorescent Hydrophobic Zippers inside Duplex DNA: Interstrand Stacking of Perylene-3,4:9,10-tetracarboxylic Acid Bisimides as Artificial DNA Base Dyes. Chemistry 2008; 14:6640-5. [DOI: 10.1002/chem.200800514] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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43
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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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44
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Nakamura M, Murakami Y, Sasa K, Hayashi H, Yamana K. Pyrene-zipper array assembled via RNA duplex formation. J Am Chem Soc 2008; 130:6904-5. [PMID: 18473465 DOI: 10.1021/ja801054t] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe a new strategy for multipyrene modification of RNA sequences to form unique structures of pyrene aromatic arrays, the "pyrene-zipper array", on duplex RNA that exhibits remarkably strong excimer fluorescence.
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Affiliation(s)
- Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2280, Japan.
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45
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Fegan A, Shirude PS, Balasubramanian S. Rigid cyanine dye nucleic acid labels. Chem Commun (Camb) 2008:2004-6. [PMID: 18536802 DOI: 10.1039/b801629a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyanine dyes attached to DNA via a rigid linker show useful fluorescence and FRET properties without altering the stability of duplex DNA.
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Affiliation(s)
- Adrian Fegan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UKCB2 1EW
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46
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Kwon T, Piton N, Grünewald C, Engels JW. Synthesis of pyrene labeled RNA for fluorescence measurements. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2008; 26:1381-6. [PMID: 18066787 DOI: 10.1080/15257770701534048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The fluorophores 1-ethynylpyrene and 1-(p-ethynyl-phenylethynyl)-pyrene were attached to RNA through a Sonogashira cross-coupling with 5-iodocytidine either in solution through phosphoamidite synthesis or via on-column conjugation during solid-phase oligonucleotide synthesis. Six probes with the sequence 5'-CUU UUC UUU CUU-3' were derivatized with both fluorophores, whereby the position of the modified cytidine was varied. Fluorescence measurements showed sensitivity of the pyrene group to its environment in the single strands and corresponding duplexes.
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Affiliation(s)
- Taewoo Kwon
- Institut für Organische Chemie und Chemische Biologie (OCCB), Johann Wolfgang Goethe-Universität, Max-von-Laue Strasse 7, D-60438 Frankfurt am Main, Germany
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47
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Samain F, Malinovskii VL, Langenegger SM, Häner R. Spectroscopic properties of pyrene-containing DNA mimics. Bioorg Med Chem 2008; 16:27-33. [PMID: 17512737 DOI: 10.1016/j.bmc.2007.04.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/16/2006] [Accepted: 04/27/2007] [Indexed: 11/27/2022]
Abstract
DNA mimics containing non-nucleosidic pyrene building blocks are described. The modified oligomers form stable hybrids, although a slight reduction in hybrid stability is observed in comparison to the unmodified DNA duplex. The nature of the interaction between the pyrene residues in single and double stranded oligomers is analyzed spectroscopically. Intra- and interstrand stacking interactions of pyrenes are monitored by UV-absorbance as well as fluorescence spectroscopy. Excimer formation is observed in both single and double strands. In general, intrastrand excimers show fluorescence emission at shorter wavelengths (approx. 5-10 nm) than excimers formed by interstrand interactions. The existence of two different forms of excimers (intra- vs. interstrand) is also revealed in temperature dependent UV-absorbance spectra.
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Affiliation(s)
- Florent Samain
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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48
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Wagenknecht HA. Fluorescent DNA base modifications and substitutes: multiple fluorophore labeling and the DETEQ concept. Ann N Y Acad Sci 2007; 1130:122-30. [PMID: 18096856 DOI: 10.1196/annals.1430.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
There is an increasing need for fluorescent nucleic acid probes that are able to sense genetic variations without the application of enzymes. The incorporation of organic fluorophores either as DNA base modifications or as DNA base substitutions represents a powerful and versatile method for such new fluorescent DNA assays. Multiple labeling of oligonucleotides using several adjacent chromophore-modified DNA bases yields fluorescence enhancement and modulation that are sensitive to single-base mismatches in the complementary oligonucleotide. Charge transfer processes that cause fluorescence quenching are DNA-base mediated and occur over several base pairs distance. Our "DETEQ" setup, consisting of a fluorescence DNA base substitution and the charge acceptor as a second modification two base pairs away, allows the homogeneous detection of single-base mutations simply by fluorescence readout. This could lead to new DNA microarrays which are based on charge transfer processes and can be analyzed by commonly used fluorescence readout techniques.
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49
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Fendt LA, Bouamaied I, Thöni S, Amiot N, Stulz E. DNA as Supramolecular Scaffold for Porphyrin Arrays on the Nanometer Scale. J Am Chem Soc 2007; 129:15319-29. [DOI: 10.1021/ja075711c] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Leslie-Anne Fendt
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Imenne Bouamaied
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Sandra Thöni
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Nicolas Amiot
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
| | - Eugen Stulz
- Contribution from the School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K., and Department of Chemistry, University of Basel, St. Johanns-Ring 19, 4056 Basel, Switzerland
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50
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Nakamura M, Shimomura Y, Ohtoshi Y, Sasa K, Hayashi H, Nakano H, Yamana K. Pyrene aromatic arrays on RNA duplexes as helical templates. Org Biomol Chem 2007; 5:1945-51. [PMID: 17551644 DOI: 10.1039/b705933g] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
RNA oligomers having multiple (2 to 4) pyrenylmethyl substituents at the 2'-O-sugar residues were synthesized. UV-melting studies showed that the pyrene-modified RNAs could form duplexes with complementary RNA sequences without loss of thermal stability. Absorption, fluorescence, and circular dichroism (CD) spectra revealed that the incorporated pyrenes projected toward the outside of A-form RNA duplexes and assembled in helical aromatic arrays along the minor grooves of the RNA duplexes. Results of computer simulations agreed with the assembled structures of the pyrenes. The helical pyrene arrays exhibited remarkably strong excimer fluorescence, which was dependent on the sequence contexts of RNA duplexes.
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Affiliation(s)
- Mitsunobu Nakamura
- Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, Himeji, Hyogo, Japan.
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