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Krebs J, Brändler L, Krummenacher I, Friedrich A, Braunschweig H, Finze M, Curchod BFE, Marder TB. Synthesis, Photophysical and Electronic Properties of a D-π-A Julolidine-Like Pyrenyl-o-Carborane. Chemistry 2024; 30:e202401704. [PMID: 38758081 DOI: 10.1002/chem.202401704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/18/2024]
Abstract
We synthesized 2-(1-1,2-dicarbadodecaboranyl(12))-6,6,12,12-tetramethyl-7,8,11,12-tetrahydro-6H,10H-phenaleno[1,9-fg]pyrido[3,2,1-ij]quinoline (4), a julolidine-like pyrenyl-o-carborane, with pyrene substituted at the 2,7-positions on the HOMO/LUMO nodal plane. Using solid state molecular structures, photophysical data, cyclic voltammetry, DFT and LR-TDDFT calculations, we compare o-carborane and B(Mes)2 (Mes=2,4,6-Me3C6H2) as acceptor groups. Whereas the π-acceptor strength of B(Mes)2 is sufficient to drop the pyrene LUMO+1 below the LUMO, the carborane does not do this. We confirm the π-donor strength of the julolidine-like moiety, however, which raises the pyrene HOMO-1 above the HOMO. In contrast to the analogous pyrene-2-yl-o-carborane, 2-(1-1,2-dicarbadodecaboranyl(12))-pyrene VI, which exhibits dual fluorescence, because the rate of internal conversion between locally-excited (LE) and charge transfer (CT) (from the pyrene to the carborane) states is faster than the radiative decay rate, leading to a thermodynamic equilibrium between the 2 states, 4 shows only single fluorescence, as the CT state involving the carborane as the acceptor moiety in not kinetically accessible, so a more localized CT emission involving the julolidine-like pyrene moiety is observed.
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Affiliation(s)
- Johannes Krebs
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Lisa Brändler
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ivo Krummenacher
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Alexandra Friedrich
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Holger Braunschweig
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Maik Finze
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Basile F E Curchod
- Centre for Computational Chemistry, School of Chemistry, Cantock's Close, University of Bristol, Bristol, BS8 1TS, United Kingdom
| | - Todd B Marder
- Institute for Inorganic Chemistry and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
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Para-N-Methylpyridinium Pyrenes: Impact of Positive Charge on ds-DNA/RNA and Protein Recognition, Photo-Induced Bioactivity, and Intracellular Localisation. Pharmaceutics 2022; 14:pharmaceutics14112499. [PMID: 36432689 PMCID: PMC9696974 DOI: 10.3390/pharmaceutics14112499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022] Open
Abstract
The 2- and 2,7- substituted para-N-methylpyridinium pyrene cations show high-affinity intercalation into ds-DNAs, whereas their non-methylated analogues interacted with ds-DNA/RNA only in the protonated form (at pH 5), but not at physiological conditions (pH 7). The fluorescence from non-methylated analogues was strongly dependent on the protonation of the pyridines; consequently, they act as fluorescence ratiometric probes for simultaneous detection of both ds-DNA and BSA at pH 5, relying on the ratio between intensities at 420 nm (BSA specific) and 520 nm (DNA specific), whereby exclusively ds-DNA sensing could be switched-off by adjustment to pH 7. Only methylated, permanently charged pyrenes show photoinduced cleavage of circular DNA, attributed to pyrene-mediated irradiation-induced production of singlet oxygen. Consequently, the moderate toxicity of these cations against human cell lines is strongly increased upon irradiation. Detailed studies revealed increased total ROS production in cells treated by the compounds studied, accompanied by cell swelling and augmentation of cellular complexity. The most photo-active 2-para-N-methylpyridinium pyrene showed significant localization at mitochondria, its photo-bioactivity likely due to mitochondrial DNA damage. Other derivatives were mostly non-selectively distributed between various cytoplasmic organelles, thus being less photoactive.
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Ucar H, Wagenknecht HA. DNA-templated control of chirality and efficient energy transport in supramolecular DNA architectures with aggregation-induced emission. Chem Sci 2021; 12:10048-10053. [PMID: 34377398 PMCID: PMC8317660 DOI: 10.1039/d1sc02351a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 06/19/2021] [Indexed: 01/15/2023] Open
Abstract
Two conjugates of tetraphenylethylene with d-2′-deoxyuridine (1d) and l-2′-deoxyuridine (1l) were synthesized to construct new supramolecular DNA-architectures by self-assembly. The non-templated assemblies of 1d and 1l show strong aggregation-induced emission and their chirality is exclusively controlled by the configuration of their sugar part. In contrast, the chirality of the DNA-templated assemblies is governed by the configuration of the DNA, and there is no configuration-selective binding of 1d to d-A20 and 1l to l-A20. The quantum yield of the assembly of 1d along the single-stranded DNA A20 is 0.40; approximately every second available binding site on the DNA template is occupied by 1d. The strong aggregation-induced emission of these DNA architectures can be efficiently quenched and the excitation energy can be transported to Atto dyes at the 5′-terminus. A multistep energy transport “hopping” precedes the final energy transfer to the terminal acceptor. The building block 1d promotes this energy transport as stepping stones. This was elucidated by reference DNA double strands in which 1d was covalently incorporated at two distinct sites in the sequences, one near the Atto dye, and one farther away. This new type of completely self-assembled supramolecular DNA architecture is hierarchically ordered and the DNA template controls not only the binding but also the energy transport properties. The high intensity of the aggregation-induced emission and the excellent energy transport properties make these DNA-based materials promising candidates for optoelectronic applications. DNA architectures with tetraphenylethylene are assembled in a non-covalent way. The strong aggregation-induced emission of the chromophores is quenched and the energy is transported to Atto dyes by a multistep energy “hopping”.![]()
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Affiliation(s)
- Hülya Ucar
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe German
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe German
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Zhang A, Kondhare D, Leonard P, Seela F. 5-Aza-7-deazaguanine-Isoguanine and Guanine-Isoguanine Base Pairs in Watson-Crick DNA: The Impact of Purine Tracts, Clickable Dendritic Side Chains, and Pyrene Adducts. Chemistry 2021; 27:7453-7466. [PMID: 33443814 PMCID: PMC8251886 DOI: 10.1002/chem.202005199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Indexed: 12/19/2022]
Abstract
The Watson-Crick coding system depends on the molecular recognition of complementary purine and pyrimidine bases. Now, the construction of hybrid DNAs with Watson-Crick and purine-purine base pairs decorated with dendritic side chains was performed. Oligonucleotides with single and multiple incorporations of 5-aza-7-deaza-2'-deoxyguanosine, its tripropargylamine derivative, and 2'-deoxyisoguanosine were synthesized. Duplex stability decreased if single modified purine-purine base pairs were inserted, but increased if pyrene residues were introduced by click chemistry. A growing number of consecutive 5-aza-7-deazaguanine-isoguanine base pairs led to strong stepwise duplex stabilization, a phenomenon not observed for the guanine-isoguanine base pair. Spacious residues are well accommodated in the large groove of purine-purine DNA tracts. Changes to the global helical structure monitored by circular dichroism spectroscopy show the impact of functionalization to the global double-helix structure. This study explores new areas of molecular recognition realized by purine base pairs that are complementary in hydrogen bonding, but not in size, relative to canonical pairs.
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Affiliation(s)
- Aigui Zhang
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Dasharath Kondhare
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Peter Leonard
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany
| | - Frank Seela
- Laboratory of Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, University of Münster, Heisenbergstrasse 11, 48149, Münster, Germany.,Laboratorium für Organische und Bioorganische Chemie, Institut für Chemie neuer Materialien, Universität Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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Burns JR, Wood JW, Stulz E. A Porphyrin-DNA Chiroptical Molecular Ruler With Base Pair Resolution. Front Chem 2020; 8:113. [PMID: 32175308 PMCID: PMC7054460 DOI: 10.3389/fchem.2020.00113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/06/2020] [Indexed: 11/13/2022] Open
Abstract
DNA-based molecular rulers enable scientists to determine important parameters across biology, from the measurement of protein binding interactions, to the study of membrane dynamics in cells. However, existing rulers can suffer from poor nanometre resolution due to the flexible nature of linkers used to tether to the DNA framework. We aimed to overcome this problem using zinc and free-base porphyrin chromophores attached via short and rigid acetylene linkers. This connectivity enables the distance and angle between the porphyrins to be fine-tuned along the DNA scaffold. The porphyrins undergo favorable energy transfer and chiral exciton coupling interactions to act as highly sensitive molecular ruler probes. To validate the system, we monitored the detection of small changes in DNA structure upon intercalation of ethidium bromide. CD spectroscopy showed the porphyrins undergo highly sensitive changes in excitation coupling to facilitate base pair resolution of the novel system.
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Affiliation(s)
- Jonathan R Burns
- Department of Chemistry, University College London, London, United Kingdom
| | - James W Wood
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Eugen Stulz
- School of Chemistry & Institute for Life Sciences, University of Southampton, Southampton, United Kingdom
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Asanuma H, Murayama K, Kamiya Y, Kashida H. The DNA Duplex as an Aqueous One-Dimensional Soft Crystal Scaffold for Photochemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2018. [DOI: 10.1246/bcsj.20180278] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hiroyuki Asanuma
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Keiji Murayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Yukiko Kamiya
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
| | - Hiromu Kashida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603, Japan
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Lubbe AS, Szymanski W, Feringa BL. Recent developments in reversible photoregulation of oligonucleotide structure and function. Chem Soc Rev 2018; 46:1052-1079. [PMID: 28128377 DOI: 10.1039/c6cs00461j] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
There is a growing interest in the photoregulation of biological functions, due to the high level of spatiotemporal precision achievable with light. Additionally, light is non-invasive and waste-free. In particular, the photoregulation of oligonucleotide structure and function is a rapidly developing study field with relevance to biological, physical and material sciences. Molecular photoswitches have been incorporated in oligonucleotides for 20 years, and the field has currently grown beyond fundamental studies on photochemistry of the switches and DNA duplex stability, and is moving towards applications in chemical biology, nanotechnology and material science. Moreover, the currently emerging field of photopharmacology indicates the relevance of photocontrol in future medicine. In recent years, a large number of publications has appeared on photoregulation of DNA and RNA structure and function. New strategies are evaluated and novel, exciting applications are shown. In this comprehensive review, the key strategies for photoswitch inclusion in oligonucleotides are presented and illustrated with recent examples. Additionally the applications that have emerged in recent years are discussed, including gene regulation, drug delivery and materials design. Finally, we identify the challenges that the field currently faces and look forward to future applications.
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Affiliation(s)
- Anouk S Lubbe
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. and Department of Radiology, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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Šmidlehner T, Badovinac M, Piantanida I. Pyrene–cyanine conjugates as multipurpose fluorescent probes for non-covalent recognition of ds-DNA, RNA and proteins. NEW J CHEM 2018. [DOI: 10.1039/c8nj00055g] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
One molecule-dual fluorescence response: pyrene emission highly selective for BSA protein and “switch-on” of cyanine fluorescence selective for DNA.
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Affiliation(s)
- T. Šmidlehner
- Ruđer Bošković Institute
- Bijenička cesta 54
- 10000 Zagreb
- Croatia
| | - M. Badovinac
- Ruđer Bošković Institute
- Bijenička cesta 54
- 10000 Zagreb
- Croatia
| | - I. Piantanida
- Ruđer Bošković Institute
- Bijenička cesta 54
- 10000 Zagreb
- Croatia
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Kashida H, Asanuma H. Development of Pseudo Base-Pairs on d-Threoninol which Exhibit Various Functions. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20160371] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hiromu Kashida
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012
| | - Hiroyuki Asanuma
- Department of Molecular Design and Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8603
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Reuss AJ, Grünewald C, Gustmann H, Engels JW, Wachtveitl J. Three-State Fluorescence of a 2-Functionalized Pyrene-Based RNA Label. J Phys Chem B 2017; 121:3032-3041. [PMID: 28301163 DOI: 10.1021/acs.jpcb.7b02027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The pyrene-based RNA-fluorescence label 2-(2-pyrenylethynyl) adenosine (2PyA) shows triexponential fluorescence, which depends strongly on the excitation wavelength. Most strikingly, a structured, long-lived fluorescence is observed in solution at room temperature after excitation into the S2 state, which is shifted hypsochromically by 30 nm compared to excitation into the S1 state. This very unusual behavior is investigated in detail with steady-state and time-resolved emission spectroscopy, ultrafast transient absorption spectroscopy, and quantum chemical calculations with both wave functions (CC2-level) and density-functional theory (DFT). 2PyA is found to emit simultaneously from two different intramolecular charge transfer states (mesomeric and twisted, MICT and TICT) which are populated most efficiently via the S1 state and a pyrene-like locally excited (LE) state. Rotational momentum derived from excess excitation energy is required to populate twisted LE configurations. Therefore, the LE state is most efficiently accessible via excitation to the S2. The stabilization of the different substates is related to two distinct reaction coordinates: the adenine-pyrene distance and the adenine-pyrene tilt angle, respectively.
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Affiliation(s)
- Andreas J Reuss
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Henrik Gustmann
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Joachim W Engels
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt , 60438 Frankfurt (Main), Germany
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12
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Thelu HVP, Albert SK, Golla M, Krishnan N, Yamijala SB, Nair SV, Srinivasula SM, Varghese R. DNA-Decorated Luminescent Vesicles as Drug Carriers. ChemistrySelect 2016. [DOI: 10.1002/slct.201600897] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hari Veera Prasad Thelu
- School of Chemistry; Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM); CET campus Trivandrum- 695016 India
| | - Shine K. Albert
- School of Chemistry; Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM); CET campus Trivandrum- 695016 India
| | - Murali Golla
- School of Chemistry; Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM); CET campus Trivandrum- 695016 India
| | - Nithiyanandan Krishnan
- School of Chemistry; Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM); CET campus Trivandrum- 695016 India
| | | | | | | | - Reji Varghese
- School of Chemistry; Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM); CET campus Trivandrum- 695016 India
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13
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201600924] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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14
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Santamaría-Díaz N, Méndez-Arriaga JM, Salas JM, Galindo MA. Highly Stable Double-Stranded DNA Containing Sequential Silver(I)-Mediated 7-Deazaadenine/Thymine Watson-Crick Base Pairs. Angew Chem Int Ed Engl 2016; 55:6170-4. [DOI: 10.1002/anie.201600924] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Noelia Santamaría-Díaz
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - José M. Méndez-Arriaga
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Juan M. Salas
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
| | - Miguel A. Galindo
- Facultad de Ciencias; Departamento Química Inorgánica; Universidad de Granada; Avd. Fuentenueva s/n 18071 Granada Spain
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15
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Maekawa S, Sato R, Hirao K, Shigeta Y. Solvent effects on excited-state electron-transfer rate of pyrene-labeled deoxyuridine: A theoretical study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2015.11.037] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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16
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Albert SK, Golla M, Thelu HVP, Krishnan N, Deepak P, Varghese R. Synthesis and self-assembly of DNA–chromophore hybrid amphiphiles. Org Biomol Chem 2016; 14:6960-9. [DOI: 10.1039/c6ob00681g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA based amphiphiles are synthesized through a modular “click” chemistry approach, and the DNA–chromophore hybrid amphiphiles undergo amphiphilicity-driven self-assembly into vesicular or micellar nanostructures having a DNA shell and functional core.
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Affiliation(s)
- Shine K. Albert
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Murali Golla
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Hari Veera Prasad Thelu
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Nithiyanandan Krishnan
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Perapaka Deepak
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
| | - Reji Varghese
- School of Chemistry
- Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM)
- Trivandrum-695016
- India
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17
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Yuan PX, Deng SY, Xin P, Ji XB, Shan D, Cosnier S. Mass effect of redox reactions: A novel mode for surface plasmon resonance-based bioanalysis. Biosens Bioelectron 2015; 74:183-9. [DOI: 10.1016/j.bios.2015.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/14/2015] [Accepted: 06/17/2015] [Indexed: 01/03/2023]
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Nakamura M, Takada T, Yamana K. Highly Ordered Pyrene π-Stacks on an RNA Duplex. ACTA ACUST UNITED AC 2015; 63:4.66.1-4.66.19. [PMID: 26623973 DOI: 10.1002/0471142700.nc0466s63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The syntheses of 2'-O-(pyren-1-ylmethyl)uridine phosphoramidite, 2'-O-(pyren-1-ylmethyl)adenosine phosphoramidite, and multiple pyrene-attached oligo-RNAs are described in this unit. The 2'-O-(pyren-1-ylmethyl)nucleosides are converted into the corresponding 2'-O-(pyren-1-ylmethyl)nucleoside 3'-phosphoramidites, which can be incorporated into the specific position of oligo-RNAs by solid-phase oligonucleotide synthesis. The multiple pyrene-attached oligo-RNA forms an A-form duplex with a complementary multiple pyrene-attached oligo-RNA; the pyrenes are associated with π-stacking along the outside of the duplex.
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Affiliation(s)
| | - Tadao Takada
- Department of Applied Chemistry, University of Hyogo, Himeji, Japan
| | - Kazushige Yamana
- Department of Applied Chemistry, University of Hyogo, Himeji, Japan
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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: 104] [Impact Index Per Article: 11.6] [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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Enzymatic Polymerization on DNA Modified Gold Nanowire for Label-Free Detection of Pathogen DNA. Int J Mol Sci 2015; 16:13653-60. [PMID: 26084045 PMCID: PMC4490515 DOI: 10.3390/ijms160613653] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 06/08/2015] [Accepted: 06/10/2015] [Indexed: 12/11/2022] Open
Abstract
This paper presents a label-free biosensor for the detection of single-stranded pathogen DNA through the target-enhanced gelation between gold nanowires (AuNW) and the primer DNAs branched on AuNW. The target DNA enables circularization of the linear DNA template, and the primer DNA is elongated continuously via rolling circle amplification. As a result, in the presence of the target DNA, a macroscopic hydrogel was fabricated by the entanglement of the elongated DNA with AuNWs as a scaffold fiber for effective gelation. In contrast, very small separate particles were generated in the absence of the target DNA. This label-free biosensor might be a promising tool for the detection of pathogen DNAs without any devices for further analysis. Moreover, the biosensor based on the weaving of AuNW and DNAs suggests a novel direction for the applications of AuNWs in biological engineering.
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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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Takada T, Tanimizu Y, Nakamura M, Yamana K. Preparation of fluorescent nucleic acids generating unique emission by primer extension reaction using pyrene-labeled deoxyuridine triphosphate derivatives. ACTA ACUST UNITED AC 2014. [DOI: 10.5857/rcp.2014.3.4.76] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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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Tedeschi T, Tonelli A, Sforza S, Corradini R, Marchelli R. A pyrenyl-PNA probe for DNA and RNA recognition: Fluorescence and UV absorption studies. ARTIFICIAL DNA, PNA & XNA 2014; 1:83-89. [PMID: 21686243 DOI: 10.4161/adna.1.2.13899] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 10/08/2010] [Accepted: 10/09/2010] [Indexed: 11/19/2022]
Abstract
The design and the synthesis of a PNA oligomer containing a pyrenyl residue in the backbone were performed. PNA sequence was chosen complementary to a "G rich" target sequence involved in G-quadruplex formation. The pyrenyl unit replaced a nucleobase in the middle of the PNA through covalent linkage to the backbone by a carboxymethyl unit. A systematic study on the binding properties of this probe towards DNA and RNA complementary strands was carried out by UV and fluorescence spectroscopy. UV melting curves indicated that the PNA probe binds more tightly to RNA rather than to DNA. Thermodynamic data obtained by Van't Hoff fitting of the melting curves indicated that, in the case of RNA, a more favorable interaction occurs between the pyrenyl unit and the RNA nucleobases, leading to a very favorable enthalpic contribution.The fluorescence analysis showed specific quenching of the pyrene emission associated to the formation of the full-match PNA-DNA or PNA-RNA duplexes. Again, this behavior was more evident in the case of RNA, consistently with the stronger interaction of the pyrenyl unit with the complementary strand. In order to study the sequence specificity of the pyrenyl-PNA probe (pyr-PNA), recognition experiments on mismatched DNA and RNA sequences were also performed.
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Affiliation(s)
- Tullia Tedeschi
- Department of Organic and Industrial Chemistry; University of Parma; Parma, Italy
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Perlíková P, Karlsen KK, Pedersen EB, Wengel J. Unlocked nucleic acids with a pyrene-modified uracil: synthesis, hybridization studies, fluorescent properties and i-motif stability. Chembiochem 2014; 15:146-56. [PMID: 24501777 DOI: 10.1002/cbic.201300567] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The synthesis of two new phosphoramidite building blocks for the incorporation of 5-(pyren-1-yl)uracilyl unlocked nucleic acid (UNA) monomers into oligonucleotides has been developed. Monomers containing a pyrene-modified nucleobase component were found to destabilize an i-motif structure at pH 5.2, both under molecular crowding and noncrowding conditions. The presence of the pyrene-modified UNA monomers in DNA strands led to decreases in the thermal stabilities of DNA*/DNA and DNA*/RNA duplexes, but these duplexes' thermal stabilities were better than those of duplexes containing unmodified UNA monomers. Pyrene-modified UNA monomers incorporated in bulges were able to stabilize DNA*/DNA duplexes due to intercalation of the pyrene moiety into the duplexes. Steady-state fluorescence emission studies of oligonucleotides containing pyrene-modified UNA monomers revealed decreases in fluorescence intensities upon hybridization to DNA or RNA. Efficient quenching of fluorescence of pyrene-modified UNA monomers was observed after formation of i-motif structures at pH 5.2. The stabilizing/destabilizing effect of pyrene-modified nucleic acids might be useful for designing antisense oligonucleotides and hybridization probes.
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Manicardi A, Guidi L, Ghidini A, Corradini R. Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA2DNA triplexes. Beilstein J Org Chem 2014; 10:1495-503. [PMID: 25161706 PMCID: PMC4142857 DOI: 10.3762/bjoc.10.154] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 06/03/2014] [Indexed: 12/17/2022] Open
Abstract
Pyrene derivatives can be incorporated into nucleic acid analogs in order to obtain switchable probes or supramolecular architectures. In this paper, peptide nucleic acids (PNAs) containing 1 to 3 1-pyreneacetic acid units (PNA1–6) with a sequence with prevalence of pyrimidine bases, complementary to cystic fibrosis W1282X point mutation were synthesized. These compounds showed sequence-selective switch-on of pyrene excimer emission in the presence of target DNA, due to PNA2DNA triplex formation, with stability depending on the number and positioning of the pyrene units along the chain. An increase in triplex stability and a very high mismatch-selectivity, derived from combined stacking and base-pairing interactions, were found for PNA2, bearing two distant pyrene units.
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Affiliation(s)
- Alex Manicardi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Lucia Guidi
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
| | - Alice Ghidini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410 ; Present Address: Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Hälsovägen 7, 14183, Huddinge, Sweden
| | - Roberto Corradini
- Department of Chemistry, University of Parma, Parco Area delle Scienze 17/A, 43124, Parma, Italy. ; Tel: +39 0521 905410
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Albert SK, Thelu HVP, Golla M, Krishnan N, Chaudhary S, Varghese R. Self-assembly of DNA-oligo(p-phenylene-ethynylene) hybrid amphiphiles into surface-engineered vesicles with enhanced emission. Angew Chem Int Ed Engl 2014; 53:8352-7. [PMID: 24962762 DOI: 10.1002/anie.201403455] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 05/19/2014] [Indexed: 11/09/2022]
Abstract
Surface-addressable nanostructures of linearly π-conjugated molecules play a crucial role in the emerging field of nanoelectronics. Herein, by using DNA as the hydrophilic segment, we demonstrate a solid-phase "click" chemistry approach for the synthesis of a series of DNA-chromophore hybrid amphiphiles and report their reversible self-assembly into surface-engineered vesicles with enhanced emission. DNA-directed surface addressability of the vesicles was demonstrated through the integration of gold nanoparticles onto the surface of the vesicles by sequence-specific DNA hybridization. This system could be converted to a supramolecular light-harvesting antenna by integrating suitable FRET acceptors onto the surface of the nanostructures. The general nature of the synthesis, surface addressability, and biocompatibility of the resulting nanostructures offer great promises for nanoelectronics, energy, and biomedical applications.
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Affiliation(s)
- Shine K Albert
- School of Chemistry, Indian Institute of Science Education and Research-Thiruvananthapuram (IISER-TVM), CET campus, Trivandrum-695016 (India)
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28
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Albert SK, Thelu HVP, Golla M, Krishnan N, Chaudhary S, Varghese R. Self-Assembly of DNA-Oligo(p-phenylene-ethynylene) Hybrid Amphiphiles into Surface-Engineered Vesicles with Enhanced Emission. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403455] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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29
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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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Tanpure AA, Srivatsan SG. Synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue based on the Lucifer chromophore. Chembiochem 2014; 15:1309-16. [PMID: 24861713 DOI: 10.1002/cbic.201402052] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Indexed: 11/10/2022]
Abstract
The majority of fluorescent nucleoside analogues used in nucleic acid studies have excitation maxima in the UV region and show very low fluorescence within oligonucleotides (ONs); hence, they cannot be utilised with certain fluorescence methods and for cell-based analysis. Here, we describe the synthesis, photophysical properties and incorporation of a highly emissive and environment-sensitive uridine analogue, derived by attaching a Lucifer chromophore (1,8-naphthalimide core) at the 5-position of uracil. The emissive nucleoside displays excitation and emission maxima in the visible region and exhibits high quantum yield. Importantly, when incorporated into ON duplexes it retains appreciable fluorescence efficiency and is sensitive to the neighbouring base environment. Notably, the nucleoside signals the presence of purine repeats in ON duplexes with an enhancement in fluorescence intensity, a property rarely displayed by other nucleoside analogues.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008 (India)
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31
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Tsuto K, Nakamura M, Takada T, Yamana K. Diketopyrrolopyrrole J-Aggregates Formed by Self-Organization with DNA. Chem Asian J 2014; 9:1618-22. [DOI: 10.1002/asia.201402063] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Indexed: 01/08/2023]
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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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Maneelun N, Vilaivan T. Dual pyrene-labeled pyrrolidinyl peptide nucleic acid as an excimer-to-monomer switching probe for DNA sequence detection. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.10.096] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Pawar MG, Srivatsan SG. Environment-responsive fluorescent nucleoside analogue probe for studying oligonucleotide dynamics in a model cell-like compartment. J Phys Chem B 2013; 117:14273-82. [PMID: 24161106 DOI: 10.1021/jp4071168] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The majority of fluorescent nucleoside analogue probes that have been used in the in vitro study of nucleic acids are not suitable for cell-based biophysical assays because they exhibit excitation maxima in the UV region and low quantum yields within oligonucleotides. Therefore, we propose that the photophysical characterization of oligonucleotides labeled with a fluorescent nucleoside analogue in reverse micelles (RM), which are good biological membrane models and UV-transparent, could provide an alternative approach to studying the properties of nucleic acids in a cell-like confined environment. In this context, we describe the photophysical properties of an environment-sensitive fluorescent uridine analogue (1), based on the 5-(benzo[b]thiophen-2-yl)pyrimidine core, in micelles and RM. The emissive nucleoside, which is polarity- and viscosity-sensitive, reports the environment of the surfactant assemblies via changes in its fluorescence properties. The nucleoside analogue, incorporated into an RNA oligonucleotide and hybridized to its complementary DNA and RNA oligonucleotides, exhibits a significantly higher fluorescence intensity, lifetime, and anisotropy in RM than in aqueous buffer, which is consistent with the environment of RM. Collectively, our results demonstrate that nucleoside 1 could be utilized as a fluorescent label to study the function of nucleic acids in a model cellular milieu.
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Affiliation(s)
- Maroti G Pawar
- Department of Chemistry, Indian Institute of Science Education and Research, Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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Evaluation of intrinsic spectroscopic properties of chromophore assemblies by shielding with cyclohexyl base pairs within a DNA duplex. Bioorg Med Chem 2013; 21:6191-7. [DOI: 10.1016/j.bmc.2013.04.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 03/28/2013] [Accepted: 04/05/2013] [Indexed: 11/21/2022]
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Murayama K, Tanaka Y, Toda T, Kashida H, Asanuma H. Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds. Chemistry 2013; 19:14151-8. [DOI: 10.1002/chem.201301578] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 11/08/2022]
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Noé MS, Sinkeldam RW, Tor Y. Oligodeoxynucleotides containing multiple thiophene-modified isomorphic fluorescent nucleosides. J Org Chem 2013; 78:8123-8. [PMID: 23859712 DOI: 10.1021/jo4008964] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
5-(Thien-2-yl)-2'-deoxyuridine, an isomorphic fluorescent nucleoside analogue, was incorporated into multiple positions within single stranded oligodeoxynucleotides. With minimal impact on duplex stability and overall structure, oligonucleotides containing three identical isomorphic fluorescent nucleosides in alternating or neighboring positions display enhanced, sequence-dependent on-signals for either duplex formation or dissociation.
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Affiliation(s)
- Mary S Noé
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093-0358, USA
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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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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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40
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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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41
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Otabe T, Matsumoto S, Nakagawa H, Hong C, Dohno C, Nakatani K. Triethynylmethane: a molecular unit inducing excimer-like emission in aggregated states of hydrocarbon fluorophores. Tetrahedron Lett 2013. [DOI: 10.1016/j.tetlet.2012.10.093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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42
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Liang F, Liu YZ, Zhang P. Universal base analogues and their applications in DNA sequencing technology. RSC Adv 2013. [DOI: 10.1039/c3ra41492b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Sargsyan G, Balaz M. Porphyrin-DNA conjugates: porphyrin induced adenine-guanine homoduplex stabilization and interduplex assemblies. Org Biomol Chem 2012; 10:5533-40. [PMID: 22692698 DOI: 10.1039/c2ob25710f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
DNA has found widespread uses as a nanosized scaffold for assembly of patterned multichomophoric nanostructures. Herein we report the synthesis, self-assembly, stability, and spectroscopic studies of short alternating non-self-complementary DNA sequences 5'-(dGdA)(4) and 5'-(dAdG)(4) with non-charged tetraarylporphyrins covalently linked to the 5' position of deoxyadenosine or deoxyguanosine via a phosphate or amide linker. The linker, the metal in the porphyrin coordination center, and the neighboring nucleobase have very distinct effects on the duplex formation of porphyrin-deoxyguanosine-deoxyadenosine oligodeoxynucleotides. At ionic strength between 5 mM and 40 mM, free base trispyridylphenylporphyrin appended to the 5' termini of 5'-(dAdG)(4) oligonucleotide via short non-polar amide linker served as a hydrophobic molecular cap inducing deoxyadenosine-deoxyguanosine antiparallel homoduplex. At ionic strength of ≥60 mM, the free base porphyrin functioned as a molecular 'glue' and induced the formation of porphyrin-DNA inter-homoduplex assemblies with characteristic tetrasignate CD Cotton effects in the porphyrin Soret band region. When the porphyrin cap was covalently attached to 5' position of deoxyguanosine or deoxyadenosine via charged phosphate linker, no significant deoxyadenosine-deoxyguanosine hybridization was observed even at elevated ionic strengths.
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Affiliation(s)
- Gevorg Sargsyan
- Department of Chemistry, University of Wyoming, 1000 E. University ave., Laramie, WY 82071, USA
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Wang S, Guo J, Ono T, Kool ET. DNA polyfluorophores for real-time multicolor tracking of dynamic biological systems. Angew Chem Int Ed Engl 2012; 51:7176-80. [PMID: 22684777 DOI: 10.1002/anie.201201928] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2012] [Revised: 04/16/2012] [Indexed: 11/07/2022]
Abstract
Dye-ing to live: Spectral limitations of common organic dyes make it difficult or impossible to visualize and follow multiple biological components in rapidly moving systems. The development of a multispectral set of improved DNA-scaffolded fluorophores is described. Their use in multicolor cellular imaging (see scheme) and in tracking of biological motions on the subsecond timescale is demonstrated.
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Affiliation(s)
- Shenliang Wang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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Wang S, Guo J, Ono T, Kool ET. DNA Polyfluorophores for Real-Time Multicolor Tracking of Dynamic Biological Systems. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201201928] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Asanuma H, Fujii T, Kato T, Kashida H. Coherent interactions of dyes assembled on DNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.04.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Yu Y, Liu J, Zhao Z, Ng KM, Luo KQ, Tang BZ. Facile preparation of non-self-quenching fluorescent DNA strands with the degree of labeling up to the theoretic limit. Chem Commun (Camb) 2012; 48:6360. [PMID: 22618018 DOI: 10.1039/c2cc32038j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
A new aggregation-induced emission (AIE) compound 1,1-dimethyl-2,5-bis[4-(isothiocyanatemethyl)phenyl]-3,4-diphenylsilole (SITC) was synthesized and used to conjugate with aminoallyl-dUTP. The SITC-dUTP can be incorporated enzymatically into DNA strands with the degree of labeling (DOL) up to the theoretic limit.
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Affiliation(s)
- Yong Yu
- Department of Chemical and Biomolecular Engineering, HKUST, Clear Water Bay, Kowloon, Hong Kong, China
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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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Neelakandan PP, McCullagh M, Schatz GC, Lewis FD. Electronic interactions in helical stacked arrays of the modified DNA base pyrrolocytosine. J Phys Chem B 2012; 116:5199-204. [PMID: 22486518 DOI: 10.1021/jp302385c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The thermal stability and ultraviolet and circular dichroism spectra of nine synthetic DNA hairpins possessing one or more (P)C-G base pairs ((P)C = pyrrolocytosine) have been investigated. One group of hairpins possess 1-5 sequential (P)C-G base pairs while another group possess two (P)C-G base pairs separated by 1-3 A-T base pairs. The first group displays a nearly linear dependence of UV and exciton-coupled circular dichroism (EC-CD) band intensity upon the number of neighboring chromophores, whereas the second group shows weak EC-CD only at the shortest distances between non-neighboring chromophores. This result stands in marked contrast to the exciton coupling seen between stilbene chromophores separated by as many as a dozen base pairs. The weak exciton coupling between non-neighboring (P)C chromophores, like that of the natural nucelobases, is attributed to their relatively weak electronic transition dipoles.
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Affiliation(s)
- Prakash P Neelakandan
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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Affiliation(s)
- Yin Nah Teo
- Department of Chemistry, Stanford University, California 94305, United States
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