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Pérez de Carvasal K, Nicollet L, Smietana M, Morvan F. Stabilization of DNA Duplexes and Hairpins by Charge-Transfer Interactions Using DAN:NDI Pairs. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:7418-7425. [PMID: 37196178 DOI: 10.1021/acs.langmuir.3c00619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Electron-rich 1,5-dialkoxynaphthalene (DAN) and electron-deficient 1,8,4,5-naphthalenetetracarboxylic diimide (NDI) are known to interact through the formation of charge-transfer complexes. The introduction of DAN and NDI into various DNA duplexes and hairpins was investigated by ultraviolet (UV) melting curve analysis. The positioning of the DAN:NDI pair was found to strongly influence the stability of DNA duplex and hairpins. In particular, while the introduction of one DAN/NDI pair in front of each other in the center of a DNA duplex led to a decrease of the thermal stability (ΔTm - 6 °C), the addition of a second pair restored or even increased the stability. In contrast, the introduction of DAN:NDI pairs at the end of a duplex always induced a strong stabilization (ΔTm up to +20 °C). Finally, a DAN:NDI pair positioned in the loop of a hairpin induced a stronger stabilization than a T4 loop (ΔTm + 10 °C). Based on charge-transfer interactions, the strong stabilizations observed allow the preparation of highly stabilized DNA nanostructures opening the way to numerous applications in nanotechnology.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Laura Nicollet
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - Michael Smietana
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
| | - François Morvan
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, 34293 Montpellier, France
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de Carvasal KP, Vergoten G, Vasseur JJ, Smietana M, Morvan F. Supramolecular Recognition of Phosphodiester-Based Donor and Acceptor Oligomers Forming Gels in Water. Biomacromolecules 2023; 24:756-765. [PMID: 36724436 DOI: 10.1021/acs.biomac.2c01203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Inspired by automated DNA synthesis, electron-rich dialkoxynaphthalene (DAN) donor and electron-deficient naphthalene-tetracarboxylic diimide (NDI) acceptor phosphodiester-linked homohexamers were synthesized by the phosphoramidite method. Two types of hexamers were prepared, one with only one phosphodiester between the aromatics (i.e., DAN or NDI) and a second with two phosphodiesters around a propanediol between the aromatics, leading to the latter more flexible and more hydrophilic hexamers. The folding properties of these homohexamers alone or mixed together, in water only, were studied by UV-visible absorption spectroscopy and atomic force microscopy (AFM). AFM imaging revealed that a 1:1 mixture of hexaDAN and hexaNDI formed fibers by charge transfer donor-acceptor recognition leading to a hydrogel after drying. The organization of the resulting structures is strongly dependent on the nature of the complementary partner, leading to the formation of mono- or multilayer hydrogel networks with different compactness.
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Affiliation(s)
- Kévan Pérez de Carvasal
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - Gérard Vergoten
- Université de Lille, Inserm, INFINITE - U1286, Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL), Faculté de Pharmacie, 3 rue du Professeur Laguesse, Lille 59006, France
| | - Jean-Jacques Vasseur
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - Michael Smietana
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
| | - François Morvan
- Université de Montpellier, CNRS, ENSCM, Institut des Biomolécules Max Mousseron, Montpellier 34293, France
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Neitz H, Bessi I, Kachler V, Michel M, Höbartner C. Tailored Tolane-Perfluorotolane Assembly as Supramolecular Base Pair Replacement in DNA. Angew Chem Int Ed Engl 2023; 62:e202214456. [PMID: 36344446 PMCID: PMC10107946 DOI: 10.1002/anie.202214456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 11/09/2022]
Abstract
Arene-fluoroarene interactions offer outstanding possibilities for engineering of supramolecular systems, including nucleic acids. Here, we implement the tolane-perfluorotolane interaction as base pair replacement in DNA. Tolane (THH) and perfluorotolane (TFF) moieties were connected to acyclic backbone units, comprising glycol nucleic acid (GNA) or butyl nucleic acid (BuNA) building blocks, that were incorporated via phosphoramidite chemistry at opposite positions in a DNA duplex. Thermodynamic analyses by UV thermal melting revealed a compelling stabilization by THH/TFF heteropairs only when connected to the BuNA backbone, but not with the shorter GNA linker. Detailed NMR studies confirmed the preference of the BuNA backbone for enhanced polar π-stacking. This work defines how orthogonal supramolecular interactions can be tailored by small constitutional changes in the DNA backbone, and it inspires future studies of arene-fluoroarene-programmed assembly of DNA.
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Affiliation(s)
- Hermann Neitz
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Irene Bessi
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Valentin Kachler
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Manuela Michel
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
| | - Claudia Höbartner
- Institute of Organic ChemistryUniversity of WürzburgAm Hubland97074WürzburgGermany
- Center for Nanosystems Chemistry (CNC)University of WürzburgTheodor-Boveri-Weg97074WürzburgGermany
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Pérez de Carvasal K, Aissaoui N, Vergoten G, Bellot G, Vasseur JJ, Smietana M, Morvan F. Folding of phosphodiester-linked donor–acceptor oligomers into supramolecular nanotubes in water. Chem Commun (Camb) 2021; 57:4130-4133. [DOI: 10.1039/d1cc01064f] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Water soluble foldamers, synthesized by DNA synthesis with dialkoxynaphthalene and naphthalene-tetracarboxylic diimide blocks, formed supramolecular nanotubes in water.
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Affiliation(s)
| | - Nesrine Aissaoui
- Université de Montpellier
- INSERM
- CNRS
- Centre de Biochimie Structurale
- Montpellier
| | - Gérard Vergoten
- Université de Lille
- Inserm
- INFINITE – U1286
- Institut de Chimie Pharmaceutique Albert Lespagnol (ICPAL)
- Faculté de Pharmacie
| | - Gaëtan Bellot
- Université de Montpellier
- INSERM
- CNRS
- Centre de Biochimie Structurale
- Montpellier
| | - Jean-Jacques Vasseur
- Université de Montpellier
- CNRS
- ENSCM
- Institut des Biomolécules Max Mousseron
- Montpellier
| | - Michael Smietana
- Université de Montpellier
- CNRS
- ENSCM
- Institut des Biomolécules Max Mousseron
- Montpellier
| | - François Morvan
- Université de Montpellier
- CNRS
- ENSCM
- Institut des Biomolécules Max Mousseron
- Montpellier
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Zhao Z, Du T, Liang F, Liu S. Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine. Int J Mol Sci 2018; 19:E2283. [PMID: 30081520 PMCID: PMC6121482 DOI: 10.3390/ijms19082283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2018] [Revised: 07/23/2018] [Accepted: 07/30/2018] [Indexed: 12/13/2022] Open
Abstract
Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic building block and then self-assemble into nanomaterials. Of particular note, a recent state-of-the-art research has turned our attention to the amphiphilic DNA organic hybrids including small molecule modified DNA (lipid-DNA, fluorescent molecule-DNA, etc.), DNA block copolymers, and DNA-dendron hybrids. This review focuses mainly on the development of their self-assembly behavior and their potential application in nanomaterial and biomedicine. The potential challenges regarding of the amphiphilic DNA organic hybrids are also briefly discussed, aiming to advance their practical applications in nanoscience and biomedicine.
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Affiliation(s)
- Zhiyong Zhao
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Ting Du
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Feng Liang
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
| | - Simin Liu
- The State Key Laboratory of Refractories and Metallurgy, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China.
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Krasheninina OA, Novopashina DS, Apartsin EK, Venyaminova AG. Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides. Molecules 2017; 22:E2108. [PMID: 29189716 PMCID: PMC6150046 DOI: 10.3390/molecules22122108] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/28/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022] Open
Abstract
In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.
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Affiliation(s)
- Olga A Krasheninina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Darya S Novopashina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Evgeny K Apartsin
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
| | - Alya G Venyaminova
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Acad. Lavrentiev Ave. 8, Novosibirsk 630090, Russia.
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Xiang Y, Zhang Q, Li Z, Chen H. Role of electrostatic complementarity between perylenediimide and porphyrin in highly stabilized GNA. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017; 70:1156-1162. [DOI: 10.1016/j.msec.2016.03.111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 02/03/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
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Doi T, Sakakibara T, Kashida H, Araki Y, Wada T, Asanuma H. Hetero-Selective DNA-Like Duplex Stabilized by Donor-Acceptor Interactions. Chemistry 2015; 21:15974-80. [PMID: 26404181 DOI: 10.1002/chem.201502653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Indexed: 01/20/2023]
Abstract
We report on the characterization of a novel hetero-selective DNA-like duplex of pyrene and anthraquinone pseudo base pairs. The pyrene/anthraquinone pairs showed excellent selectivity in hetero-recognition and even trimers were found to form a hetero-duplex. Pyrene and anthraquinone moieties were tethered on acyclic D-threoninol linkers and linked to adjacent residues by using standard phosphoramidite chemistry. When pyrene and anthraquinone were incorporated at pairing positions in complementary strands of natural DNA oligonucleotides, the duplex was stabilized significantly. Moreover, a pyrene hexamer and an anthraquinone hexamer formed a stable artificial hetero-duplex without the assistance of natural base pairs. The pyrene/anthraquinone pair was so stable that even trimers formed a hetero-duplex under conditions in which natural DNA strands of three residues do not.
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Affiliation(s)
- Tetsuya Doi
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
| | - Takumi Sakakibara
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).,PRESTO (Japan) Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan)
| | - Yasuyuki Araki
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577 (Japan)
| | - Takehiko Wada
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1, Katahira, Aoba-ku, Sendai 980-8577 (Japan)
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).
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Winiger CB, Langenegger SM, Calzaferri G, Häner R. Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks. Angew Chem Int Ed Engl 2015; 54:3643-7. [DOI: 10.1002/anie.201410041] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 11/18/2014] [Indexed: 12/21/2022]
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Winiger CB, Langenegger SM, Calzaferri G, Häner R. Formation of Two Homo-chromophoric H-Aggregates in DNA-Assembled Alternating Dye Stacks. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410041] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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