1
|
Kole GK, Košćak M, Amar A, Majhen D, Božinović K, Brkljaca Z, Ferger M, Michail E, Lorenzen S, Friedrich A, Krummenacher I, Moos M, Braunschweig H, Boucekkine A, Lambert C, Halet JF, Piantanida I, Müller-Buschbaum K, Marder TB. Methyl Viologens of Bis-(4'-Pyridylethynyl)Arenes - Structures, Photophysical and Electrochemical Studies, and their Potential Application in Biology. Chemistry 2022; 28:e202200753. [PMID: 35502627 PMCID: PMC9400870 DOI: 10.1002/chem.202200753] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Indexed: 12/20/2022]
Abstract
A series of bis‐(4’‐pyridylethynyl)arenes (arene=benzene, tetrafluorobenzene, and anthracene) were synthesized and their bis‐N‐methylpyridinium compounds were investigated as a class of π‐extended methyl viologens. Their structures were determined by single crystal X‐ray diffraction, and their photophysical and electrochemical properties (cyclic voltammetry), as well as their interactions with DNA/RNA were investigated. The dications showed bathochromic shifts in emission compared to the neutral compounds. The neutral compounds showed very small Stokes shifts, which are a little larger for the dications. All of the compounds showed very short fluorescence lifetimes (<4 ns). The neutral compound with an anthracene core has a quantum yield of almost unity. With stronger acceptors, the analogous bis‐N‐methylpyridinium compound showed a larger two‐photon absorption cross‐section than its neutral precursor. All of the dicationic compounds interact with DNA/RNA; while the compounds with benzene and tetrafluorobenzene cores bind in the grooves, the one with an anthracene core intercalates as a consequence of its large, condensed aromatic linker moiety, and it aggregates within the polynucleotide when in excess over DNA/RNA. Moreover, all cationic compounds showed highly specific CD spectra upon binding to ds‐DNA/RNA, attributed to the rare case of forcing the planar, achiral molecule into a chiral rotamer, and negligible toxicity toward human cell lines at ≤10 μM concentrations. The anthracene‐analogue exhibited intracellular accumulation within lysosomes, preventing its interaction with cellular DNA/RNA. However, cytotoxicity was evident at 1 μM concentration upon exposure to light, due to singlet oxygen generation within cells. These multi‐faceted features, in combination with its two‐photon absorption properties, suggest it to be a promising lead compound for development of novel light‐activated theranostic agents.
Collapse
Affiliation(s)
- Goutam Kumar Kole
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany.,Department of Chemistry, College of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Tamil Nadu, 603203, India
| | - Marta Košćak
- Ruđer Bošković Institute, 10000, Zagreb, Croatia
| | - Anissa Amar
- Laboratoire de Physique et Chimie Quantiques, Université Mouloud Mammeri, Tizi Ouzou, 15000 Tizi-Ouzou, Algeria
| | | | | | | | - Matthias Ferger
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Evripidis Michail
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Sabine Lorenzen
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Alexandra Friedrich
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Ivo Krummenacher
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Michael Moos
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Holger Braunschweig
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Abdou Boucekkine
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, Institut des Sciences Chimiques de Rennes UMR 6226, 35000, Rennes, France
| | - Christoph Lambert
- Institut für Organische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Jean-François Halet
- Univ Rennes, Ecole Nationale Supérieure de Chimie de Rennes, CNRS, Institut des Sciences Chimiques de Rennes UMR 6226, 35000, Rennes, France.,CNRS-Saint-Gobain-NIMS, IRL 3629, Laboratory for Innovative Key Materials and Structures (LINK), National Institute for Materials Science (NIMS), Tsukuba, 305-0044, Japan
| | | | - Klaus Müller-Buschbaum
- Institut für Anorganische und Analytische Chemie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 17, 35392, Gießen, Germany
| | - Todd B Marder
- Institut für Anorganische Chemie, and, Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074, Würzburg, Germany
| |
Collapse
|
2
|
Weißenstein A, Vysotsky MO, Piantanida I, Würthner F. Naphthalene diimide–amino acid conjugates as novel fluorimetric and CD probes for differentiation between ds-DNA and ds-RNA. Beilstein J Org Chem 2020; 16:2032-2045. [PMID: 32874350 PMCID: PMC7445415 DOI: 10.3762/bjoc.16.170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/04/2020] [Indexed: 11/23/2022] Open
Abstract
Two novel unnatural amino acids, prepared by linking a dicationic purple-coloured and fluorescent naphthalene diimide (NDI) at core position to amino acid side chains of variable length, strongly interacted with ds-DNA/RNA by threading intercalation. Different from a reference NDI dye with identical visible range absorbance (520–540 nm) and Stokes shifts in emission (+60 nm, quantum yield > 0.2), only these amino acid–NDI conjugates showed selective fluorimetric response for GC-DNA in respect to AT(U)-polynucleotides. The DNA/RNA binding-induced circular dichroism (ICD) response of NDI at 450–550 nm strongly depended on the length and rigidity of the linker to the amino acid unit, which controls the orientation of the NDI unit inside within the intercalative binding site. The ICD selectivity also depends on the type of polynucleotide, thus the studied NDI dyes act as dual fluorimetric/ICD probes for sensing the difference between here used GC-DNA, AT-DNA and AU-RNA.
Collapse
Affiliation(s)
- Annike Weißenstein
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Myroslav O Vysotsky
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, PO Box 180, 10002 Zagreb, Croatia
| | - Frank Würthner
- Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany
- Center for Nanosystems Chemistry (CNC), Universität Würzburg, Theodor-Boveri-Weg, 97074 Würzburg, Germany
| |
Collapse
|
3
|
Zhirov AM, Kovalev DA, Ulshina DV, Pisarenko SV, Demidov OP, Borovlev IV. Diazapyrenes: interaction with nucleic acids and biological activity. Chem Heterocycl Compd (N Y) 2020; 56:674-693. [PMID: 32836316 PMCID: PMC7366485 DOI: 10.1007/s10593-020-02717-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/26/2019] [Indexed: 12/22/2022]
Abstract
The review summarizes data on the practical aspects of the interaction of nucleic acids with diazapyrene derivatives. The information on biological activity is given and the probable mechanisms underlying the action of diazapyrenes are analyzed. It contains 119 references.
Collapse
Affiliation(s)
- Andrey M. Zhirov
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Dmitry A. Kovalev
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Diana V. Ulshina
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Sergey V. Pisarenko
- Stavropol Research Anti-Plague Institute, 13-15 Sovetskaya St, Stavropol, 355035 Russia
| | - Oleg P. Demidov
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| | - Ivan V. Borovlev
- North Caucasus Federal University, 1a Pushkina St, Stavropol, 355017 Russia
| |
Collapse
|
4
|
Mansour AM, Ragab MS. DNA/lysozyme binding propensity and nuclease properties of benzimidazole/2,2'-bipyridine based binuclear ternary transition metal complexes. RSC Adv 2019; 9:30879-30887. [PMID: 35529371 PMCID: PMC9072361 DOI: 10.1039/c9ra07188a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 09/25/2019] [Indexed: 12/21/2022] Open
Abstract
In the present contribution, new binuclear ternary complexes; [M2(bpy)4L](ClO4)4 (M = Co(ii) (1) and Ni(ii) (2); bpy = 2,2'-bipyridine; L = 1,1'-(hexane-1,6-diyl)bis[2-(pyridin-2-yl)1H-benzimidazole] and [Cu2(bpy)2(OH2)2L](BF4)4 (3) were synthesized, characterized and screened for their antimicrobial activity and cytotoxicity against human liver carcinoma cells (HepG-2) as well as non-malignant human embryonic kidney cells (HEK-293). The structural studies were complemented by density functional theory (DFT) calculations. DNA binding of 1-3 was spectrophotometrically studied. The DNA cleavage ability of 1-3 towards the supercoiled plasmid DNA (pBR322 DNA) was examined through gel electrophoresis. Compound 3 has the highest cytotoxic activity (IC50 = 3.5 μg mL-1) against HepG-2 among the investigated complexes and is non cytotoxic to noncancerous HEK-293. Complexes (1 and 2) exhibited toxicity to HEK-293 with IC50 values of 30.3 and 23.5 μg mL-1 in that order. While compound 1 showed antifungal activity against Cryptococcus neoformans, complex 2 exhibited its toxicity against Candida albicans.
Collapse
Affiliation(s)
- Ahmed M Mansour
- Department of Chemistry, Faculty of Science, Cairo University Gamma Street, Giza Cairo 12613 Egypt
| | - Mona S Ragab
- Department of Chemistry, Faculty of Science, Cairo University Gamma Street, Giza Cairo 12613 Egypt
| |
Collapse
|
5
|
Fairbanks SD, Robertson CC, Keene FR, Thomas JA, Williamson MP. Structural Investigation into the Threading Intercalation of a Chiral Dinuclear Ruthenium(II) Polypyridyl Complex through a B-DNA Oligonucleotide. J Am Chem Soc 2019; 141:4644-4652. [PMID: 30799603 DOI: 10.1021/jacs.8b12280] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Herein we report the separation of the three stereoisomers of the DNA light-switch compound [{Ru(bpy)2}2(tpphz)]4+ (tpphz = tetrapyrido[3,2-a:2',3'-c:3″,2″-h:2‴,3‴-j]phenazine) by column chromatography and the characterization of each stereoisomer by X-ray crystallography. The interaction of these compounds with a DNA octanucleotide d(GCATATCG).d(CGATATGC) has been studied using NMR techniques. Selective deuteration of the bipyridyl rings was needed to provide sufficient spectral resolution to characterize structures. NMR-derived structures for these complexes show a threading intercalation binding mode with slow and chirality-dependent rates. This represents the first solution structure of an intercalated bis-ruthenium ligand. Intriguingly, we find that the binding site selectivity is dependent on the nature of the stereoisomer employed, with Λ RuII centers showing a better intercalation fit.
Collapse
Affiliation(s)
- Simon D Fairbanks
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K.,Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
| | - Craig C Robertson
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - F Richard Keene
- Department of Chemistry, School of Physical Sciences , University of Adelaide , Adelaide , SA 5005 , Australia
| | - Jim A Thomas
- Department of Chemistry , University of Sheffield , Brook Hill , Sheffield , S3 7HF , U.K
| | - Mike P Williamson
- Department of Molecular Biology and Biotechnology , University of Sheffield , Western Bank , Sheffield , S10 2TN , U.K
| |
Collapse
|
6
|
Basak S, Léon JC, Ferranco A, Sharma R, Hebenbrock M, Lough A, Müller J, Kraatz HB. AgI
-Induced Switching of DNA Binding Modes via Formation of a Supramolecular Metallacycle. Chemistry 2018; 24:3729-3732. [DOI: 10.1002/chem.201800440] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Indexed: 12/18/2022]
Affiliation(s)
- Shibaji Basak
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - J. Christian Léon
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Annaleizle Ferranco
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Renu Sharma
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
| | - Marian Hebenbrock
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Alan Lough
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
| | - Jens Müller
- Institut für Anorganische und Analytische Chemie; Westfälische Wilhelms-Universität Münster; Corrensstraße 28/30 48149 Münster Germany
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences; University of Toronto; Scarborough 1265 Military Trail Toronto Ontario M1C 1A4 Canada
- Department of Chemistry; University of Toronto; 80 St. George Street Toronto Ontario M5S 3H6 Canada
| |
Collapse
|
7
|
Mansour AM, Shehab OR. Lysozyme and DNA binding affinity of Pd(ii) and Pt(ii) complexes bearing charged N,N-pyridylbenzimidazole bidentate ligands. Dalton Trans 2018; 47:3459-3468. [DOI: 10.1039/c7dt04347c] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The 2-pyridylbenzimidazole Pt(ii) complex functionalized with triphenylphosphonium interacts covalently with lysozyme via the loss of labile ligands and the departure of the TPP+ part.
Collapse
Affiliation(s)
- Ahmed M. Mansour
- Department of Chemistry
- Faculty of Science
- Cairo University
- Cairo 12613
- Egypt
| | - Ola R. Shehab
- Department of Chemistry
- Faculty of Science
- Cairo University
- Cairo 12613
- Egypt
| |
Collapse
|
8
|
Islam MM, Fujii S, Sato S, Okauchi T, Takenaka S. Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs. Bioorg Med Chem 2015; 23:4769-4776. [PMID: 26081762 DOI: 10.1016/j.bmc.2015.05.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/22/2015] [Accepted: 05/24/2015] [Indexed: 10/23/2022]
Abstract
Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation from dsDNA than cNDI 2.
Collapse
Affiliation(s)
- Md Monirul Islam
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Satoshi Fujii
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
| | - Shinobu Sato
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Tatsuo Okauchi
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan
| | - Shigeori Takenaka
- Department of Applied Chemistry, Kyushu Institute of Technology, Kitakyushu, Fukuoka 804-8550, Japan.
| |
Collapse
|
9
|
Evans K, Bhamra I, Wheelhouse RT, Arnold JRP, Cosstick R, Fisher J. Stabilization of a Bimolecular Triplex by 3'-S-Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation. Chemistry 2015; 21:7278-84. [PMID: 25802084 DOI: 10.1002/chem.201500369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/08/2022]
Abstract
Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson-Crick (W-C) base-paired DNA duplexes and a Hoogsteen base-paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA-like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3'-S-phosphorothiolate (3'-SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. (1) H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3'-SP modifications is more compact. The 3'-SP modification was previously shown to stabilise G-quadruplex and i-motif structures and therefore is now proposed as a generic solution to stabilising multi-stranded DNA structures.
Collapse
Affiliation(s)
- Kathryn Evans
- School of Chemistry, University of Leeds, Leeds, LS2 9JT (UK)
| | | | | | | | | | | |
Collapse
|
10
|
Panesar HK, Solano J, Minehan TG. Synthesis and DNA binding profile of N-mono- and N,N'-disubstituted indolo[3,2-b]carbazoles. Org Biomol Chem 2015; 13:2879-83. [PMID: 25633133 PMCID: PMC4339310 DOI: 10.1039/c4ob02566k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of N-monosubstituted and N,N'-disubstituted derivatives of the indolo[3,2-b]carbazole chromophore have been prepared, and their binding affinity for duplex DNA has been evaluated by ultraviolet and fluorescence spectroscopies. It has been found that indolo[3,2-b]carbazoles bearing basic N-alkyl substituents are intercalators that bind DNA with affinities in the micromolar and submicromolar range and a preference for associating with sequences of mixed composition and purine-pyrimidine steps.
Collapse
Affiliation(s)
- Harmanpreet Kaur Panesar
- Department of Chemistry and Biochemistry, California State University, Northridge, 18111 Nordhoff Street, Northridge, CA 91330, USA.
| | | | | |
Collapse
|
11
|
The stacking geometries and association thermodynamics of oxalyl acid N,N ′-dibenzoyl-hydrazide derivatives studied by NMR. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
12
|
Rhoden Smith A, Iverson BL. Threading polyintercalators with extremely slow dissociation rates and extended DNA binding sites. J Am Chem Soc 2013; 135:12783-9. [PMID: 23919778 DOI: 10.1021/ja4057344] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-vis spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid-based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.
Collapse
Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | | |
Collapse
|
13
|
Haldar R, Maji TK. Metal–organic frameworks (MOFs) based on mixed linker systems: structural diversities towards functional materials. CrystEngComm 2013. [DOI: 10.1039/c3ce41438h] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
14
|
Smith AR, Ikkanda BA, Holman GG, Iverson BL. Subtle recognition of 14-base pair DNA sequences via threading polyintercalation. Biochemistry 2012; 51:4445-52. [PMID: 22554127 PMCID: PMC3369501 DOI: 10.1021/bi300317n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules that bind DNA in a sequence-specific manner could act as antibiotic, antiviral, or anticancer agents because of their potential ability to manipulate gene expression. Our laboratory has developed threading polyintercalators based on 1,4,5,8-naphthalene diimide (NDI) units connected in a head-to-tail fashion by flexible peptide linkers. Previously, a threading tetraintercalator composed of alternating minor-major-minor groove-binding modules was shown to bind specifically to a 14 bp DNA sequence with a dissociation half-life of 16 days [Holman, G. G., et al. (2011) Nat. Chem. 3, 875-881]. Herein are described new NDI-based tetraintercalators with a different major groove-binding module and a reversed N to C directionality of one of the minor groove-binding modules. DNase I footprinting and kinetic analyses revealed that these new tetraintercalators are able to discriminate, by as much as 30-fold, 14 bp DNA binding sites that differ by 1 or 2 bp. Relative affinities were found to correlate strongly with dissociation rates, while overall C(2) symmetry in the DNA-binding molecule appeared to contribute to enhanced association rates.
Collapse
Affiliation(s)
- Amy Rhoden Smith
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | | | | | | |
Collapse
|
15
|
Wu K, Luo Q, Hu W, Li X, Wang F, Xiong S, Sadler PJ. Mechanism of interstrand migration of organoruthenium anticancer complexes within a DNA duplex. Metallomics 2012; 4:139-48. [PMID: 22262368 DOI: 10.1039/c2mt00162d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Organometallic ruthenium(ii) anticancer complexes [(η(6)-arene)Ru(en)Cl][PF(6)] (e.g. arene = biphenyl (bip, 1), indane (ind, 2); en = ethylenediamine) bind to N7 of guanine (G) in DNA selectively. The fragment {(η(6)-bip)Ru(en)}(2+) (1') bound to N7 of one guanine residue at a 14-mer duplex DNA migrates readily to other guanine residues in both the same strand and the complementary strand when the strands are hybridized at elevated temperature. In this work, by applying HPLC coupled to mass spectrometry, the mechanism of such intra- and interstrand migration was investigated using a 15-mer duplex, in which one strand 5'-CTCTCTTG(8)TCTTCTC-3' (I) contained a single guanine (G(8)). The results show that the interstrand migration of complexes 1 and 2 within the duplex involves an SN1 pathway, firstly solvent-assisted dissociation of the initially G(8)-bound adducts I-G(8)-1' and I-G(8)-2' (2' = {(η(6)-ind)Ru(en)}(2+)) as the rate-controlling step, and secondly the coordination of the dissociated 1' and 2' to guanine bases (G(21) for 1', either G(21) or G(18) for 2') on strand II. The high temperature used to anneal the single strands was found to increase the migration rate. The formation of the duplex acts as a key driving force to promote the dissociation of G(8)-bound 1' and 2' due to the competition of cytosine in II with the en-NH(2) groups in 1' and 2' for H-bonding with C6O of guanine. Complex 2 (t(1/2) = 18 h) containing a mono-ringed arene ligand dissociates more readily from the initially binding site G(8) than complex 1 (t(1/2) = 23 h). The extended biphenyl arene ligand which is intercalated into DNA stabilizes the adduct I-G(8)-1'. These results provide new insight into this unusual metal migration, and are of significance for the design and development of more active organometallic ruthenium anticancer complexes.
Collapse
Affiliation(s)
- Kui Wu
- CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, PR China
| | | | | | | | | | | | | |
Collapse
|
16
|
|
17
|
Holman GG, Zewail-Foote M, Smith AR, Johnson KA, Iverson BL. A sequence-specific threading tetra-intercalator with an extremely slow dissociation rate constant. Nat Chem 2011; 3:875-81. [PMID: 22024884 PMCID: PMC3209807 DOI: 10.1038/nchem.1151] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2011] [Accepted: 08/17/2011] [Indexed: 12/02/2022]
Abstract
A long-lived and sequence specific ligand-DNA complex would make possible the modulation of biological processes for extended periods. We have been investigating the threading polyintercalation approach to DNA recognition in which chains of aromatic units thread back and forth repeatedly through the double helix. Here we report the preliminary sequence specificity and detailed kinetic analysis of a structurally characterized threading tetraintercalator. Specific binding on a relatively long DNA strand was observed, strongly favoring a predicted 14-base pair sequence. Kinetic studies revealed a multi-step association process and specificity was found to derive primarily from large differences in dissociation rates. Importantly, the rate-limiting dissociation rate constant of the tetraintercalator complex dissociating from its preferred binding site was extremely slow, corresponding to a 16 day half-life, making it one of the longer non-covalent complex half-lives yet measured, and, to the best of our knowledge, the longest for a DNA binding molecule.
Collapse
Affiliation(s)
- Garen G Holman
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | | | | | | | | |
Collapse
|
18
|
McKnight RE, Reisenauer E, Pintado MV, Polasani SR, Dixon DW. Substituent effect on the preferred DNA binding mode and affinity of a homologous series of naphthalene diimides. Bioorg Med Chem Lett 2011; 21:4288-91. [DOI: 10.1016/j.bmcl.2011.05.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2011] [Revised: 05/16/2011] [Accepted: 05/18/2011] [Indexed: 11/15/2022]
|
19
|
Abstract
DNA has a strong affinity for many heterocyclic aromatic dyes, such as acridine and its derivatives. Lerman in 1961 first proposed intercalation as the source of this affinity, and this mode of DNA binding has since attracted considerable research scrutiny. Organic intercalators can inhibit nucleic acid synthesis in vivo, and they are now common anticancer drugs in clinical therapy. The covalent attachment of organic intercalators to transition metal coordination complexes, yielding metallointercalators, can lead to novel DNA interactions that influence biological activity. Metal complexes with σ-bonded aromatic side arms can act as dual-function complexes: they bind to DNA both by metal coordination and through intercalation of the attached aromatic ligand. These aromatic side arms introduce new modes of DNA binding, involving mutual interactions of functional groups held in close proximity. The biological activity of both cis- and trans-diamine Pt(II) complexes is dramatically enhanced by the addition of σ-bonded intercalators. We have explored a new class of organometallic "piano-stool" Ru(II) and Os(II) arene anticancer complexes of the type [(η(6)-arene)Ru/Os(XY)Cl](+). Here XY is, for example, ethylenediamine (en), and the arene ligand can take many forms, including tetrahydroanthracene, biphenyl, or p-cymene. Arene-nucleobase stacking interactions can have a significant influence on both the kinetics and thermodynamics of DNA binding. In particular, the cytotoxic activity, conformational distortions, recognition by DNA-binding proteins, and repair mechanisms are dependent on the arene. A major difficulty in developing anticancer drugs is cross-resistance, a phenomenon whereby a cell that is resistant to one drug is also resistant to another drug in the same class. These new complexes are non-cross-resistant with cisplatin towards cancer cells: they constitute a new class of anticancer agents, with a mechanism of action that differs from the anticancer drug cisplatin and its analogs. The Ru-arene complexes with dual functions are more potent towards cancer cells than their nonintercalating analogs. In this Account, we focus on recent studies of dual-function organometallic Ru(II)- and Os(II)-arene complexes and the methods used to detect arene-DNA intercalation. We relate these interactions to the mechanism of anticancer activity and to structure-activity relationships. The interactions between these complexes and DNA show close similarities to those of covalent polycyclic aromatic carcinogens, especially to N7-alkylating intercalation compounds. However, Ru-arene complexes exhibit some new features. Classical intercalation and base extrusion next to the metallated base is observed for {(η(6)-biphenyl)Ru(ethylenediamine)}(2+) adducts of a 14-mer duplex, while penetrating arene intercalation occurs for adducts of the nonaromatic bulky intercalator {(η(6)-tetrahydroanthracene)Ru(ethylenediamine)}(2+) with a 6-mer duplex. The introduction of dual-function Ru-arene complexes introduces new mechanisms of antitumor activity, novel mechanisms for attack on DNA, and new concepts for developing structure- activity relationships. We hope this discussion will stimulate thoughtful and focused research on the design of anticancer chemotherapeutic agents using these unique approaches.
Collapse
Affiliation(s)
- Hong-Ke Liu
- Jiangsu Key Laboratory of Biofunctional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210046, China
| | - Peter J. Sadler
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, U.K
| |
Collapse
|
20
|
Abstract
Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.
Collapse
|
21
|
Doria F, di Antonio M, Benotti M, Verga D, Freccero M. Substituted heterocyclic naphthalene diimides with unexpected acidity. Synthesis, properties, and reactivity. J Org Chem 2010; 74:8616-25. [PMID: 19848382 DOI: 10.1021/jo9017342] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Naphthalene bisimides (NDIs) with a heterocyclic 1,4-dihydro-2,3-pyrazinedione moiety have been synthesized from both 2,6-dibromonaphthalene and 2,3,6,7-tetrabromonaphthalene bisanhydrides by means of a stepwise protocol including imidization, nucleophilic displacement of the bromine atoms by ethane-1,2-diamine, in situ reductive dehalogenation, and further oxidation. These heterocycles (R = n-pentyl, cyclohexyl) are yellow dyes with green emission in organic solvent, where the acid form dominates. The orange nonfluorescent conjugate base can be generated quantitatively by CH(3)COONBu(4) addition in DMSO, where it exhibits a pK(a) = 7.63. The conjugate base becomes the only detectable species (by UV-vis spectroscopy), in water solution, even under acid conditions (pH 1). In aqueous DMSO the acid/base equilibrium is a function of the DMSO/water ratio. The unexpected acidity of these heterocyclic NDIs, which justifies the reactivity with CH(2)N(2), has been rationalized by DFT computational means [PBE0/6-31+G(d,p)] in aqueous solvent (PCM models) as a result of a strong specific solvation effect, modeled by the inclusion of three water molecules.
Collapse
Affiliation(s)
- Filippo Doria
- Dipartimento di Chimica Organica, Università di Pavia, V. le Taramelli 10, 27100 Pavia, Italy
| | | | | | | | | |
Collapse
|
22
|
Liu HK, Parkinson JA, Bella J, Wang F, Sadler PJ. Penetrative DNA intercalation and G-base selectivity of an organometallic tetrahydroanthracene RuII anticancer complex. Chem Sci 2010. [DOI: 10.1039/c0sc00175a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
|
23
|
Recent developments in the chemistry of deoxyribonucleic acid (DNA) intercalators: principles, design, synthesis, applications and trends. Molecules 2009; 14:1725-46. [PMID: 19471193 PMCID: PMC6254398 DOI: 10.3390/molecules14051725] [Citation(s) in RCA: 104] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 04/20/2009] [Accepted: 05/05/2009] [Indexed: 01/17/2023] Open
Abstract
In the present overview, we describe the bases of intercalation of small molecules (cationic and polar neutral compounds) in DNA. We briefly describe the importance of DNA structure and principles of intercalation. Selected syntheses, possibilities and applications are shown to exemplify the importance, drawbacks and challenges in this pertinent, new, and exciting research area. Additionally, some clinical applications (molecular processes, cancer therapy and others) and trends are described.
Collapse
|
24
|
Chu Y, Hoffman DW, Iverson BL. A pseudocatenane structure formed between DNA and A cyclic bisintercalator. J Am Chem Soc 2009; 131:3499-508. [PMID: 19236098 PMCID: PMC2733282 DOI: 10.1021/ja805676w] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting double-stranded DNA with small molecules remains an active area of basic research. Herein is described a cyclic DNA bisintercalator that is based on two naphthalene diimide (NDI) intercalating units tethered by one linking element specific for binding in the minor groove and the other linking element specific for binding in the major groove. DNase I footprinting revealed a strong preference for binding the sequence 5'-GGTACC-3'. NMR structural studies of the complex with d(CGGTACCG)(2) verified a pseudocatenane structure in which the NDI units reside four base pairs apart, with one linker segment located in the minor groove and the other in the major groove consistent with the linker designs. To the best of our knowledge, this is the first structurally well-characterized pseudocatenane complex between a sequence specific cyclic bisintercalator and intact DNA.
Collapse
Affiliation(s)
- Yongjun Chu
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - David W. Hoffman
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Brent L. Iverson
- Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
25
|
Kim MB, Dixon DW. Hydrolysis of aliphatic naphthalene diimides: effect of charge placement in the side chains. J PHYS ORG CHEM 2008. [DOI: 10.1002/poc.1334] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
26
|
Tri- and tetra-substituted naphthalene diimides as potent G-quadruplex ligands. Bioorg Med Chem Lett 2008; 18:1668-73. [DOI: 10.1016/j.bmcl.2008.01.050] [Citation(s) in RCA: 115] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Revised: 01/10/2008] [Accepted: 01/14/2008] [Indexed: 12/11/2022]
|
27
|
Malinovskii VL, Samain F, Häner R. Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework. Angew Chem Int Ed Engl 2007; 46:4464-7. [PMID: 17510989 DOI: 10.1002/anie.200700891] [Citation(s) in RCA: 140] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Vladimir L Malinovskii
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | | | |
Collapse
|
28
|
Malinovskii V, Samain F, Häner R. Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200700891] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
29
|
Spillane CB, Smith JA, Morgan JL, Keene FR. DNA affinity binding studies using a fluorescent dye displacement technique: the dichotomy of the binding site. J Biol Inorg Chem 2007; 12:819-24. [PMID: 17486377 DOI: 10.1007/s00775-007-0235-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2006] [Accepted: 03/30/2007] [Indexed: 10/23/2022]
Abstract
We have observed a number of discrepancies and contradictions in the use of a fluorescent intercalator displacement assay in surveying the binding affinities of dinuclear polypyridyl ruthenium(II) complexes with DNA. By a modification of the assay using the fluorescent minor-groove binder 4',6-diamidino-2-phenylindole, rather than intercalating dyes (ethidium bromide or thiazole orange), results were obtained for all complexes studied which were consistent with relative affinities and stereoselectivities observed with other techniques, including NMR, affinity chromatography and equilibrium dialysis. It is believed that the difference in binding mode between the minor groove-binding Ru(II) complexes and the intercalating fluorescent dyes they are displacing may contribute to these discrepancies.
Collapse
Affiliation(s)
- Caitriona B Spillane
- School of Pharmacy and Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
| | | | | | | |
Collapse
|
30
|
Mazzitelli CL, Chu Y, Reczek JJ, Iverson BL, Brodbelt JS. Screening of threading bis-intercalators binding to duplex DNA by electrospray ionization tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:311-21. [PMID: 17098442 PMCID: PMC1853371 DOI: 10.1016/j.jasms.2006.09.021] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Revised: 09/21/2006] [Accepted: 09/26/2006] [Indexed: 05/11/2023]
Abstract
The DNA binding of novel threading bis-intercalators V1, trans-D1, and cis-C1, which contain two naphthalene diimide (NDI) intercalation units connected by a scaffold, was evaluated using electrospray ionization mass spectrometry (ESI-MS) and DNAse footprinting techniques. ESI-MS experiments confirmed that V1, the ligand containing the -Gly3-Lys- peptide scaffold, binds to a DNA duplex containing the 5'-GGTACC-3' specific binding site identified in previous NMR-based studies. The ligand formed complexes with a ligand/DNA binding stoichiometry of 1:1, even when there was excess ligand in solution. Trans-D1 and cis-C1 are new ligands containing a rigid spiro-tricyclic scaffold in the trans- and cis- orientations, respectively. Preliminary DNAse footprinting experiments identified possible specific binding sites of 5'-CAGTGA-5' for trans-D1 and 5'-GGTACC-3' for cis-C1. ESI-MS experiments revealed that both ligands bound to DNA duplexes containing the respective specific binding sequences, with cis-C1 exhibiting the most extensive binding based on a higher fraction of bound DNA value. Cis-C1 formed complexes with a dominant 1:1 binding stoichiometry, whereas trans-D1 was able to form 2:1 complexes at ligand/DNA molar ratios >or=1 which is suggestive of nonspecific binding. Collisional activated dissociation (CAD) experiments indicate that DNA complexes containing V1, trans-D1, and cis-C1 have a unique fragmentation pathway, which was also observed for complexes containing the commercially available bis-intercalator echinomycin, as a result of similar binding interactions, marked by intercalation in addition to hydrogen bonding by the scaffold with the DNA major or minor groove.
Collapse
Affiliation(s)
- Carolyn L Mazzitelli
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, Texas 78712-0165, USA
| | | | | | | | | |
Collapse
|
31
|
Liu HK, Wang F, Parkinson JA, Bella J, Sadler PJ. Ruthenation of duplex and single-stranded d(CGGCCG) by organometallic anticancer complexes. Chemistry 2007; 12:6151-65. [PMID: 16807967 DOI: 10.1002/chem.200600110] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have studied the interaction of the organometallic anticancer ruthenium(II) complexes [(eta(6)-p-cymene)Ru(en)Cl][PF(6)] (1) and [(eta(6)-biphenyl)Ru(en)Cl][PF(6)] (2) (en=ethylenediamine) with the single-stranded (ss) DNA hexamer d(CGGCCG) (I) and the duplex d(CGGCCG)(2) (II) by HPLC, ESI-MS, and one- and two-dimensional (1)H and (15)N NMR spectroscopy. For ss-DNA, all three G's are readily ruthenated with [(eta(6)-arene)Ru(en)](2+), but for duplex DNA there is preferential ruthenation of G3 and G6, and no binding to G2 was detected. For monoruthenated duplexes, N7 ruthenation of G is accompanied by strong hydrogen bonding between G-O6 and en-NH for the p-cymene adducts. Intercalation of the non-coordinated phenyl ring between G3 and C4 or G6 and C5 was detected in the biphenyl adducts of mono- and diruthenated duplexes, together with weakening of the G-O6NH-en hydrogen bonding. The arene ligand plays a major role in distorting the duplex either through steric interactions (p-cymene) or through intercalation (biphenyl).
Collapse
Affiliation(s)
- Hong-Ke Liu
- School of Chemistry, University of Edinburgh, King's Buildings, West Mains Road, Edinburgh EH9 3 JJ, UK
| | | | | | | | | |
Collapse
|
32
|
Gorteau V, Bollot G, Mareda J, Matile S. Rigid-rod anion–π slides for multiion hopping across lipid bilayers. Org Biomol Chem 2007; 5:3000-12. [PMID: 17728867 DOI: 10.1039/b708337h] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Shape-persistent oligo-p-phenylene-N,N-naphthalenediimide (O-NDI) rods are introduced as anion-pi slides for chloride-selective multiion hopping across lipid bilayers. Results from end-group engineering and covalent capture as O-NDI hairpins suggested that self-assembly into transmembrane O-NDI bundles is essential for activity. A halide topology VI (Cl > F > Br approximately I, Cl/Br approximately Cl/I > 7) implied strong anion binding along the anion-pi slides with relatively weak contributions from size exclusion (F >or= OAc). Anomalous mole fraction effects (AMFE) supported the occurrence of multiion hopping along the pi-acidic O-NDI rods. The existence of anion-pi interactions was corroborated by high-level ab initio and DFT calculations. The latter revealed positive NDI quadrupole moments far beyond the hexafluorobenzene standard. Computational studies further suggested that anion binding occurs at the confined, pi-acidic edges of the sticky NDI surface and is influenced by the nature of the phenyl spacer between two NDIs. With regard to methods development, a detailed analysis of the detection of ion selectivity with the HPTS assay including AMFE in vesicles is provided.
Collapse
Affiliation(s)
- Virginie Gorteau
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | | | | | | |
Collapse
|
33
|
Tanaka H, Bollot G, Mareda J, Litvinchuk S, Tran DH, Sakai N, Matile S. Synthetic pores with sticky π-clamps. Org Biomol Chem 2007; 5:1369-80. [PMID: 17464406 DOI: 10.1039/b702255g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this report, we describe design, synthesis, evaluation and molecular dynamics simulations of synthetic multifunctional pores with pi-acidic naphthalenediimide clamps. Experimental evidence is provided for the formation of unstable but inert, heterogeneous and acid-insensitive dynamic tetrameric pores that are sensitive to base and ionic strength. Blockage experiments reveal that the introduction of aromatic electron donor-acceptor interactions provides access to the selective recognition of pi-basic intercalators within the pore. This breakthrough is important for the application of synthetic pores as multianalyte sensors.
Collapse
Affiliation(s)
- Hiroyuki Tanaka
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | | | | | | | | | | | | |
Collapse
|
34
|
Sun H, Ye K, Wang C, Qi H, Li F, Wang Y. The π−π Stacked Geometries and Association Thermodynamics of Quinacridone Derivatives Studied by 1H NMR. J Phys Chem A 2006; 110:10750-6. [PMID: 16970367 DOI: 10.1021/jp057232a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pi-pi stacked associations of three N,N'-di(n-butyl) quinacridone derivatives, widely used dopants in organic light-emitting diodes, with different sizes of substituents were investigated in solution at various temperatures by (1)H NMR spectroscopy. The pi-pi stacked geometries were estimated by both the magnitudes of peak shifts with concentration and the directions of peak shifts induced by polar solvents. Two patterns of geometries with different pi-pi interaction strengths were found to coexist in solution for all the three samples. In both of the patterns, the preferential orientation of the stacking is the approach of the carbonyl groups on one molecule to the nitrogen atoms on the stacked partner, which makes the pi-deficient aromatic atoms interact with both pi-rich and pi-deficient aromatic atoms of the stacked partner to maximize the electrostatic complementarity. Differently, whereas the molecules in one pattern are face-to-face stacked in a parallel fashion and slip two rings relative to one another along with the long axis of the conjugated ring systems, the molecules in the other are either face-to-face stacked in an antiparallel fashion with slight slipping between layers or stacked in a turning fashion. Both association constants obtained by fitting the dilution curves and thermodynamic parameters obtained from van't Hoff analyses revealed unexpectedly three thermodynamic processes of aggregations for all the three samples in the temperature region of 298-213 K. The size of substituents on the outer aromatic rings significantly influences the pi-pi stacked structures and association thermodynamics.
Collapse
Affiliation(s)
- Hui Sun
- Key Laboratory for Supramolecular Structure and Materials of Ministry of Education, Jilin University, Changchun 130012, People's Republic of China
| | | | | | | | | | | |
Collapse
|
35
|
Chu Y, Lynch V, Iverson BL. Synthesis and DNA binding studies of bis-intercalators with a novel spiro-cyclic linker. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.038] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
36
|
Mizukami J, Sugiura H, Yamaguchi M, Mushiake K. Synthesis of Helicenediamine Oligomers and Their Formation of Multilayer Structures in Aqueous Solvents. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.317] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
37
|
Bhosale S, Sisson AL, Sakai N, Matile S. Synthetic functional π-stack architecture in lipid bilayers. Org Biomol Chem 2006; 4:3031-9. [PMID: 16886067 DOI: 10.1039/b606487f] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neglected until recently, pi-stack architecture is rapidly emerging as a powerful strategy to create function in lipid bilayer membranes. Recent reports describe supramolecular rosettes acting as hosts of intercalating guests, to assemble in bilayer membranes and, in the case of stacked guanosine and folate quartets, to form ion channels. The introduction of rigid-rod pi-stack architecture allowed us to address one of the great challenges in the field, i.e. ligand gating. Inspiring pi-stack chemistry from related fields, covering rainbow coloration, conductivity, as well as the critical dependence of charge mobilities on the precision of supramolecular organization is summarized to zoom in on arguably the most promising application of functional pi-stack architecture in lipid bilayers, that is the creation of multifunctional photosystems.
Collapse
Affiliation(s)
- Sheshanath Bhosale
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | | | | | | |
Collapse
|
38
|
Abstract
Supramolecular pi-stack architecture is fundamental in DNA chemistry but absent in biological and synthetic ion channels and pores. Here, a novel rigid-rod pi-stack architecture is introduced to create synthetic ion channels with characteristics that are at the forefront of rational design, that is, ligand gating by a conformational change of the functional supramolecule. Namely, the intercalation of electron-rich aromatics is designed to untwist inactive electron-poor helical pi-stacks without internal space into open barrel-stave ion channels. Conductance experiments in planar lipid bilayers corroborate results from spherical bilayers and molecular modeling: Highly cooperative and highly selective ligand gating produces small, long-lived, weakly anion selective, ohmic ion channels. Structural studies conducted under conditions relevant for function provide experimental support for helix-barrel transition as origin of ligand gating. Control experiments demonstrate that minor structural changes leading to internal decrowding suffice to cleanly annihilate chiral self-organization and function.
Collapse
Affiliation(s)
- Pinaki Talukdar
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | | | | | | | | |
Collapse
|