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Kwon HC, Lee DH, Yoon M, Nayab S, Lee H, Han JH. Novel Cu(II) complexes as DNA-destabilizing agents and their DNA nuclease activity. Dalton Trans 2023; 52:16802-16811. [PMID: 37902974 DOI: 10.1039/d3dt02615a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
Here, we report a series of four novel Cu complexes, namely 2-(piperidin-1-ylmethyl)quinoline copper(II) nitrate, [LACu(NO3)2] (Cu1), 4-(quinolin-2-ylmethyl)morpholine copper(II) nitrate, [LBCu(NO3)2] (Cu2), 4-(quinolin-2-ylmethyl)morpholine copper(II) chloride, [LBCuCl2] (Cu3), and 2-(piperidin-1-ylmethyl)pyridine copper(II) chloride, [LCCu(μ-Cl)Cl]2 (Cu4). X-ray diffraction studies revealed that the geometry around the Cu(II) center could be best described as distorted octahedral in Cu1 and Cu2, whereas Cu3 and Cu4 showed distorted tetrahedral and square pyramidal geometries, respectively. DNA binding studies showed that Cu complexes Cu1-3 containing quinoline interacted via minor groove binding, whereas the Cu4 complex containing pyridine interacted via intercalation. All Cu complexes containing quinoline and pyridine caused destabilization of DNA at specific homogeneous G-C regions. The Cu1-3 complexes as groove binders destabilized the DNA structure much more than the Cu4 complex as an intercalator. Regarding groove binders, the Cu2 complex containing quinoline and morpholine caused the highest distortion and destabilization of the DNA structure, leading to high DNA cleavage efficiency.
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Affiliation(s)
- Hee Chang Kwon
- Department of Chemical and Biological Engineering, Andong National University, 1375 Gyeongdong-ro, Andong, Gyeongbuk, Korea, 36729.
| | - Da Hyun Lee
- Department of Chemical and Biological Engineering, Andong National University, 1375 Gyeongdong-ro, Andong, Gyeongbuk, Korea, 36729.
| | - Minyoung Yoon
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea.
| | - Saira Nayab
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea.
- Department of Chemistry, Shaheed Benazir Bhutto University (SBBU), Sheringal Upper Dir (18050), Khyber Pakhtunkhwa, Islamic Republic of Pakistan
| | - Hyosun Lee
- Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Bukgu, Daegu 41566, Republic of Korea.
| | - Ji Hoon Han
- Department of Chemical and Biological Engineering, Andong National University, 1375 Gyeongdong-ro, Andong, Gyeongbuk, Korea, 36729.
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Chemical structures and biological activities of bis- and tetrakis-acridine derivatives: A review. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2017.05.042] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Mukherjee S, Dohno C, Nakatani K. Design and Synthesis of Cyclic Mismatch-Binding Ligands (CMBLs) with Variable Linkers by Ring-Closing Metathesis and their Photophysical and DNA Repeat Binding Properties. Chemistry 2017; 23:11385-11396. [DOI: 10.1002/chem.201702064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
- National Centre for Biological Sciences (NCBS); Tata Institute of Fundamental Research (TIFR); Bellary Road Bangalore 560065 India
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
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Mukherjee S, Dohno C, Asano K, Nakatani K. Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base. Nucleic Acids Res 2016; 44:7090-9. [PMID: 27466390 PMCID: PMC5009760 DOI: 10.1093/nar/gkw672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022] Open
Abstract
A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaori Asano
- Comprehensive Analysis Center, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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Gasiorek M, Schneider HJ. Unwinding DNA and RNA with Synthetic Complexes: On the Way to Artificial Helicases. Chemistry 2015; 21:18328-32. [PMID: 26503404 DOI: 10.1002/chem.201502738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Indexed: 01/04/2023]
Abstract
Synthetic helicases can be designed on the basis of ligands that bind more strongly to single-stranded nucleic acids than to double-stranded nucleic acids. This can be achieved with ligands containing phenyl groups, which intercalate into single strands, but due to their small size not into double strands. Moreover, two phenyl rings are combined with a distance that allows bis-intercalation with only single strands and not double strands. In this respect, such ligands also mimic single-strand binding (SSB) proteins. Exploration with more than 23 ligands, mostly newly synthesised, shows that the distance between the phenyl rings and between those and the linker influence the DNA unwinding efficiency, which can reach a melting point decrease of almost ΔTm =50 °C at much lower concentrations than that with any other known artificial helicases. Conformational pre-organisation of the ligand plays a decisive role in optimal efficiency. Substituents at the phenyl rings have a large effect, and increase, for example, in the order of H<F<Cl<Br, which illustrates the strong role of dispersive interactions in intercalation. Studies with homopolymers revealed significant selectivity: for example, with a ligand concentration of 40 μM at 35 °C, only GC double strands melt (ΔTm =48 °C), whereas the AT strand remains untouched, and with poly(rA)-poly(rU) as an RNA model one observes unfolding at 29 °C with a concentration of only 30 μM.
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Affiliation(s)
- Martin Gasiorek
- FR Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken (Germany)
| | - Hans-Jörg Schneider
- FR Organische Chemie, Universität des Saarlandes, 66041 Saarbrücken (Germany).
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Rednic MI, Hădade ND, Bogdan E, Grosu I. Macrocycles embedding phenothiazine or similar nitrogen and/or sulphur containing heterocycles. J INCL PHENOM MACRO 2014. [DOI: 10.1007/s10847-014-0455-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Granzhan A, Kotera N, Teulade-Fichou MP. Finding needles in a basestack: recognition of mismatched base pairs in DNA by small molecules. Chem Soc Rev 2014; 43:3630-65. [DOI: 10.1039/c3cs60455a] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Jourdan M, Granzhan A, Guillot R, Dumy P, Teulade-Fichou MP. Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine-thymine mismatch. Nucleic Acids Res 2012; 40:5115-28. [PMID: 22362757 PMCID: PMC3367172 DOI: 10.1093/nar/gks067] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
The macrocyclic bis-naphthalene macrocycle (2,7-BisNP), belonging to the cyclobisintercalator family of DNA ligands, recognizes T–T mismatch sites in duplex DNA with high affinity and selectivity, as evidenced by thermal denaturation experiments and NMR titrations. The binding of this macrocycle to an 11-mer DNA oligonucleotide containing a T–T mismatch was studied using NMR spectroscopy and NMR-restrained molecular modeling. The ligand forms a single type of complex with the DNA, in which one of the naphthalene rings of the ligand occupies the place of one of the mismatched thymines, which is flipped out of the duplex. The second naphthalene unit of the ligand intercalates at the A-T base pair flanking the mismatch site, leading to encapsulation of its thymine residue via double stacking. The polyammonium linking chains of the macrocycle are located in the minor and the major grooves of the oligonucleotide and participate in the stabilization of the complex by formation of hydrogen bonds with the encapsulated thymine base and the mismatched thymine remaining inside the helix. The study highlights the uniqueness of this cyclobisintercalation binding mode and its importance for recognition of DNA lesion sites by small molecules.
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Affiliation(s)
- Muriel Jourdan
- CNRS UMR5250, ICMG FR2607, Département de Chimie Moléculaire, Université Joseph Fourier, 570 rue de la Chimie, 38041 Grenoble Cedex 9, France.
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9
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Lenglet G, David-Cordonnier MH. DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences. J Nucleic Acids 2010; 2010. [PMID: 20725618 PMCID: PMC2915751 DOI: 10.4061/2010/290935] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2010] [Revised: 05/27/2010] [Accepted: 06/03/2010] [Indexed: 01/06/2023] Open
Abstract
DNA targeting drugs represent a large proportion of the actual anticancer drug pharmacopeia, both in terms of drug brands and prescription volumes. Small DNA-interacting molecules share the ability of certain proteins to change the DNA helix's overall organization and geometrical orientation via tilt, roll, twist, slip, and flip effects. In this ocean of DNA-interacting compounds, most stabilize both DNA strands and very few display helix-destabilizing properties. These types of DNA-destabilizing effect are observed with certain mono- or bis-intercalators and DNA alkylating agents (some of which have been or are being developed as cancer drugs). The formation of locally destabilized DNA portions could interfere with protein/DNA recognition and potentially affect several crucial cellular processes, such as DNA repair, replication, and transcription. The present paper describes the molecular basis of DNA destabilization, the cellular impact on protein recognition, and DNA repair processes and the latter's relationships with antitumour efficacy.
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Affiliation(s)
- Gaëlle Lenglet
- INSERM U-837, Jean-Pierre Aubert Research Center (JPARC), Team 4 Molecular and Cellular Targeting for Cancer Treatment, Institute for Research on Cancer of Lille (IRCL), Lille F-59045, France
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10
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Granzhan A, Monchaud D, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One Ring to Bind Them All"-Part II: Identification of Promising G-Quadruplex Ligands by Screening of Cyclophane-Type Macrocycles. J Nucleic Acids 2010; 2010. [PMID: 20725622 PMCID: PMC2915812 DOI: 10.4061/2010/460561] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/10/2010] [Indexed: 11/30/2022] Open
Abstract
A collection of 26 polyammonium cyclophane-type macrocycles with a large structural diversity has been screened for G-quadruplex recognition. A two-step selection procedure based on the FRET-melting assay was carried out enabling identification of macrocycles of high affinity (ΔT1/2 up to 30°C) and high selectivity for the human telomeric G-quadruplex. The four selected hits possess sophisticated architectures, more particularly the presence of a pendant side-arm as well as the existence of a particular topological arrangement appear to be strong determinants of quadruplex binding. These compounds are thus likely to create multiple contacts with the target that may be at the origin of their high selectivity, thereby suggesting that this class of macrocycles offers unique advantages for targeting G-quadruplex-DNA.
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Affiliation(s)
- Anton Granzhan
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Bat. 110, 91405 Orsay, France
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11
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Piazza A, Boulé JB, Lopes J, Mingo K, Largy E, Teulade-Fichou MP, Nicolas A. Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae. Nucleic Acids Res 2010; 38:4337-48. [PMID: 20223771 PMCID: PMC2910037 DOI: 10.1093/nar/gkq136] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
G-quadruplexes are nucleic acid secondary structures for which many biological roles have been proposed but whose existence in vivo has remained elusive. To assess their formation, highly specific G-quadruplex ligands are needed. Here, we tested Phen-DC3 and Phen-DC6, two recently released ligands of the bisquinolinium class. In vitro, both compounds exhibit high affinity for the G4 formed by the human minisatellite CEB1 and inhibit efficiently their unwinding by the yeast Pif1 helicase. In vivo, both compounds rapidly induced recombination-dependent rearrangements of CEB1 inserted in the Saccharomyces cerevisiae genome, but did not affect the stability of other tandem repeats lacking G-quadruplex forming sequences. The rearrangements yielded simple-deletion, double-deletion or complex reshuffling of the polymorphic motif units, mimicking the phenotype of the Pif1 inactivation. Treatment of Pif1-deficient cells with the Phen-DC compounds further increased CEB1 instability, revealing additional G4 formation per cell. In sharp contrast, the commonly used N-methyl-mesoporphyrin IX G-quadruplex ligand did not affect CEB1 stability. Altogether, these results demonstrate that the Phen-DC bisquinolinium compounds are potent molecular tools for probing the formation of G-quadruplexes in vivo, interfere with their processing and elucidate their biological roles.
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Affiliation(s)
- Aurèle Piazza
- Recombinaison et Instabilité Génétique, Institut Curie Centre de Recherche, CNRS UMR3244, Université Pierre et Marie Curie, 26 rue d'Ulm, 75248 Paris Cedex 05, France
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12
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Kuruvilla E, Joseph J, Ramaiah D. Novel Bifunctional Acridine−Acridinium Conjugates: Synthesis and Study of Their Chromophore-Selective Electron-Transfer and DNA-Binding Properties. J Phys Chem B 2005; 109:21997-2002. [PMID: 16853857 DOI: 10.1021/jp0543532] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Novel bifunctional conjugates 1-3, with varying polymethylene spacer groups, were synthesized, and their DNA interactions have been investigated by various biophysical techniques. The absorption spectra of these systems showed bands in the regions of 300-375 and 375-475 nm, corresponding to acridine and acridinium chromophores, respectively. When compared to 1 (Phi(f) = 0.25), bifunctional derivatives 2 and 3 exhibited quantitative fluorescence yields (Phi(f) = 0.91 and 0.98) and long lifetimes (tau = 38.9 and 33.2 ns). The significant quenching of fluorescence and lifetimes observed in the case of 1 is attributed to intramolecular electron transfer from the excited state of the acridine chromophore to the acridinium moiety. DNA-binding studies through spectroscopic investigations, viscosity, and thermal denaturation temperature measurements indicate that these systems interact with DNA preferentially through intercalation of the acridinium chromophore and exhibit significant DNA association constants (K(DNA) = 10(5)-10(7) M(-1)). Compound 1 exhibits chromophore-selective electron-transfer reactions and DNA binding, wherein only the acridinium moiety of 1 interacts with DNA, whereas optical properties of the acridine chromophore remain unperturbed. Among bifunctional derivatives 2 and 3, the former undergoes DNA mono-intercalation, whereas the latter exhibits bis-intercalation; however both of them interact through mono-intercalation at higher ionic strength. Results of these investigations demonstrate that these novel water-soluble systems, which exhibit quantitative fluorescence yields, chromophore-selective electron transfer, and DNA intercalation, can have potential use as probes in biological applications.
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Affiliation(s)
- Elizabeth Kuruvilla
- Photosciences and Photonics Division, Regional Research Laboratory, Trivandrum 695 019, India
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13
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Interactions of acyclic and cyclic bis-phenanthridinium derivatives with ss- and ds-polynucleotides. Tetrahedron 2004. [DOI: 10.1016/j.tet.2004.05.009] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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14
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David A, Bleimling N, Beuck C, Lehn JM, Weinhold E, Teulade-Fichou MP. DNA mismatch-specific base flipping by a bisacridine macrocycle. Chembiochem 2004; 4:1326-31. [PMID: 14661275 DOI: 10.1002/cbic.200300693] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Most, if not all, enzymes that chemically modify nucleobases in DNA flip their target base from the inside of the double helix into an extrahelical position. This energetically unfavorable conformation is partly stabilized by specific binding of the apparent abasic site being formed. Thus, DNA base-flipping enzymes, like DNA methyltransferases and DNA glycosylases, generally bind very strongly to DNA containing abasic sites or abasic-site analogues. The macrocyclic bisacridine BisA has previously been shown to bind abasic sites. Herein we demonstrate that it is able to specifically recognize DNA base mismatches and most likely induces base flipping. Specific binding of BisA to DNA mismatches was studied by thermal denaturation experiments by using short duplex oligodeoxynucleotides containing central TT, TC, or TG mismatches or a TA match. In the presence of the macrocycle a strong increase in the melting temperature of up to 7.1 degrees C was observed for the mismatch-containing duplexes, whereas the melting temperature of the fully matched duplex was unaffected. Furthermore, BisA binding induced an enhanced reactivity of the mispaired thymine residue in the DNA toward potassium permanganate oxidation. A comparable reactivity has previously been observed for a TT target base mismatch in the presence of DNA methyltransferase M.TaqI. This similarity to a known base-flipping enzyme suggests that insertion of BisA into the DNA helix displaces the mispaired thymine residue into an extrahelical position, where it should be more prone to chemical oxidation. Thus, DNA base flipping does not appear to be limited to DNA-modifying enzymes but it is likely to also be induced by a small synthetic molecule binding to a thermodynamically weakened site in DNA.
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Affiliation(s)
- Arnaud David
- Laboratoire de Chimie des Interactions Moléculaires, Collège de France, CNRS UPR 285, 11 place Marcelin Berthelot, 75005 Paris, France
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15
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Boyer G, Tuan Lormier A, Faure R, Pierre Galy J. Synthesis of New Atropisomers Derived from Methoxychloroacridine. Preparation of Enantiomerically Pure (aR)-(-)-2,2'-Dihydroxy-9,9'-biacridine. HETEROCYCLES 2002. [DOI: 10.3987/com-01-9408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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16
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Alberti P, Ren J, Teulade-Fichou MP, Guittat L, Riou JF, Chaires J, Hélène C, Vigneron JP, Lehn JM, Mergny JL. Interaction of an acridine dimer with DNA quadruplex structures. J Biomol Struct Dyn 2001; 19:505-13. [PMID: 11790148 DOI: 10.1080/07391102.2001.10506758] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The reactivation of telomerase activity in most cancer cells supports the concept that telomerase is a relevant target in oncology, and telomerase inhibitors have been proposed as new potential anticancer agents. The telomeric G-rich single-stranded DNA can adopt an intramolecular G-quadruplex structure in vitro, which has been shown to inhibit telomerase activity. The C-rich sequence can also adopt a quadruplex (intercalated) structure (i-DNA). Two acridine derivatives were shown to increase the melting temperature of the G- quadruplex and the C-quadruplex at 1 microM dye concentration. The increase in Tm value of the G-quadruplex was associated with telomerase inhibition in vitro. The most active compound, "BisA", showed an IC(50) value of 0.75 microM in a standard TRAP assay.
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Affiliation(s)
- P Alberti
- Laboratoire de Biophysique, Muséum National d'Histoire Naturelle, INSERM U 201,CNRS UMR 8646, Paris, France
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Piantanida I, Palm BS, Cudic P, Zinic M, Schneider HJ. Phenanthridinium cyclobisintercalands. Fluorescence sensing of AMP and selective binding to single-stranded nucleic acids. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01386-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Teulade-Fichou MP, Fauquet M, Baudoin O, Vigneron JP, Lehn JM. DNA double helix destabilizing properties of cyclobisintercaland compounds and competition with a single strand binding protein. Bioorg Med Chem 2000; 8:215-22. [PMID: 10968280 DOI: 10.1016/s0968-0896(99)00283-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The DNA helix destabilizing activity of a series of cyclobisintercaland compounds (CBIs) has been evaluated by measuring their ability to displace a 32P-labelled oligonucleotide primer (17-mer) hybridized to the single stranded DNA of M13. This destabilizing activity appears to be strongly dependent on the cyclic structure (the linear acyclic references are inactive) and the size of the macrocycle; both features being known to determine the preferential binding of the compound to ssDNA. Interestingly, CBIs induced the dissociation of the duplex template in a concentration range (0.5-1 microM) close to that required for the destabilizing activity of single stranded DNA binding proteins (SSBs). Therefore competition experiments between CBIs and an SSB protein (Eco SSB) for binding to a single stranded oligonucleotide target (36-mer) have been performed through gel electrophoresis and nitrocellulose binding assays and strong inhibitory effects on the formation of the SSB:36-mer complex have been observed.
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Affiliation(s)
- M P Teulade-Fichou
- Laboratoire de Chimie des Iteractions Molécullaires, CNRS UPR 285, Collège de France, Paris
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19
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Supramolecular Bioorganic Chemistry: Nucleic Acids Recognition and Synthetic Vectors for Gene Transfer. Molecules 1999. [DOI: 10.3390/40700180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Slama-Schwok A, Brossalina E, Demchenko Y, Best-Belpomme M, Vlassov V. Structural flexibility of a DNA hairpin located in the long terminal repeat of the Drosophila 1731 retrotransposon. Nucleic Acids Res 1998; 26:5142-51. [PMID: 9801312 PMCID: PMC147971 DOI: 10.1093/nar/26.22.5142] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The structure of the DNA binding site of the Nuclear single-stranded Binding Factor (NssBF), located in the long terminal repeat of the Drosophila 1731 retrotransposon, was investigated by melting temperature experiments, chemical probing and fluorescence measurements using a macrocyclic bis-acridine. The most probable structure of this element, named Bc, mainly involves two hairpins in equilibrium at pH 6.0 at low concentration. The hairpins differ in their apical loop size; 4 and 8 nt. The structural flexibility of Bc probably derives from the three consecutive CATA repeats complementary to the GTAT nucleotides of the palindrome. In contrast, the Bc complementary strand adopts a single hairpin. Since Bc is implicated in repression of transcription via binding of two specific factors, its structural flexibility could be associated with this process.
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Affiliation(s)
- A Slama-Schwok
- INSERM U310, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.
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21
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Blacker AJ, Teulade-Fichou MP, Vigneron JP, Fauquet M, Lehn JM. Selective photocleavage of single-stranded nucleic acids by cyclobisintercaland molecules. Bioorg Med Chem Lett 1998; 8:601-6. [PMID: 9871568 DOI: 10.1016/s0960-894x(98)00085-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Irradiation of mixtures of a single-stranded circular plasmid and of a double-stranded supercoiled DNA in presence of the cyclobisintercaland compounds 2 or 3 shows that these reagents effect the selective photocleavage of the single-stranded entity. Furthermore, 2 also cleaves tRNAasp preferentially at single-stranded domains.
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Affiliation(s)
- A J Blacker
- Laboratoire de Chimie Supramoléculaire, ISIS, Université Louis Pasteur, Strasbourg, France
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Raspaud E, Olvera de la Cruz M, Sikorav JL, Livolant F. Precipitation of DNA by polyamines: a polyelectrolyte behavior. Biophys J 1998; 74:381-93. [PMID: 9449338 PMCID: PMC1299390 DOI: 10.1016/s0006-3495(98)77795-1] [Citation(s) in RCA: 330] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Conditions of double-stranded DNA precipitation by the polyamines spermidine and spermine have been determined experimentally and compared to theoretical predictions. The influence of the concentrations of DNA and added monovalent salt, and of the DNA length has been investigated in a systematic manner. Three regimes of DNA concentrations are observed. We clarify the dependence of these regimes on the monovalent salt concentration and on the DNA length. Our observations make possible a rationalization of the experimental results reported in the literature. A comparison of the precipitation conditions of different kinds of polyelectrolytes suggests a general process. Our experimental data are compared to the "ion-bridging" model based on short-range electrostatic attractions. By starting from the spinodal equation, predicted by this model, and using the limiting form of Manning's fractions of condensed counterions, analytical expressions of the precipitation conditions have been found in the three regimes. Experimental and theoretical results are in good agreement.
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Affiliation(s)
- E Raspaud
- Laboratoire de Physique des Solides, CNRS URA D0002, Université Paris Sud, France.
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