101
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Shan C, Tan JH, Ou TM, Huang ZS. Natural products and their derivatives as G-quadruplex binding ligands. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4920-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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102
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Novotná J, Goncharova I, Urbanová M. Guanosine assemblies: newly used matrices for chiroptical studies on biliverdin. Supramol Chem 2013. [DOI: 10.1080/10610278.2013.814774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Jana Novotná
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
| | - Iryna Goncharova
- Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
| | - Marie Urbanová
- Department of Physics and Measurements, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
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103
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Le VH, Nagesh N, Lewis EA. Bcl-2 promoter sequence G-quadruplex interactions with three planar and non-planar cationic porphyrins: TMPyP4, TMPyP3, and TMPyP2. PLoS One 2013; 8:e72462. [PMID: 23977303 PMCID: PMC3748076 DOI: 10.1371/journal.pone.0072462] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 07/18/2013] [Indexed: 12/31/2022] Open
Abstract
The interactions of three related cationic porphyrins, TMPyP4, TMPyP3 and TMPyP2, with a WT 39-mer Bcl-2 promoter sequence G-quadruplex were studied using Circular Dichroism, ESI mass spectrometry, Isothermal Titration Calorimetry, and Fluorescence spectroscopy. The planar cationic porphyrin TMPyP4 (5, 10, 15, 20-meso-tetra (N-methyl-4-pyridyl) porphine) is shown to bind to a WT Bcl-2 G-quadruplex via two different binding modes, an end binding mode and a weaker mode attributed to intercalation. The related non-planar ligands, TMPyP3 and TMPyP2, are shown to bind to the Bcl-2 G-quadruplex by a single mode. ESI mass spectrometry experiments confirmed that the saturation stoichiometry is 4:1 for the TMPyP4 complex and 2:1 for the TMPyP2 and TMPyP3 complexes. ITC experiments determined that the equilibrium constant for formation of the (TMPyP4)1/DNA complex (K1 = 3.7 × 10(6)) is approximately two orders of magnitude greater than the equilibrium constant for the formation of the (TMPyP2)1/DNA complex, (K1 = 7.0 × 10(4)). Porphyrin fluorescence is consistent with intercalation in the case of the (TMPyP4)3/DNA and (TMPyP4)4/DNA complexes. The non-planar shape of the TMPyP2 and TMPyP3 molecules results in both a reduced affinity for the end binding interaction and the elimination of the intercalation binding mode.
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Affiliation(s)
- Vu H. Le
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States of America
| | - Narayana Nagesh
- Centre for Cellular and Molecular Biology, Hyderabad, Andhra Pradesh, India
| | - Edwin A. Lewis
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi, United States of America
- * E-mail:
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104
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Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Biochim Biophys Acta Gen Subj 2013; 1830:4189-201. [DOI: 10.1016/j.bbagen.2013.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 01/24/2023]
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105
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von Grebe P, Suntharalingam K, Vilar R, Sanz Miguel PJ, Herres-Pawlis S, Lippert B. A conformationally flexible dinuclear Pt(II) complex with differential behavior of its two states toward quadruplex DNA. Chemistry 2013; 19:11429-38. [PMID: 23852779 DOI: 10.1002/chem.201301400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Indexed: 01/09/2023]
Abstract
The reaction of tetrakis(pyridine-2-yl)pyrazine (tppz) with 2 equiv of (2,2'-bpy)Pt(II) in water yields two isomeric dinuclear cations, [{Pt(2,2'-bpy)}2 (tppz)](4+) , in which Pt coordination exclusively takes place through the two pairs of pyridine-2-yl nitrogen atoms. The two conformational isomers differ in their overall shape, with the formation of "Z" and "U" shapes, which are formed at 40 °C (Z isomer, 1) and under reflux conditions (U isomer, 2), respectively. X-ray crystal-structure analyses of the Z isomer, [{Pt(2,2'-bpy)}2 (tppz)](PF6 )4 ⋅3 CHCl3 ⋅4 H2 O (1 a), and of the U isomer, [{Pt(2,2'-bpy)}2 ](PF6 )4 ⋅2 CH3 CN⋅1.5 H2 O (2 a), were carried out. Co-crystallization of compound 2 with PtCl2 (2,2'-bpy) yielded [{Pt(2,2'-bpy)}2 (tppz)](BF4 )4 ⋅[PtCl2 (2,2'-bpy)]⋅4.5 H2 O (3), in which the PtCl2 (2,2'-bpy) entity was sandwiched between the two 2,2'-bpy faces of the U-shaped cation (2). Quantum chemical calculations revealed that the U isomer was more stable than the Z isomer, both in the gas phase and in an aqueous environment. These two isomers display different affinities toward duplex DNA and human telomeric quadruplex DNA (Htelo), as concluded from CD spectroscopy and FID assays. Thus, the U isomer binds significantly more strongly to quadruplex DNA (DC50 =0.38 μM) than the Z isomer (DC50 =8.50 μM).
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Affiliation(s)
- Philipp von Grebe
- Fakultät Chemie, Technische Universität Dortmund, Otto-Hahn-Str. 6, 44221 Dortmund, Germany
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106
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Ghosh S, Kar A, Chowdhury S, Dasgupta D. Ellipticine binds to a human telomere sequence: an additional mode of action as a putative anticancer agent? Biochemistry 2013; 52:4127-37. [PMID: 23697684 DOI: 10.1021/bi400080t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polyguanine sequences fold into G-quadruplex structures in the presence of monovalent cations. It is accepted that the telomeric DNA region consists of G-quadruplex structure. There are reports that potential G-quadruplex forming motifs are also present in the promoter region of some proto-oncogenes such as c-myc, c-kit, KRAS, etc. Small molecules with the potential to stabilize the telomeric DNA quadruplex have emerged as potential anticancer agents. We have studied the interaction of ellipticine, a putative anticancer agent from a plant source, with a human telomeric DNA sequence (H24). Spectroscopic and calorimetric studies indicate that the association of ellipticine with H24 is an entropically driven phenomenon with a 2:3 (H24:ellipticine) stoichiometry. Though ellipticine binding does not induce any major structural perturbation in H24, the association leads to formation of a complex with enhanced thermal stability. An assay with the telomerase repeat amplification protocol shows that ellipticine inhibits telomerase activity in MDAMB-231 breast cancer cell line extracts. This is the first report of the quadruplex binding ability of ellipticine. Using the results, we propose that along with DNA intercalation and/or topoisomerase II inhibition, interaction with the telomeric DNA region and the resultant inhibition of telomerase activity might be an additional mode of action for its anticancer property.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics Division, Saha Institute of Nuclear Physics , Block-AF, Sector- I, Bidhan Nagar, Kolkata 700064, India
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107
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Liu ZQ, Zhuo ST, Tan JH, Ou TM, Li D, Gu LQ, Huang ZS. Facile syntheses of disubstituted bis(vinylquinolinium)benzene derivatives as G-quadruplex DNA binders. Tetrahedron 2013. [DOI: 10.1016/j.tet.2013.04.045] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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108
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Bortolozzi R, Ihmels H, Thomas L, Tian M, Viola G. 9-(4-Dimethylaminophenyl)benzo[b]quinolizinium: a near-infrared fluorophore for the multicolor analysis of proteins and nucleic acids in living cells. Chemistry 2013; 19:8736-41. [PMID: 23703698 DOI: 10.1002/chem.201301164] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Roberta Bortolozzi
- Dipartimento di Salute della Donna e del Bambino, Laboratorio di Oncoematologia, University of Padova, via Giustiniani 3, I-35128 Padova, Italy
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109
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Iida K, Majima S, Nakamura T, Seimiya H, Nagasawa K. Evaluation of the interaction between long telomeric DNA and macrocyclic hexaoxazole (6OTD) dimer of a G-quadruplex ligand. Molecules 2013; 18:4328-41. [PMID: 23584054 PMCID: PMC6269967 DOI: 10.3390/molecules18044328] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 04/02/2013] [Accepted: 04/09/2013] [Indexed: 11/19/2022] Open
Abstract
Macrocyclic hexaoxazole dimer of L2H2-6OTD-dimer (3) was newly synthesized as a telomeric G-quadruplex (G4) ligand, and interaction with long telomeric DNAs telo48, 72, and 96 was evaluated by means of electrophoresis mobility shift assay, CD spectra analysis, and CD melting experiments. The L2H2-6OTD-dimer (3) interacted with the long telomeric DNAs by inducing anti-parallel type G4 structure of each unit of 24 bases, i.e., (TTAGGG)₄ sequences. Dimer 3 stabilizes long telomeric DNAs more efficiently than the corresponding monomer of L2H2-6OTD (2). It showed potent inhibitory activity against telomerase, with an IC₅₀ value of 7.5 nm.
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Affiliation(s)
- Keisuke Iida
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Satoki Majima
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Takahiro Nakamura
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
| | - Hiroyuki Seimiya
- Cancer Chemotherapy Center, Japanese Foundation for Cancer Research (JFCR), 3-8-31 Ariake, Koto-ku, Tokyo 135-8550, Japan
| | - Kazuo Nagasawa
- Faculty of Technology, Tokyo University of Agriculture and Technology (TUAT), 2-24-16 Naka-cho, Koganei-shi, Tokyo 185-0031, Japan
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110
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Wei C, Ren L, Gao N. Interactions of terpyridines and their Pt(II) complexes with G-quadruplex DNAs and telomerase inhibition. Int J Biol Macromol 2013; 57:1-8. [PMID: 23434432 DOI: 10.1016/j.ijbiomac.2013.02.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Revised: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 12/29/2022]
Abstract
Three terpyridine derivatives L1-L3 and their Pt(II) complexes 1-3 have been prepared, the binding interactions with human telomeric (h-telo) and the promoter c-kit2 and c-myc G-quadruplex DNAs were investigated. All the ligands and the complexes are potent stabilisers of the G-quadruplex structures and exhibit the G-quadruplex selectivity over duplex. The binding affinities of these compounds to G-quadruplexes are higher than to calf thymus DNA. Three Pt(II) complexes are also potent telomerase inhibitors. CD spectra show that both the ligands and the complexes can induce the formation of anti-parallel G-quadruplex structure of h-telo in the absence and presence of K(+). Each h-telo G-quadruplex binds two ligand or complex molecules using Job plot analysis.
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Affiliation(s)
- Chunying Wei
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Molecular Science, Shanxi University, Taiyuan 030006, PR China.
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111
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He JH, Liu HY, Li Z, Tan JH, Ou TM, Huang SL, An LK, Li D, Gu LQ, Huang ZS. New quinazoline derivatives for telomeric G-quadruplex DNA: effects of an added phenyl group on quadruplex binding ability. Eur J Med Chem 2013; 63:1-13. [PMID: 23454529 DOI: 10.1016/j.ejmech.2013.01.051] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Revised: 01/19/2013] [Accepted: 01/24/2013] [Indexed: 01/06/2023]
Abstract
To improve the selectivity of indoloquinoline or benzofuroquinoline derivatives, we previously reported several quinazoline derivatives [17]. These compounds could mimic a tetracyclic aromatic system through intramolecular hydrogen bond. Studies showed that these quinazoline derivatives were effective and selective telomeric G-quadruplex ligands. With this encouragement, here we synthesized a series of N-(2-(quinazolin-2-yl)phenyl)benzamide (QPB) compounds as modified quinazoline derivatives. In this modification, a phenyl group was introduced to the aromatic core. The evaluation results showed that part of QPB derivatives had stronger binding ability and better selectivity for telomeric G-quadruplex DNA than LZ-11, the most potential compound of reported quinazoline derivatives. Furthermore, telomerase inhibition of QPB derivatives and their cellular effects were studied.
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Affiliation(s)
- Jin-Hui He
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510006, People's Republic of China
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112
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Long X, Parks JW, Bagshaw CR, Stone MD. Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy. Nucleic Acids Res 2013; 41:2746-55. [PMID: 23303789 PMCID: PMC3575832 DOI: 10.1093/nar/gks1341] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-molecule techniques facilitate analysis of mechanical transitions within nucleic acids and proteins. Here, we describe an integrated fluorescence and magnetic tweezers instrument that permits detection of nanometer-scale DNA structural rearrangements together with the application of a wide range of stretching forces to individual DNA molecules. We have analyzed the force-dependent equilibrium and rate constants for telomere DNA G-quadruplex (GQ) folding and unfolding, and have determined the location of the transition state barrier along the well-defined DNA-stretching reaction coordinate. Our results reveal the mechanical unfolding pathway of the telomere DNA GQ is characterized by a short distance (<1 nm) to the transition state for the unfolding reaction. This mechanical unfolding response reflects a critical contribution of long-range interactions to the global stability of the GQ fold, and suggests that telomere-associated proteins need only disrupt a few base pairs to destabilize GQ structures. Comparison of the GQ unfolded state with a single-stranded polyT DNA revealed the unfolded GQ exhibits a compacted non-native conformation reminiscent of the protein molten globule. We expect the capacity to interrogate macromolecular structural transitions with high spatial resolution under conditions of low forces will have broad application in analyses of nucleic acid and protein folding.
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Affiliation(s)
- Xi Long
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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113
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Xia Y, Chen Q, Qin X, Sun D, Zhang J, Liu J. Studies of ruthenium(ii)-2,2′-bisimidazole complexes on binding to G-quadruplex DNA and inducing apoptosis in HeLa cells. NEW J CHEM 2013. [DOI: 10.1039/c3nj00542a] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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114
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Yu Q, Liu Y, Zhang J, Yang F, Sun D, Liu D, Zhou Y, Liu J. Ruthenium(ii) polypyridyl complexes as G-quadruplex inducing and stabilizing ligands in telomeric DNA. Metallomics 2013; 5:222-31. [DOI: 10.1039/c3mt20214c] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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115
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Iida K, Tsubouchi G, Nakamura T, Majima S, Seimiya H, Nagasawa K. Interaction of long telomeric DNAs with macrocyclic hexaoxazole as a G-quadruplex ligand. MEDCHEMCOMM 2013. [DOI: 10.1039/c2md20234d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interactions of long telomeric DNAs, which mimic telomeres in living cells, with a macrocyclic hexaoxazole ligand L2H2-6OTD (2) were investigated by means of electrophoresis mobility shift assay, circular dichroism (CD) titration analysis, and DNA melting measurements.
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Affiliation(s)
- Keisuke Iida
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Gen Tsubouchi
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Takahiro Nakamura
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Satoki Majima
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
| | - Hiroyuki Seimiya
- Cancer Chemotherapy Center
- Japanese Foundation for Cancer Research (JFCR)
- Koto-ku
- Japan
| | - Kazuo Nagasawa
- Faculty of Technology
- Tokyo University of Agriculture and Technology (TUAT)
- Koganei-shi
- Japan
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116
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Chung CYS, Yam VWW. Selective label-free detection of G-quadruplex structure of human telomere by emission spectral changes in visible-and-NIR region under physiological condition through the FRET of a two-component PPE-SO3−–Pt(ii) complex ensemble with Pt⋯Pt, electrostatic and π–π interactions. Chem Sci 2013. [DOI: 10.1039/c2sc20897k] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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117
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Yao JL, Gao X, Sun W, Shi S, Yao TM. [Ru(bpy)2dppz-idzo]2+: a colorimetric molecular “light switch” and powerful stabilizer for G-quadruplex DNA. Dalton Trans 2013; 42:5661-72. [DOI: 10.1039/c3dt32640c] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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118
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Wei C, Wang Y, Zhang M. Synthesis and binding studies of novel di-substituted phenanthroline compounds with genomic promoter and human telomeric DNA G-quadruplexes. Org Biomol Chem 2013; 11:2355-64. [DOI: 10.1039/c3ob27426h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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119
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Mohanty J, Barooah N, Dhamodharan V, Harikrishna S, Pradeepkumar PI, Bhasikuttan AC. Thioflavin T as an Efficient Inducer and Selective Fluorescent Sensor for the Human Telomeric G-Quadruplex DNA. J Am Chem Soc 2012; 135:367-76. [DOI: 10.1021/ja309588h] [Citation(s) in RCA: 459] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Jyotirmayee Mohanty
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - Nilotpal Barooah
- Radiation & Photochemistry Division, Bhabha Atomic Research Centre, Mumbai 400 085, India
| | - V. Dhamodharan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai
400 076, India
| | - S. Harikrishna
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai
400 076, India
| | - P. I. Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai
400 076, India
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120
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Czerwinska I, Sato S, Takenaka S. Improving the affinity of naphthalene diimide ligand to telomeric DNA by incorporating Zn2+ ions into its dipicolylamine groups. Bioorg Med Chem 2012; 20:6416-22. [DOI: 10.1016/j.bmc.2012.08.055] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Revised: 08/23/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022]
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121
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Sassano MF, Schlesinger AP, Jarstfer MB. Identification of G-Quadruplex Inducers Usinga Simple, Inexpensiveand Rapid High Throughput Assay, and TheirInhibition of Human Telomerase. THE OPEN MEDICINAL CHEMISTRY JOURNAL 2012; 6:20-8. [PMID: 23173022 PMCID: PMC3502892 DOI: 10.2174/1874104501206010020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2012] [Revised: 07/17/2012] [Accepted: 07/18/2012] [Indexed: 11/22/2022]
Abstract
Telomeres are protein and DNA complexes located atchromosome ends. Telomeric DNA is composed of a double stranded region of repetitive DNA followed by single-stranded 3' extension of aG-rich sequence. Single-stranded G-rich sequencescan fold into G-quadruplex structures,and molecules that stabilize G-quadruplexes are known to inhibit the enzyme telomerase and disrupt telomere maintenance. Because telomere maintenance is required for proliferation of cancer cells, G-quadruplex stabilizers have become attractive prospects for anticancer drug discovery.However, telomere-targeting G-quadruplex ligands have yet to enter the clinic owing in part to poor pharmacokinetics and target selectivity. Increasing the pharmacophore diversity of G-quadruplex and specifically telomeric-DNA targeting agents should assist in overcoming these shortcomings. In this work, we report the identification and validation ofligands that bind telomeric DNA and induce G-quadruplex formationusing the NCI Diversity Set I, providing validation of anextremely simple, rapid and high-throughput screen using FRET technology. Hits from the screen were validated by examining telomerase inhibition and G-quadruplex inductionusing CD spectroscopy and DNA polymerase stop assays. We show that two known DNA binding molecules, ellipticine derivativeNSC 176327 (apyridocarbazole) and NSC 305831 (an antiparasitic hetero-cyclediamidine referred to as furamidine and DB75),are selective induceG-quadruplex formation in the human telomeric sequence and bind telomeric DNA quadruplexes in the absence of stabilizing monovalent cations with molar ratios(molecule: DNA)of 4:1and 1.5:1, respectively.
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Affiliation(s)
- Maria Florencia Sassano
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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122
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Nanjunda R, Owens EA, Mickelson L, Alyabyev S, Kilpatrick N, Wang S, Henary M, Wilson WD. Halogenated pentamethine cyanine dyes exhibiting high fidelity for G-quadruplex DNA. Bioorg Med Chem 2012; 20:7002-11. [PMID: 23127491 DOI: 10.1016/j.bmc.2012.10.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2012] [Revised: 10/05/2012] [Accepted: 10/10/2012] [Indexed: 11/29/2022]
Abstract
Design and optimization of quadruplex-specific small molecules is developing into an attractive strategy for anti-cancer therapeutics with some promising candidates in clinical trials. A number of therapeutically favorable features of cyanine molecules can be effectively exploited to develop them as promising quadruplex-targeting agents. Herein, the design, synthesis and evaluation of a series of dimethylindolenine cyanine dyes with varying halogen substitutions are reported. Their interactions with telomeric and c-myc quadruplexes as well as a reference duplex sequence have been evaluated using thermal melting, biosensor-surface plasmon resonance, circular dichroism, isothermal titration calorimetry and mass spectrometry. Thermal melting analysis indicates that these ligands exhibit significant quadruplex stabilization and a very low duplex binding, with the dimethyl incorporation of paramount importance for decreased duplex affinity. Circular dichroism studies showed that the interaction of cyanines with quadruplex structures are primarily through stacking at one or both ends of the terminal tetrads with the two (trimethylammonium)propyl groups interacting in the accessible quadruplex grooves. Surface plasmon resonance and mass spectral studies shows the formation of an initial strong 1:1 complex followed by a significantly weaker secondary binding. Isothermal calorimetry studies show that the interaction of cyanines is predominantly entropy driven. In line with the design principles, this work provides new insights for further developing potent, highly selective cyanines as promising quadruplex-specific agents.
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Affiliation(s)
- Rupesh Nanjunda
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
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123
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Abstract
In addition to the canonical double helix, DNA can fold into various other inter- and intramolecular secondary structures. Although many such structures were long thought to be in vitro artefacts, bioinformatics demonstrates that DNA sequences capable of forming these structures are conserved throughout evolution, suggesting the existence of non-B-form DNA in vivo. In addition, genes whose products promote formation or resolution of these structures are found in diverse organisms, and a growing body of work suggests that the resolution of DNA secondary structures is critical for genome integrity. This Review focuses on emerging evidence relating to the characteristics of G-quadruplex structures and the possible influence of such structures on genomic stability and cellular processes, such as transcription.
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124
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Shi S, Lv C, Gao X, Zhao J, Yao J, Sun W, Huang H, Yao T, Ji L. [Ru(bpy)2(bppp)]2+ binds two different forms of the human telomeric G-quadruplex structure. INORG CHEM COMMUN 2012. [DOI: 10.1016/j.inoche.2012.07.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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125
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Long Y, Li Z, Tan JH, Ou TM, Li D, Gu LQ, Huang ZS. Benzofuroquinoline derivatives had remarkable improvement of their selectivity for telomeric G-quadruplex DNA over duplex DNA upon introduction of peptidyl group. Bioconjug Chem 2012; 23:1821-31. [PMID: 22871222 DOI: 10.1021/bc300123m] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In order to improve the selectivity of 5-N-methyl quindoline (cryptolepine) derivatives as telomeric quadruplex binding ligands versus duplex DNA, a series of peptidyl-benzofuroquinoline (P-BFQ) conjugates (2a-2n) were designed and synthesized. Their interactions with telomeric quadruplex and duplex DNA were examined by using the fluorescence resonance energy transfer (FRET) melting assay, surface plasmon resonance (SPR), circular dichroism spectroscopy (CD), and molecular modeling studies. Introduction of a peptidyl group at 11-position of the aromatic benzofuroquinoline scaffold not only effectively increased its binding affinity, but also significantly improved its selectivity toward telomeric quadruplex versus duplex DNA. Combined with the data for their inhibitory effects on telomerase activity, their structure-activity relationships (SARs) studies showed that the types of amino acid residues and the length of the peptidyl side chains were important for the improvement of their interactions with the telomeric G-quadruplex. Long-term exposure of human cancer cells to 2c showed a remarkable cessation in population growth and cellular senescence phenotype, and accompanied by a shortening of the telomere length.
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Affiliation(s)
- Yi Long
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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126
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Larsen AF, Nielsen MC, Ulven T. Tetrasubstituted Phenanthrolines as Highly Potent, Water-Soluble, and Selective G-Quadruplex Ligands. Chemistry 2012; 18:10892-902. [DOI: 10.1002/chem.201200081] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/29/2012] [Indexed: 11/11/2022]
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127
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Zheng XH, Chen HY, Tong ML, Ji LN, Mao ZW. Platinum squares with high selectivity and affinity for human telomeric G-quadruplexes. Chem Commun (Camb) 2012; 48:7607-9. [PMID: 22728887 DOI: 10.1039/c2cc32942e] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two new Pt(II) squares with quinoxaline-bridges selectively stabilize human telomeric G-quadruplexes with high binding constants (10(7)-10(9) M(-1)) and an unprecedented binding stoichiometric ratio of Pt(II) square/G-quadruplex (6 : 1). This selectivity is likely due to the Pt(II) squares' cube-like shape. Both Pt(II) squares also show significant telomerase inhibition and anticancer efficacy.
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Affiliation(s)
- Xiao-Hui Zheng
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-Sen University, Guangzhou 510275, China
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128
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Liu D, Liu Y, Wang C, Shi S, Sun D, Gao F, Zhang Q, Liu J. Polypyridyl Complexes of Ruthenium(II): Stabilization of G-quadruplex DNA and Inhibition of Telomerase Activity. Chempluschem 2012. [DOI: 10.1002/cplu.201200039] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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129
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Xu N, Yang H, Cui M, Song F, Liu Z, Liu S. A Study of Interaction between Flavonoids and the Parallel Quadruplex Structure [d(TGGGGT)]
4
by Electrospray Ionization Mass Spectrometry. CHINESE J CHEM 2012. [DOI: 10.1002/cjoc.201100641] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Niusheng Xu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Hongmei Yang
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Graduate School of the Chinese Academy of Sciences, Beijing 100039, China
| | - Meng Cui
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Fengrui Song
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Zhiqiang Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
| | - Shuying Liu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
- Changchun University of Chinese Medicine, Changchun, Jilin 130117, China
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130
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Wang SR, Zhang D, Luo FL, Liu L, Weng XC, Huang J, Li GR, Zhang XL, Zhou X. Some cationic porphyrins: synthesis, stabilization of G-quadruplexes, and down-regulation of c-myc in Hep G2 cells. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The stabilization of G-quadruplex DNA represents an attractive strategy for the design and development of novel antitumor drugs. In the present work, we have designed and synthesized nine cationic porphyrins, each with four side arms at their meso positions. The interactions of these porphyrins with both human telomeric DNA and NHE III1 G-quadruplexes were measured by various DNA binding assays, including polymerase stop assay, circular dichroism (CD) and CD melting assay. We then proceeded to investigate their effects on the expression of c-myc oncogene in the Hep G2 cell line. The experimental results indicate that these porphyrins are capable of effectively inducing or stabilizing both human telomeric and NHE III1 G-quadruplexes in the presence or absence of metal ions. Furthermore, we have discovered that porphyrins with a stronger stabilizing effect on c-myc G-quadruplexes lead to more pronounced down-regulation of the c-myc oncogene in the Hep G2 cell line.
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Affiliation(s)
- Shao R. Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Dan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Feng L. Luo
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Lin Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao C. Weng
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Jing Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Guo R. Li
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao L. Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
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131
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Xu L, Xu Z, Shang Y, Feng S, Zhou X. Structural polymorphism of human telomere G-quadruplex induced by a pyridyl carboxamide molecule. Bioorg Med Chem Lett 2012; 22:2988-92. [DOI: 10.1016/j.bmcl.2012.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 01/02/2023]
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132
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Liao SR, Zhou CX, Wu WB, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. 12-N-Methylated 5,6-dihydrobenzo[c]acridine derivatives: a new class of highly selective ligands for c-myc G-quadruplex DNA. Eur J Med Chem 2012; 53:52-63. [PMID: 22513122 DOI: 10.1016/j.ejmech.2012.03.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 03/16/2012] [Accepted: 03/17/2012] [Indexed: 11/19/2022]
Abstract
12-N-Methylated and non-methylated 5,6-dihydrobenzo[c]acridine derivatives were designed and synthesized as new series of c-myc G-quadruplex binding ligands. Their interactions with c-myc G-quadruplex were evaluated using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), polymerase chain reaction (PCR) stop assay, and molecular modeling. Compared with the non-methylated derivatives, 12-N-methylated derivatives had stronger binding affinity and stabilizing ability to c-myc G-quadruplex structure, and could more effectively stack on the G-quartet surface. All these derivatives had high selectivity for c-myc G-quadruplex DNA over duplex DNA. The reverse transcription (RT) PCR assay showed that compound 21c could down-regulate transcription of c-myc gene in Ramos cell line containing NHE III(1) element, but had no effect in CA46 cell line with NHE III(1) element removed.
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Affiliation(s)
- Sheng-Rong Liao
- School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou University City, Waihuan East Road 132, Guangzhou 510006, People's Republic of China
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133
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Sun D, Liu Y, Liu D, Zhang R, Yang X, Liu J. Stabilization of G-Quadruplex DNA, Inhibition of Telomerase Activity and Live Cell Imaging Studies of Chiral Ruthenium(II) Complexes. Chemistry 2012; 18:4285-95. [DOI: 10.1002/chem.201103156] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Indexed: 11/11/2022]
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134
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Nagesh N, Ganesh Kumar A. Interaction of TMPyP4, TMPyP3, and TMPyP2 with Intramolecular G-Quadruplex Formed by Promoter Region of Bcl2 and KRAS NHPPE. ACTA ACUST UNITED AC 2012. [DOI: 10.5402/2012/786596] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Oncogenes are rich in guanine and capable of forming quadruplex structure. Promoter regions oncogenes such as Bcl2 and KRAS NHPPE are rich in guanine content and they can form quadruplex structures. Alterations in the mode and nature of molecular binding to DNA, certainly has effect on the posttranscriptional activities. Recent experiments indicate that structure of quadruplex complex and ligand has predominant role on ligand-quadruplex DNA interaction. In order to understand the nature of each ligand interaction with quadruplex DNA, Bcl2, KRAS NHPPE quadruplex DNA interaction with three porphyrin was studied using spectroscopy, microcalorimetry and mass spectrometry. Our studies, indicate that mode of ligand interaction varies with structure, environment and concentration of ligand. Fluorescence quenching experiments show that TMPyP4 interaction is ligand concentration dependent. Job plots and ITC experiments demonstrate that four molecules of TMPyP4 and two molecules of TMPyP3, TMPyP2 interact with each quadruplex complex. Through ITC titrations, ligand binding constant are higher for TMPyP4 (≈107 M−1) compared to TMPyP3, TMPyP2 (≈105 M−1). ESI-MS experiments confirm the stoichiometry of TMPyP4 : 39Bcl2 is 4 : 1 at saturation and it is 2 : 1 in case of KRAS NHPPE quadruplex.
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Affiliation(s)
- Narayana Nagesh
- Department of Medicinal Chemistry, Centre for Cellular and Molecular Biology, Hyderabad 500007, India
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135
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Abstract
G-quartets are square planar arrangements of four guanine bases, which can form extraordinarily stable stacks when present in nucleic acid sequences. Such G-quadruplex structures were long regarded as an in vitro phenomenon, but the widespread presence of suitable sequences in genomes and the identification of proteins that stabilize, modify or resolve these nucleic acid structures have provided circumstantial evidence for their physiological relevance. The therapeutic potential of small molecules that can stabilize or disrupt G-quadruplex structures has invigorated the field in recent years. Here we review some of the key observations that support biological functions for G-quadruplex DNA as well as the techniques and tools that have enabled researchers to probe these structures and their interactions with proteins and small molecules.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, University of Sydney, 214 Hawkesbury Road, Westmead, Sydney, NSW 2145, Australia.
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136
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Nagasawa K, Iida K, Majima S, Ohtake T, Tera M, Shin-ya K. Design and Synthesis of G-Quadruplex Ligands Bearing Macrocyclic Hexaoxazoles with Four-Way Side Chains. HETEROCYCLES 2012. [DOI: 10.3987/com-11-s(p)88] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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137
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Zhang Z, He X, Yuan G. Formation and recognition of G-quadruplex relevant for pilin antigenic variation in Neisseria gonorrhoeae. CAN J CHEM 2012. [DOI: 10.1139/v11-092] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In this research, NMR, ESI-MS, and circular dichroism (CD) spectroscopies were used to investigate the formation and recognition of G-quadruplex by a G-rich sequence that has been demonstrated to be relevant for pilin variation in Neisseria gonorrhoeae . The NMR spectra provided strong evidence that the G-quadruplex structure was formed from this G-rich sequence, and this result was confirmed by CD spectroscopy. In addition, two small-molecule natural products (jatrorrhizine hydrochloride (J) and dehydrocorydaline (D)) were found to bind to this G-quadruplex over the corresponding duplex DNA with high selectivity by ESI-MS.
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Affiliation(s)
- Zhenjiang Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Xiangwei He
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
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138
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Sun D, Zhang R, Yuan F, Liu D, Zhou Y, Liu J. Studies on characterization, telomerase inhibitory properties and G-quadruplex binding of η6-arene ruthenium complexes with 1,10-phenanthroline-derived ligands. Dalton Trans 2012; 41:1734-41. [DOI: 10.1039/c1dt11676b] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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139
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Yaku H, Fujimoto T, Murashima T, Miyoshi D, Sugimoto N. Phthalocyanines: a new class of G-quadruplex-ligands with many potential applications. Chem Commun (Camb) 2012; 48:6203-16. [DOI: 10.1039/c2cc31037f] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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140
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Zheng XH, Zhong YF, Tan CP, Ji LN, Mao ZW. Pt(ii) squares as selective and effective human telomeric G-quadruplex binders and potential cancer therapeutics. Dalton Trans 2012; 41:11807-12. [DOI: 10.1039/c2dt31303k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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141
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Dhamodharan V, Harikrishna S, Jagadeeswaran C, Halder K, Pradeepkumar PI. Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1,8-Naphthyridine. J Org Chem 2011; 77:229-42. [DOI: 10.1021/jo201816g] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- V. Dhamodharan
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - S. Harikrishna
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - C. Jagadeeswaran
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - K. Halder
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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142
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Li Z, Tan JH, He JH, Long Y, Ou TM, Li D, Gu LQ, Huang ZS. Disubstituted quinazoline derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Eur J Med Chem 2011; 47:299-311. [PMID: 22104971 DOI: 10.1016/j.ejmech.2011.10.057] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 10/25/2011] [Accepted: 10/28/2011] [Indexed: 12/12/2022]
Abstract
A series of 2,4-disubstituted quinazoline derivatives found to be a new type of highly selective ligand to bind with telomeric G-quadruplex DNA, and their biological properties were reported for the first time.Their interactions with telomeric G-quadruplex DNA were evaluated by using fluorescence resonance energy transfer (FRET) melting assay, circular dichroism (CD) spectroscopy, surface plasmon resonance (SPR), nuclear magnetic resonance (NMR), and molecular modeling. Our results showed that these derivatives could well recognize G-quadruplex and have high selectivity toward G-quadruplex over duplex DNA. The structure-activity relationships (SARs) study revealed that the disubstitution of quinazoline and the length of the amide side chain were important for its interaction with the G-quadruplex. Furthermore, telomerase inhibition of the quinazoline derivatives and their cellular effects were studied.
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Affiliation(s)
- Zeng Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, People's Republic of China
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143
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Castor KJ, Mancini J, Fakhoury J, Weill N, Kieltyka R, Englebienne P, Avakyan N, Mittermaier A, Autexier C, Moitessier N, Sleiman HF. Platinum(II) Phenanthroimidazoles for Targeting Telomeric G-Quadruplexes. ChemMedChem 2011; 7:85-94. [DOI: 10.1002/cmdc.201100453] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Indexed: 11/10/2022]
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144
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Chu JF, Wang ZF, Tseng TY, Chang TC. A Novel Method for Screening G-quadruplex Stabilizers to Human Telomeres. J CHIN CHEM SOC-TAIP 2011. [DOI: 10.1002/jccs.201190028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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145
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Sun H, Xiang J, Liu Y, Li L, Li Q, Xu G, Tang Y. A stabilizing and denaturing dual-effect for natural polyamines interacting with G-quadruplexes depending on concentration. Biochimie 2011; 93:1351-6. [DOI: 10.1016/j.biochi.2011.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 06/07/2011] [Indexed: 01/31/2023]
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146
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Manet I, Manoli F, Donzello MP, Ercolani C, Vittori D, Cellai L, Masi A, Monti S. Tetra-2,3-pyrazinoporphyrazines with Externally Appended Pyridine Rings. 10. A Water-Soluble Bimetallic (ZnII/PtII) Porphyrazine Hexacation as Potential Plurimodal Agent for Cancer Therapy: Exploring the Behavior as Ligand of Telomeric DNA G-Quadruplex Structures. Inorg Chem 2011; 50:7403-11. [DOI: 10.1021/ic200514z] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti 101, 40129 Bologna, Italy
| | - Francesco Manoli
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti 101, 40129 Bologna, Italy
| | - Maria Pia Donzello
- Dipartimento di Chimica, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Claudio Ercolani
- Dipartimento di Chimica, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Daniela Vittori
- Dipartimento di Chimica, Università degli Studi di Roma “La Sapienza”, P.le A. Moro 5, 00185 Roma, Italy
| | - Luciano Cellai
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Area della Ricerca di Roma 1, 00015 Monterotondo Scalo, Rome, Italy
| | - Annalisa Masi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Area della Ricerca di Roma 1, 00015 Monterotondo Scalo, Rome, Italy
| | - Sandra Monti
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti 101, 40129 Bologna, Italy
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147
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Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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148
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Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011; 50:8046-50. [DOI: 10.1002/anie.201101759] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/30/2011] [Indexed: 12/18/2022]
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149
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Zhang AYQ, Bugaut A, Balasubramanian S. A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry 2011; 50:7251-8. [PMID: 21744844 DOI: 10.1021/bi200805j] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
G-Quadruplexes are noncanonical nucleic acid secondary structures based on guanine association that are readily adopted by G-rich RNA and DNA sequences. Naturally occurring genomic G-quadruplex-forming sequences have functional roles in biology that are mediated through structure. To appreciate how this is achieved, an understanding of the likelihood of G-quadruplex formation and the structural features of the folded species under a defined set of conditions is informative. We previously systematically investigated the thermodynamic stability and folding topology of DNA G-quadruplexes and found a strong dependence of these properties on loop length and loop arrangement [Bugaut, A., and Balasubramanian, S. (2008) Biochemistry 47, 689-697]. Here we report on a complementary analysis of RNA G-quadruplexes using UV melting and circular dichroism spectroscopy that also serves as a comparison to the equivalent DNA G-quadruplex-forming sequences. We found that the thermodynamic stability of G-quadruplex RNA can be modulated by loop length while the overall structure is largely unaffected. The systematic design of our study also revealed subtle loop length dependencies in RNA G-quadruplex structure.
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Affiliation(s)
- Amy Y Q Zhang
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
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150
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Prakash A, Kieken F, Marky LA, Borgstahl GEO. Stabilization of a G-Quadruplex from Unfolding by Replication Protein A Using Potassium and the Porphyrin TMPyP4. J Nucleic Acids 2011; 2011:529828. [PMID: 21772995 PMCID: PMC3136172 DOI: 10.4061/2011/529828] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/17/2011] [Accepted: 04/01/2011] [Indexed: 11/20/2022] Open
Abstract
Replication protein A (RPA) plays an essential role in DNA replication by binding and unfolding non-canonical single-stranded DNA (ssDNA) structures. Of the six RPA ssDNA binding domains (labeled A-F), RPA-CDE selectively binds a G-quadruplex forming sequence (5′-TAGGGGAAGGGTTGGAGTGGGTT-3′ called Gq23). In K+, Gq23 forms a mixed parallel/antiparallel conformation, and in Na+ Gq23 has a less stable (TM lowered by ∼20°C), antiparallel conformation. Gq23 is intramolecular and 1D NMR confirms a stable G-quadruplex structure in K+. Full-length RPA and RPA-CDE-core can bind and unfold the Na+ form of Gq23 very efficiently, but complete unfolding is not observed with the K+ form. Studies with G-quadruplex ligands, indicate that TMPyP4 has a thermal stabilization effect on Gq23 in K+, and inhibits complete unfolding by RPA and RPA-CDE-core. Overall these data indicate that G-quadruplexes present a unique problem for RPA to unfold and ligands, such as TMPyP4, could possibly hinder DNA replication by blocking unfolding by RPA.
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Affiliation(s)
- Aishwarya Prakash
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
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