101
|
Lu C, Smith-Carpenter JE, Taylor JSA. Evidence for Reverse Hoogsteen Hairpin Intermediates in the Photocrosslinking of Human Telomeric DNA Sequences. Photochem Photobiol 2018; 94:685-697. [PMID: 29418001 DOI: 10.1111/php.12898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 01/04/2018] [Indexed: 12/28/2022]
Abstract
UVB irradiation of human telomeric d(GGGTTA)3 GGG sequences in potassium ion solution crosslinks the first and third TTA segments through anti cyclobutane pyrimidine dimer (CPD) formation. The photocrosslinking reaction was first proposed to occur through a form 3 two-tetrad G-quadruplex in which the lateral four-nucleotide GTTA loop can interact with an adjacent TTA loop. Curiously, the reaction does not occur with sodium ion, which was explained by the formation of a basket structure which only has three-nucleotide TTA loops that cannot interact. Sequences known or expected to favor the two-tetrad basket did not show enhanced photocrosslinking, suggesting that some other structure was the reactive intermediate. Herein, we report that anti CPDs form in human telomeric DNA sequences with lithium ion that is known to disfavor G-quadruplex formation, as well as with potassium ion when the bases are modified to interfere with G-quartet formation. We also show that anti CPDs form in sequences containing A's in place of G's that cannot form Hoogsteen hairpins, but can form reverse Hoogsteen hairpins. These results suggest that reverse Hoogsteen hairpins may play a hitherto unrecognized role in the biology and photoreactivity of DNA in telomeres, and possibly in other purine-rich sequences found in regulatory regions.
Collapse
Affiliation(s)
- Chen Lu
- Department of Chemistry, Washington University, St. Louis, MO
| | | | | |
Collapse
|
102
|
Probing the interaction of copper cofactor and azachalcone substrate with G-quadruplex of DNA based Diels-Alderase by site-specific fluorescence quenching titration. Biochimie 2018; 146:20-27. [DOI: 10.1016/j.biochi.2017.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/02/2017] [Indexed: 01/18/2023]
|
103
|
Cozzoli L, Gjonaj L, Stuart MCA, Poolman B, Roelfes G. Responsive DNA G-quadruplex micelles. Chem Commun (Camb) 2018; 54:260-263. [PMID: 29231221 DOI: 10.1039/c7cc07899d] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A novel and versatile design of DNA-lipid conjugates is presented. The assembly of the DNA headgroups into G-quadruplex structures is essential for the formation of micelles and their stability. By hybridization with a complementary oligonucleotide the micelles were destabilized, resulting in cargo release. In combination with a hairpin DNA aptamer as complementary strand, the release is obtained selectively by the presence of ATP.
Collapse
Affiliation(s)
- Liliana Cozzoli
- Stratingh Institute for Chemistry, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
| | | | | | | | | |
Collapse
|
104
|
Padmapriya K, Barthwal R. WITHDRAWN: Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and circular dichroism spectroscopy. Biochimie 2018:S0300-9084(18)30042-7. [PMID: 29474974 DOI: 10.1016/j.biochi.2018.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/05/2018] [Accepted: 01/07/2018] [Indexed: 11/17/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.biochi.2018.02.002. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Kumar Padmapriya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ritu Barthwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| |
Collapse
|
105
|
Zhang J, Li X, Sun X, Song A, Tan Y, Hao J. GMP-quadruplex-based hydrogels stabilized by lanthanide ions. Sci China Chem 2018. [DOI: 10.1007/s11426-017-9187-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
106
|
García-Iglesias M, Torres T, González-Rodríguez D. Well-defined, persistent, chiral phthalocyanine nanoclusters via G-quadruplex assembly. Chem Commun (Camb) 2018; 52:9446-9. [PMID: 27377372 DOI: 10.1039/c6cc04152c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Octameric near-IR dye nanoclusters are produced by complexation of potassium cations with a phthalocyanine-guanosine conjugate. The combination of hydrogen-bonding, K(+) coordination, π-π stacking and steric interactions between the chiral side groups is responsible for defining a specific helical chromophore arrangement in the clusters, which display high stability and maintain their supramolecular identity onto substrates.
Collapse
Affiliation(s)
- Miguel García-Iglesias
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| | - Tomas Torres
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. and IMDEA Nanociencia, c/Faraday 9, Campus de Cantoblanco, 28049, Spain
| | - David González-Rodríguez
- Departamento de Química Orgánica, Facultad de Ciencias, Universidad Autónoma de Madrid, E-28049 Madrid, Spain.
| |
Collapse
|
107
|
Konda M, Maiti S, Jadhav RG, Das AK. Redox-Active Peptide-Functionalized Quinquethiophene-Based Electrochromic π-Gel. Chem Asian J 2018; 13:204-209. [PMID: 29266836 DOI: 10.1002/asia.201701460] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Indexed: 12/13/2022]
Abstract
An electrochromic system based on a self-assembled dipeptide-appended redox-active quinquethiophene π-gel is reported. The designed peptide-quinquethiophene consists of a symmetric bolaamphiphile that has two segments: a redox-active π-conjugated quinquethiophene core for electrochromism, and peptide motif for the involvement of molecular self-assembly. Investigations reveal that self-assembly and electrochromic properties of the π-gel are strongly dependent on the relative orientation of peptidic and quinquethiophene scaffolds in the self-assembly system. The colors of the π-gel film are very stable with fast and controlled switching speed at room temperature.
Collapse
Affiliation(s)
- Maruthi Konda
- Department of Chemistry, Indian Institute of Technology Indore, Indore, India
| | - Sayan Maiti
- Department of Chemistry, Indian Institute of Technology Indore, Indore, India
| | - Rohit G Jadhav
- Department of Chemistry, Indian Institute of Technology Indore, Indore, India
| | - Apurba K Das
- Department of Chemistry, Indian Institute of Technology Indore, Indore, India
| |
Collapse
|
108
|
Zhu X, Zou R, Sun P, Wang Q, Wu J. A supramolecular peptide polymer from hydrogen-bond and coordination-driven self-assembly. Polym Chem 2018. [DOI: 10.1039/c7py01901g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A terpyridine- and guanine-functionalized peptide was developed that could form different morphologies by self-assembly or coordination with Fe2+ in dimethyl sulfoxide.
Collapse
Affiliation(s)
- Xiaomin Zhu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| | - Rongfeng Zou
- Division of Theoretical Chemistry and Biology
- School of Biotechnology
- Royal Institute of Technology (KTH)
- AlbaNova University Center
- 106 91 Stockholm
| | - Peng Sun
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan
- China
| | - Qi Wang
- College of Public Health
- Nantong University
- Nantong
- China
| | - Junchen Wu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals
- School of Chemistry and Molecular Engineering
- East China University of Science and Technology
- Shanghai 200237
- China
| |
Collapse
|
109
|
Sahakyan AB, Chambers VS, Marsico G, Santner T, Di Antonio M, Balasubramanian S. Machine learning model for sequence-driven DNA G-quadruplex formation. Sci Rep 2017; 7:14535. [PMID: 29109402 PMCID: PMC5673958 DOI: 10.1038/s41598-017-14017-4] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/05/2017] [Indexed: 11/25/2022] Open
Abstract
We describe a sequence-based computational model to predict DNA G-quadruplex (G4) formation. The model was developed using large-scale machine learning from an extensive experimental G4-formation dataset, recently obtained for the human genome via G4-seq methodology. Our model differentiates many widely accepted putative quadruplex sequences that do not actually form stable genomic G4 structures, correctly assessing the G4 folding potential of over 700,000 such sequences in the human genome. Moreover, our approach reveals the relative importance of sequence-based features coming from both within the G4 motifs and their flanking regions. The developed model can be applied to any DNA sequence or genome to characterise sequence-driven intramolecular G4 formation propensities.
Collapse
Affiliation(s)
- Aleksandr B Sahakyan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Vicki S Chambers
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Giovanni Marsico
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tobias Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Marco Di Antonio
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK.
| |
Collapse
|
110
|
Dvořáková Z, Vorlíčková M, Renčiuk D. Spectroscopic insights into quadruplexes of five-repeat telomere DNA sequences upon G-block damage. Biochim Biophys Acta Gen Subj 2017; 1861:2750-2757. [DOI: 10.1016/j.bbagen.2017.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/16/2017] [Accepted: 07/24/2017] [Indexed: 11/26/2022]
|
111
|
Virgilio A, Russo A, Amato T, Russo G, Mayol L, Esposito V, Galeone A. Monomolecular G-quadruplex structures with inversion of polarity sites: new topologies and potentiality. Nucleic Acids Res 2017; 45:8156-8166. [PMID: 28666330 PMCID: PMC5737522 DOI: 10.1093/nar/gkx566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
In this paper, we report investigations, based on circular dichroism, nuclear magnetic resonance spectroscopy and electrophoresis methods, on three oligonucleotide sequences, each containing one 3′-3′ and two 5′-5′ inversion of polarity sites, and four G-runs with a variable number of residues, namely two, three and four (mTG2T, mTG3T and mTG4T with sequence 3′-TGnT-5′-5′-TGnT-3′-3′-TGnT-5′-5′-TGnT-3′ in which n = 2, 3 and 4, respectively), in comparison with their canonical counterparts (TGnT)4 (n = 2, 3 and 4). Oligonucleotides mTG3T and mTG4T have been proven to form very stable unprecedented monomolecular parallel G-quadruplex structures, characterized by three side loops containing the inversion of polarity sites. Both G-quadruplexes have shown an all-syn G-tetrad, while the other guanosines adopt anti glycosidic conformations. All oligonucleotides investigated have shown a noteworthy antiproliferative activity against lung cancer cell line Calu 6 and colorectal cancer cell line HCT-116 p53−/−. Interestingly, mTG3T and mTG4T have proven to be mostly resistant to nucleases in a fetal bovine serum assay. The whole of the data suggest the involvement of specific pathways and targets for the biological activity.
Collapse
Affiliation(s)
- Antonella Virgilio
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Annapina Russo
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Teresa Amato
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Giulia Russo
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Veronica Esposito
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Aldo Galeone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| |
Collapse
|
112
|
Riccardi C, Russo Krauss I, Musumeci D, Morvan F, Meyer A, Vasseur JJ, Paduano L, Montesarchio D. Fluorescent Thrombin Binding Aptamer-Tagged Nanoparticles for an Efficient and Reversible Control of Thrombin Activity. ACS APPLIED MATERIALS & INTERFACES 2017; 9:35574-35587. [PMID: 28849915 DOI: 10.1021/acsami.7b11195] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Progress in understanding and treatment of thrombotic diseases requires new effective methods for the easy, rapid, and reversible control of coagulation processes. In this framework, the use of aptamers, and particularly of the thrombin binding aptamer (TBA), has aroused strong interest, due to its enormous therapeutic potential, associated with a large number of possible applications in biotechnological and bioanalytical fields. Here, we describe a new TBA analogue (named tris-mTBA), carrying three different pendant groups: a dansyl residue at the 3'- and a β-cyclodextrin moiety at the 5'-end-providing a host-guest system which exhibits a marked fluorescence enhancement upon TBA G-quadruplex folding-and a biotin tag, allowing the attachment of the aptamer onto biocompatible streptavidin-coated silica nanoparticles (NPs) of 50 nm hydrodynamic diameter (Sicastar). The use of nanoparticles for the in vivo delivery of TBA, expected to induce per se increased nuclease resistance and improved pharmacokinetic properties of this oligonucleotide, offers as an additional advantage the possibility to exploit multivalency effects, due to the presence of multiple copies of TBA on a single scaffold. In addition, the selected fluorescent system allows monitoring both the presence of TBA on the functionalized NPs and its correct folding upon immobilization, also conferring enhanced enzymatic resistance and bioactivity. The anticoagulant activity of the new tris-mTBA, free or conjugated to Sicastar NPs, was evaluated by dynamic light scattering experiments. Highly effective and reversible inhibition of thrombin activity toward fibrinogen was found for the free tris-mTBA and especially for the tris-mTBA-conjugated NPs, demonstrating great potential for the biomedical control of blood clotting.
Collapse
Affiliation(s)
- Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia 21, I-80126, Napoli, Italy
| | - Irene Russo Krauss
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia 21, I-80126, Napoli, Italy
- CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase , Via della Lastruccia 3, I-50019, Sesto Fiorentino, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia 21, I-80126, Napoli, Italy
- Institute of Biostructures and Bioimages, CNR , Via Mezzocannone 16, I-80134 Napoli, Italy
| | - François Morvan
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, University of Montpellier , place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Albert Meyer
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, University of Montpellier , place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier, CNRS, ENSCM, University of Montpellier , place E. Bataillon, 34095 Montpellier Cedex 5, France
| | - Luigi Paduano
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia 21, I-80126, Napoli, Italy
- CSGI - Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase , Via della Lastruccia 3, I-50019, Sesto Fiorentino, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia 21, I-80126, Napoli, Italy
| |
Collapse
|
113
|
Bhattacharyya T, Kumar YP, Dash J. Supramolecular Hydrogel Inspired from DNA Structures Mimics Peroxidase Activity. ACS Biomater Sci Eng 2017; 3:2358-2365. [DOI: 10.1021/acsbiomaterials.7b00563] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tanima Bhattacharyya
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Y. Pavan Kumar
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| |
Collapse
|
114
|
Kejnovská I, Bednárová K, Renciuk D, Dvoráková Z, Školáková P, Trantírek L, Fiala R, Vorlícková M, Sagi J. Clustered abasic lesions profoundly change the structure and stability of human telomeric G-quadruplexes. Nucleic Acids Res 2017; 45:4294-4305. [PMID: 28369584 PMCID: PMC5416849 DOI: 10.1093/nar/gkx191] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 03/21/2017] [Indexed: 01/02/2023] Open
Abstract
Ionizing radiation produces clustered damage to DNA which is difficult to repair and thus more harmful than single lesions. Clustered lesions have only been investigated in dsDNA models. Introducing the term 'clustered damage to G-quadruplexes' we report here on the structural effects of multiple tetrahydrofuranyl abasic sites replacing loop adenines (A/AP) and tetrad guanines (G/AP) in quadruplexes formed by the human telomere d[AG3(TTAG3)3] (htel-22) and d[TAG3(TTAG3)3TT] (htel-25) in K+ solutions. Single to triple A/APs increased the population of parallel strands in their structures by stabilizing propeller type loops, shifting the antiparallel htel-22 into hybrid or parallel quadruplexes. In htel-25, the G/APs inhibited the formation of parallel strands and these adopted antiparallel topologies. Clustered G/AP and A/APs reduced the thermal stability of the wild-type htel-25. Depending on position, A/APs diminished or intensified the damaging effect of the G/APs. Taken together, clustered lesions can disrupt the topology and stability of the htel quadruplexes and restrict their conformational space. These in vitro results suggest that formation of clustered lesions in the chromosome capping structure can result in the unfolding of existing G-quadruplexes which can lead to telomere shortening.
Collapse
Affiliation(s)
- Iva Kejnovská
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Klára Bednárová
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Daniel Renciuk
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Zuzana Dvoráková
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Petra Školáková
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Lukáš Trantírek
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625 00 Brno, Czech Republic
| | - Michaela Vorlícková
- Institute of Biophysics, Czech Academy of Sciences, v.v.i., Královopolská 135, CZ-612 65 Brno, Czech Republic
| | - Janos Sagi
- Rimstone Laboratory, RLI, Carlsbad, CA 92010, USA
| |
Collapse
|
115
|
Wu J, Meng Z, Lu Y, Shao F. Efficient Long-Range Hole Transport Through G-Quadruplexes. Chemistry 2017; 23:13980-13985. [PMID: 28703459 DOI: 10.1002/chem.201702478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Indexed: 01/09/2023]
Abstract
DNA offers a means of long-range charge transport for biology and electric nanodevices. Here, a series of tetra-stranded G-quadruplexes were assembled within a dendritic DNA architecture to explore oxidative charge transport (hole transport) through the G-quadruplex. Efficient charge transport was achieved over 28 Å upon UV irradiation. Over a longer G-quadruplex bridge, hole transport was escalated to a higher efficiency, which resulted in a higher yield than that of the optimal duplex DNA for charge transport, that is, the adenine tract. Efficient long-range hole transport suggests tetra-stranded G-quadruplexes, instead of an oxidation hotspot, hold better potential as an electron conduit than duplex DNA.
Collapse
Affiliation(s)
- Jingyuan Wu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Zhenyu Meng
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Yunpeng Lu
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| | - Fangwei Shao
- Division of Chemistry & Biological Chemistry, Nanyang Technological University, SPMS-CBC-04-22, 21 Nanyang Link, Singapore, 637371, Singapore
| |
Collapse
|
116
|
Papi F, Bazzicalupi C, Ferraroni M, Massai L, Bertrand B, Gratteri P, Colangelo D, Messori L. [Au(9-methylcaffein-8-ylidene)2
]+
/DNA Tel23 System: Solution, Computational, and Biological Studies. Chemistry 2017; 23:13784-13791. [DOI: 10.1002/chem.201702854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco, Salute del Bambino (NEUROFARBA); Laboratory of Molecular Modeling Cheminformatics & QSAR; Università degli Studi di Firenze; Via Ugo Schiff 6 50019 Sesto Fiorentino (FI Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | - Marta Ferraroni
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | - Lara Massai
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | | | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco, Salute del Bambino (NEUROFARBA); Laboratory of Molecular Modeling Cheminformatics & QSAR; Università degli Studi di Firenze; Via Ugo Schiff 6 50019 Sesto Fiorentino (FI Italy
| | - Donato Colangelo
- Dipartimento di Scienze della Salute; Università del Piemonte Orientale ‘A. Avogadro'; Via Solaroli 17 28100 Novara Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| |
Collapse
|
117
|
Platella C, Guida S, Bonmassar L, Aquino A, Bonmassar E, Ravagnan G, Montesarchio D, Roviello GN, Musumeci D, Fuggetta MP. Antitumour activity of resveratrol on human melanoma cells: A possible mechanism related to its interaction with malignant cell telomerase. Biochim Biophys Acta Gen Subj 2017; 1861:2843-2851. [PMID: 28780124 DOI: 10.1016/j.bbagen.2017.08.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 07/31/2017] [Accepted: 08/01/2017] [Indexed: 12/19/2022]
Abstract
BACKGROUND trans-Resveratrol (tRES) is a polyphenolic stilbene found in plant products which has attracted great attention because of its antioxidant, anti-inflammatory and anticancer properties. METHODS The possible correlation between tRES-induced suppression of melanoma cell growth and its influence on telomerase expression has been investigated by biological assays. Moreover, in order to gain new knowledge about possible mechanisms of action of tRES as antineoplastic agent, its interaction with biologically relevant secondary structure-forming DNA sequences, its aggregation properties and copper-binding activity have been studied by CD, UV and fluorescence spectroscopies. RESULTS Biological assays have confirmed that growth inhibitory properties of tRES well correlate with the reduction of telomerase activity and hTERT gene transcript levels in human melanoma cells. Biophysical studies in solution have proved that tRES binds all the studied DNA model systems with low affinity, however showing high ability to discriminate G-quadruplex vs. duplex DNA. In addition, tRES has shown no propensity to form aggregates in the explored concentration range and has been found able to bind Cu2+ ions with a 2:1 stoichiometry. CONCLUSIONS From these biological and biophysical analyses it has emerged that tRES produces cytotoxic effects on human melanoma cells and, at a molecular level, is able to bind Cu2+ and cancer-involved G-quadruplexes, suggesting that multiple mechanisms of action could be involved in its antineoplastic activity. GENERAL SIGNIFICANCE Expanding the knowledge on the putative mechanisms of action of tRES as antitumour agent can help to develop novel, effective tRES-based anticancer drugs.
Collapse
Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy
| | - Serena Guida
- Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, I-00133 Rome, Italy
| | - Laura Bonmassar
- Laboratory of Molecular Oncology, Istituto Dermopatico dell'Immacolata-IRCCS, Via Monti di Creta, Rome, Italy
| | - Angelo Aquino
- School of Medicine, Department of Systems Medicine, University of Rome Tor Vergata, Via Montpellier, Rome, Italy
| | - Enzo Bonmassar
- Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, I-00133 Rome, Italy
| | - Giampiero Ravagnan
- Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, I-00133 Rome, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
| | - Maria Pia Fuggetta
- Institute of Translational Pharmacology, CNR, Via Fosso del Cavaliere 100, I-00133 Rome, Italy.
| |
Collapse
|
118
|
Effects of monovalent cations on folding kinetics of G-quadruplexes. Biosci Rep 2017; 37:BSR20170771. [PMID: 28588052 PMCID: PMC5567087 DOI: 10.1042/bsr20170771] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/02/2017] [Accepted: 06/06/2017] [Indexed: 01/29/2023] Open
Abstract
G-quadruplexes are special structures existing at the ends of human telomeres,
the folding kinetics of which are essential for their functions, such as in the
maintenance of genome stability and the protection of chromosome ends. In the
present study, we investigated the folding kinetics of G-quadruplex in different
monovalent cation environments and determined the detailed kinetic parameters
for Na+- and K+-induced G-quadruplex folding, and for its
structural transition from the basket-type Na+ form to the
hybrid-type K+ form. More interestingly, although Li+ was
often used in previous studies of G-quadruplex folding as a control ion supposed
to have no effect, we have found that Li+ can actually influence the
folding kinetics of both Na+- and K+-induced
G-quadruplexes significantly and in different ways, by changing the folding
fraction of Na+-induced G-quadruplexes and greatly increasing the
folding rates of K+-induced G-quadruplexes. The present study may
shed new light on the roles of monovalent cations in G-quadruplex folding and
should be useful for further studies of the underlying folding mechanism.
Collapse
|
119
|
Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
| |
Collapse
|
120
|
D'Urso A, Randazzo R, Rizzo V, Gangemi CMA, Romanucci V, Zarrelli A, Tomaselli G, Milardi D, Borbone N, Purrello R, Piccialli G, Di Fabio G, Oliviero G. Stabilization vs. destabilization of G-quadruplex superstructures: the role of the porphyrin derivative having spermine arms. Phys Chem Chem Phys 2017. [PMID: 28650039 DOI: 10.1039/c7cp02816d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction of the porphyrin derivative H2TCPPSpm4, having spermine pendants in the four meso positions, with the G-quadruplex (GQ) structure formed by the DNA aptamer TGGGAG has been investigated by means of UV, electronic circular dichroism and PAGE studies. The results reported here demonstrate that the porphyrin derivative is capable of stabilizing or destabilizing the higher-ordered structures of parallel GQs, depending on the method used to reach their relative stoichiometry (titration vs. single addition). Noteworthily, when two equivalents of H2TCPPSpm4 were mixed directly with one equivalent of the (TGGGAG)4 GQ to reach a 2 : 1 H2TCPPSpm4 : GQ ratio T1/2 higher than 80 °C was also observed confirming the presence of higher-ordered GQ structures.
Collapse
Affiliation(s)
- A D'Urso
- Department of Chemical Science, University of Catania, V.le A Doria 6, 95125, Catania, Italy.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
121
|
Zhou J, Amrane S, Rosu F, Salgado GF, Bian Y, Tateishi-Karimata H, Largy E, Korkut DN, Bourdoncle A, Miyoshi D, Zhang J, Ju H, Wang W, Sugimoto N, Gabelica V, Mergny JL. Unexpected Position-Dependent Effects of Ribose G-Quartets in G-Quadruplexes. J Am Chem Soc 2017; 139:7768-7779. [PMID: 28523907 DOI: 10.1021/jacs.7b00648] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
To understand the role of ribose G-quartets and how they affect the properties of G-quadruplex structures, we studied three systems in which one, two, three, or four deoxyribose G-quartets were substituted with ribose G-quartets. These systems were a parallel DNA intramolecular G-quadruplex, d(TTGGGTGGGTTGGGTGGGTT), and two tetramolecular G-quadruplexes, d(TGGGT) and d(TGGGGT). Thermal denaturation experiments revealed that ribose G-quartets have position-dependent and cumulative effects on G-quadruplex stability. An unexpected destabilization was observed when rG quartets were presented at the 5'-end of the G stack. This observation challenges the general belief that RNA residues stabilize G-quadruplexes. Furthermore, in contrast to past proposals, hydration is not the main factor determining the stability of our RNA/DNA chimeric G-quadruplexes. Interestingly, the presence of rG residues in a central G-quartet facilitated the formation of additional tetramolecular G-quadruplex topologies showing positive circular dichroism signals at 295 nm. 2D NMR analysis of the tetramolecular TGgGGT (lowercase letter indicates ribose) indicates that Gs in the 5'-most G-quartet adopt the syn conformation. These analyses highlight several new aspects of the role of ribose G-quartets on G-quadruplex structure and stability, and demonstrate that the positions of ribose residues are critical for tuning G-quadruplex properties.
Collapse
Affiliation(s)
- Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University , Nanjing 210023, China.,Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Samir Amrane
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Université de Bordeaux , CNRS UMS 3033, INSERM US001, IECB, F-33600 Pessac, France
| | - Gilmar F Salgado
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Yunqiang Bian
- Shandong Provincial Key Laboratory of Functional Macromolecular Biophysics, Institute of Biophysics, Dezhou University , Dezhou 253023, China
| | - Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Eric Largy
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Dursun Nizam Korkut
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Anne Bourdoncle
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Daisuke Miyoshi
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Jian Zhang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University , Nanjing 210093, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry & Chemical Engineering, Nanjing University , Nanjing 210023, China
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures and Department of Physics, Nanjing University , Nanjing 210093, China
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Graduate School of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | - Valérie Gabelica
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France
| | - Jean-Louis Mergny
- Université de Bordeaux , INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac, France.,Institute of Biophysics of the CAS , v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
122
|
Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme. Biochim Biophys Acta Gen Subj 2017; 1861:1913-1920. [PMID: 28533132 DOI: 10.1016/j.bbagen.2017.05.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/26/2017] [Accepted: 05/18/2017] [Indexed: 01/11/2023]
Abstract
The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K+, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. 1D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.
Collapse
|
123
|
Dickerhoff J, Haase L, Langel W, Weisz K. Tracing Effects of Fluorine Substitutions on G-Quadruplex Conformational Changes. ACS Chem Biol 2017; 12:1308-1315. [PMID: 28318229 DOI: 10.1021/acschembio.6b01096] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A human telomere sequence that folds into an intramolecular (3 + 1)-hybrid G-quadruplex was modified by the incorporation of 2'-fluoro-2'-deoxyriboguanosines (FG) into syn positions of its outer tetrad. A circular dichroism and NMR spectral analysis reveals a nearly quantitative switch of the G-tetrad polarity with concerted syn↔anti transitions of all four G residues. These observations follow findings on a FG-substituted (3 + 1)-hybrid quadruplex with a different fold, suggesting a more general propensity of hybrid-type quadruplexes to undergo a tetrad polarity reversal. Two out of the three FG analogs in both modified quadruplexes adopt an S-type sugar pucker, challenging a sole contribution of N-type sugars in enforcing an anti glycosidic torsion angle associated with the tetrad flip. NMR restrained three-dimensional structures of the two substituted quadruplexes reveal a largely conserved overall fold but significant rearrangements of the overhang and loop nucleotides capping the flipped tetrad. Sugar pucker preferences of the FG analogs may be rationalized by different orientations of the fluorine atom and its resistance to be positioned within the narrow groove with its highly negative electrostatic potential and spine of water molecules.
Collapse
Affiliation(s)
- Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Walter Langel
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Str. 4, D-17487 Greifswald, Germany
| |
Collapse
|
124
|
Salvati E, Botta L, Amato J, Di Leva FS, Zizza P, Gioiello A, Pagano B, Graziani G, Tarsounas M, Randazzo A, Novellino E, Biroccio A, Cosconati S. Lead Discovery of Dual G-Quadruplex Stabilizers and Poly(ADP-ribose) Polymerases (PARPs) Inhibitors: A New Avenue in Anticancer Treatment. J Med Chem 2017; 60:3626-3635. [PMID: 28445046 DOI: 10.1021/acs.jmedchem.6b01563] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G-quadruplex stabilizers are an established opportunity in anticancer chemotherapy. To circumvent the antiproliferative effects of G4 ligands, cancer cells recruit PARP enzymes at telomeres. Herein, starting from the structural similarity of a potent G4 ligand previously discovered by our group and a congeneric PARP inhibitor, a library of derivatives was synthesized to discover the first dual G4/PARP ligand. We demonstrate that a properly decorated thieno[3,2-c]quinolin-4(5H)-one stabilizes the G4 fold in vitro and in cells, induces a DNA damage response localized to telomeres, inhibits PARylation in cells, and has an antiproliferative effect in BRCA2 deficient tumor cells.
Collapse
Affiliation(s)
- Erica Salvati
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Lorenzo Botta
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | | | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Antimo Gioiello
- Department of Pharmaceutical Science, University of Perugia , I-06123 Perugia, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Grazia Graziani
- Department of Systems Medicine, University of "Tor Vergata" , 00173 Rome, Italy
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford , Old Road Campus Research Building, Oxford OX3 7DQ, U.K
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , 80131 Naples, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute , 00158 Rome, Italy
| | - Sandro Cosconati
- DiSTABiF, University of Campania Luigi Vanvitelli , 81100 Caserta, Italy
| |
Collapse
|
125
|
Buchholz I, Karg B, Dickerhoff J, Sievers-Engler A, Lämmerhofer M, Weisz K. Selective Targeting of G-Quadruplex Structures by a Benzothiazole-Based Binding Motif. Chemistry 2017; 23:5814-5823. [PMID: 28276093 DOI: 10.1002/chem.201700298] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Indexed: 12/28/2022]
Abstract
A benzothiazole derivative was identified as potent ligand for DNA G-quadruplex structures. Fluorescence titrations revealed selective binding to quadruplexes of different topologies including parallel, antiparallel, and (3+1) hybrid structures. The parallel c-MYC sequence was found to constitute the preferred target with dissociation constants in the micromolar range. Binding of the benzothiazole-based ligand to c-MYC was structurally and thermodynamically characterized in detail by employing a comprehensive set of spectroscopic and calorimetric techniques. Job plot analyses and mass spectral data indicate noncooperative ligand binding to form complexes with 1:1 and 2:1 stoichiometries. Whereas stacking interactions are suggested by optical methods, NMR chemical shift perturbations also indicate significant rearrangements of both 5'- and 3'-flanking sequences upon ligand binding. Additional isothermal calorimetry studies yield a thermodynamic profile of the ligand-quadruplex association and reveal enthalpic contributions to be the major driving force for binding. Structural and thermodynamic information obtained in the present work provides the basis for the rational development of benzothiazole derivatives as promising quadruplex binding agents.
Collapse
Affiliation(s)
- Ina Buchholz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| | - Adrian Sievers-Engler
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Eberhard Karls University Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald, Felix-Hausdorff-Strasse 4, 17487, Greifswald, Germany
| |
Collapse
|
126
|
Lomidze L, Kelley S, Gogichaishvili S, Metreveli N, Musier-Forsyth K, Kankia B. Sr(2+) induces unusually stable d(GGGTGGGTGGGTGGG) quadruplex dimers. Biopolymers 2017; 105:811-8. [PMID: 27416320 DOI: 10.1002/bip.22916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 02/03/2023]
Abstract
Guanine-rich sequences are able to form quadruplexes consisting of G-quartet structural units. Quadruplexes play an important role in the regulation of gene expression and have therapeutic and biotechnological potential. The HIV-1 integrase inhibitor, (GGGT)4 , and its variants demonstrate unusually high thermal stability. This property has been exploited in the use of quadruplex formation to drive various endergonic reactions of nucleic acids such as isothermal DNA amplification. Quadruplex stability is mainly determined by cations, which specifically bind into the inner core of the structure. In the present work, we report a systematic study of a variant of the HIV-1 integrase inhibitor, GGGTGGGTGGGTGGG (G3T), in the presence of alkali and alkaline-earth cations. We show that Sr(2+) -G3T is characterized by the highest thermal stability and that quadruplex formation requires only one Sr(2+) ion that binds with low micromolar affinity. These concentrations are sufficient to drive robust isothermal quadruplex priming DNA amplification reaction. The Sr(2+) -quadruplexes are also able to form unusually stable dimers through end-to-end stacking. The multimerization can be induced by a combination of quadruplex forming cations (i.e., K(+) or Sr(2+) ) and non-specific Mg(2+) .
Collapse
Affiliation(s)
- Levan Lomidze
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Sean Kelley
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| | - Shota Gogichaishvili
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Nunu Metreveli
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| | - Besik Kankia
- Institute of Biophysics, Ilia State University, Tbilisi, 0162, Republic of Georgia.,Department of Chemistry and Biochemistry, Center for RNA Biology, The Ohio State University, Columbus, OH, 43210
| |
Collapse
|
127
|
Musumeci D, Amato J, Zizza P, Platella C, Cosconati S, Cingolani C, Biroccio A, Novellino E, Randazzo A, Giancola C, Pagano B, Montesarchio D. Tandem application of ligand-based virtual screening and G4-OAS assay to identify novel G-quadruplex-targeting chemotypes. Biochim Biophys Acta Gen Subj 2017; 1861:1341-1352. [PMID: 28130159 DOI: 10.1016/j.bbagen.2017.01.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2016] [Revised: 01/16/2017] [Accepted: 01/23/2017] [Indexed: 11/29/2022]
Abstract
BACKGROUND G-quadruplex (G4) structures are key elements in the regulation of cancer cell proliferation and their targeting is deemed to be a promising strategy in anticancer therapy. METHODS A tandem application of ligand-based virtual screening (VS) calculations together with the experimental G-quadruplex on Oligo Affinity Support (G4-OAS) assay was employed to discover novel G4-targeting compounds. The interaction of the selected compounds with the investigated G4 in solution was analysed through a series of biophysical techniques and their biological activity investigated by immunofluorescence and MTT assays. RESULTS A focused library of 60 small molecules, designed as putative G4 groove binders, was identified through the VS. The G4-OAS experimental screening led to the selection of 7 ligands effectively interacting with the G4-forming human telomeric DNA. Evaluation of the biological activity of the selected compounds showed that 3 ligands of this sub-library induced a marked telomere-localized DNA damage response in human tumour cells. CONCLUSIONS The combined application of virtual and experimental screening tools proved to be a successful strategy to identify new bioactive chemotypes able to target the telomeric G4 DNA. These compounds may represent useful leads for the development of more potent and selective G4 ligands. GENERAL SIGNIFICANCE Expanding the repertoire of the available G4-targeting chemotypes with improved physico-chemical features, in particular aiming at the discovery of novel, selective G4 telomeric ligands, can help in developing effective anti-cancer drugs with fewer side effects. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | | | - Chiara Cingolani
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, Regina Elena National Cancer Institute, Rome 00144, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples 80131, Italy.
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy.
| |
Collapse
|
128
|
Abstract
Minima of the electric field and positions of K+ and Na+ (zero of the x-coordinate is the center of the cavity).
Collapse
Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici
- ICCOM – UOS Pisa
- Area della Ricerca del CNR
- I-56124 Pisa
- Italy
| |
Collapse
|
129
|
Rotaru A, Pricope G, Plank TN, Clima L, Ursu EL, Pinteala M, Davis JT, Barboiu M. G-Quartet hydrogels for effective cell growth applications. Chem Commun (Camb) 2017; 53:12668-12671. [DOI: 10.1039/c7cc07806d] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functional G-quartet hydrogels formed from natural guanosine cross linked with benzene-1,4-diboronic acid and Mg2+ support cell growth with no visible signs of gel degradation.
Collapse
Affiliation(s)
- Alexandru Rotaru
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
| | - Gabriela Pricope
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
| | - Taylor N. Plank
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Lilia Clima
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
| | - Elena L. Ursu
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
| | - Mariana Pinteala
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
| | - Jeffery T. Davis
- Department of Chemistry and Biochemistry
- University of Maryland
- College Park
- USA
| | - Mihail Barboiu
- “Petru Poni” Institute of Macromolecular Chemistry
- Centre Advanced Research in Bionanoconjugates and Biopolymers
- Romania
- Institut Europeen Membranes
- Adaptive Supramolecular Nanosystems Group
| |
Collapse
|
130
|
Anjong TF, Kim G, Jang HY, Yoon J, Kim J. Diiridium(iii) complexes: luminescent probes and sensors for G-quadruplex DNA and endoplasmic reticulum imaging. NEW J CHEM 2017. [DOI: 10.1039/c6nj02890j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Two new dinuclear iridium (Ir) complexes bridged by a conjugated aromatic tppz ligand, (bhq)2Ir(tppz)Ir(bhq)2(1) and (ppy)2Ir(tppz)Ir(ppy)2(2) (bhq = benzo(h)quinolone, ppy = phenyl-pyridine, tppz = tetrapyrido[3,2-a:2′,3′-c:3′′,2′′-h:2′′′,3′′′-j]phenazine), were prepared.
Collapse
Affiliation(s)
| | - Gyoungmi Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Korea
| | - Ha Yoon Jang
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Korea
| | - Juyoung Yoon
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Korea
| | - Jinheung Kim
- Department of Chemistry and Nano Science
- Ewha Womans University
- Seoul 120-750
- Korea
| |
Collapse
|
131
|
Krafčíková P, Demkovičová E, Víglaský V. Ebola virus derived G-quadruplexes: Thiazole orange interaction. Biochim Biophys Acta Gen Subj 2016; 1861:1321-1328. [PMID: 27979676 DOI: 10.1016/j.bbagen.2016.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 12/05/2016] [Accepted: 12/11/2016] [Indexed: 10/20/2022]
Abstract
The Ebola and Marburg viruses are some of the deadliest viruses in the world. In this study a series of G-rich DNA sequences derived from these types of viruses which possess the potential to form G-quadruplex structures are analyzed. A set of DNA oligonucleotides derived from original viral isolates was used as a representative modeling sequence with which to demonstrate the influence of thiazole orange on circular dichroism (CD) spectral profiles. The results show the unique profile of the induced CD (ICD) signal in the visible region caused by interactions between the ligand and G-quadruplexes. This ligand was found to stabilize the G-quadruplex structure and can also induce topological changes and facilitate G-quadruplex multimerization. Thus, the ICD signatures can be used to determine whether specific unknown sequences can form G-quadruplex motifs. The viral sequences were analyzed using standard spectral and electrophoretic methods. In addition, the ability to target G-quadruplexes located in filoviruses offers researchers attractive therapeutic targets which would be of particular use in the development of novel antiviral therapies. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Petra Krafčíková
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia
| | - Erika Demkovičová
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia
| | - Viktor Víglaský
- Department of Biochemistry, Institute of Chemistry, Faculty of Sciences, P. J. Safarik University, 04001, Kosice, Slovakia.
| |
Collapse
|
132
|
Padmapriya K, Barthwal R. Binding of the alkaloid coralyne to parallel G-quadruplex DNA [d(TTGGGGT)]4 studied by multi-spectroscopic techniques. Biophys Chem 2016; 219:49-58. [DOI: 10.1016/j.bpc.2016.09.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 08/17/2016] [Accepted: 09/17/2016] [Indexed: 11/16/2022]
|
133
|
Karg B, Haase L, Funke A, Dickerhoff J, Weisz K. Observation of a Dynamic G-Tetrad Flip in Intramolecular G-Quadruplexes. Biochemistry 2016; 55:6949-6955. [PMID: 27951645 DOI: 10.1021/acs.biochem.6b00925] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A MYC sequence forming an intramolecular G-quadruplex with a parallel topology was modified by the incorporation of 8-bromoguanosine (BrG) analogues in one of its outer G-tetrads. The propensity of the BrG analogues to adopt a syn glycosidic torsion angle results in an exceptional monomolecular quadruplex conformation featuring a complete flip of one tetrad while keeping a parallel orientation of all G-tracts as shown by circular dichroism and nuclear magnetic resonance spectroscopic studies. When substituting three of the four G-tetrad residues with BrG analogues, two coexisting quadruplex conformational isomers with an all-syn and all-anti outer G-quartet are approximately equally populated in solution. A dynamic interconversion of the two quadruplexes with an exchange rate (kex) of 0.2 s-1 is demonstrated through the observation of exchange crosspeaks in rotating frame Overhauser effect spectroscopy and nuclear Overhauser effect spectroscopy experiments at 50 °C. The kinetic properties suggest disruption of the corresponding outer G-tetrad but not of the whole quadruplex core during the tetrad flip. Conformational syn-anti isomers with homopolar and heteropolar stacking interactions are nearly isoenergetic with a transition enthalpy of 18.2 kJ/mol in favor of the all-syn isomer.
Collapse
Affiliation(s)
- Beatrice Karg
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Linn Haase
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Andrea Funke
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Jonathan Dickerhoff
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| | - Klaus Weisz
- Institute of Biochemistry, Ernst-Moritz-Arndt University Greifswald , Felix-Hausdorff-Strasse 4, D-17487 Greifswald, Germany
| |
Collapse
|
134
|
Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
| |
Collapse
|
135
|
Amato J, Pagano A, Cosconati S, Amendola G, Fotticchia I, Iaccarino N, Marinello J, De Magis A, Capranico G, Novellino E, Pagano B, Randazzo A. Discovery of the first dual G-triplex/G-quadruplex stabilizing compound: a new opportunity in the targeting of G-rich DNA structures? Biochim Biophys Acta Gen Subj 2016; 1861:1271-1280. [PMID: 27836755 DOI: 10.1016/j.bbagen.2016.11.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 11/03/2016] [Accepted: 11/05/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND Guanine-rich DNA motifs can form non-canonical structures known as G-quadruplexes, whose role in tumorigenic processes makes them attractive drug-target candidates for cancer therapy. Recent studies revealed that the folding and unfolding pathways of G-quadruplexes proceed through a quite stable intermediate named G-triplex. METHODS Virtual screening was employed to identify a small set of putative G-triplex ligands. The G-triplex stabilizing properties of these compounds were analyzed by CD melting assay. DSC, non-denaturing gel electrophoresis, NMR and molecular modeling studies were performed to investigate the interaction between the selected compound 1 and G-rich DNA structures. Cytotoxic activity of 1 was evaluated by MTT cell proliferation assay. RESULTS The experiments led to the identification of a promising hit that was shown to bind preferentially to G-triplex and parallel-stranded G-quadruplexes over duplex and antiparallel G-quadruplexes. Molecular modeling results suggested a partial end-stacking of 1 to the external G-triad/G-tetrads as a binding mode. Biological assays showed that 1 is endowed with cytotoxic effect on human osteosarcoma cells. CONCLUSIONS A tandem application of virtual screening along with the experimental investigation was employed to discover a G-triplex-targeting ligand. Experiments revealed that the selected compound actually acts as a dual G-triplex/G-quadruplex stabilizer, thus stimulating further studies aimed at its optimization. GENERAL SIGNIFICANCE The discovery of molecules able to bind and stabilize G-triplex structures is highly appealing, but their transient state makes challenging their recognition. These findings suggest that the identification of ligands with dual G-triplex/G-quadruplex stabilizing properties may represent a new route for the design of anticancer agents targeting the G-rich DNA structures. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Alessia Pagano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Sandro Cosconati
- DiSTABiF, Second University of Naples, via Vivaldi 43, 81100 Caserta, Italy
| | - Giorgio Amendola
- DiSTABiF, Second University of Naples, via Vivaldi 43, 81100 Caserta, Italy
| | - Iolanda Fotticchia
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Alessio De Magis
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy.
| |
Collapse
|
136
|
Padula D, Jurinovich S, Di Bari L, Mennucci B. Simulation of Electronic Circular Dichroism of Nucleic Acids: From the Structure to the Spectrum. Chemistry 2016; 22:17011-17019. [PMID: 27699878 DOI: 10.1002/chem.201602777] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Indexed: 12/18/2022]
Abstract
We present a quantum mechanical (QM) simulation of the electronic circular dichroism (ECD) of nucleic acids (NAs). The simulation combines classical molecular dynamics, to obtain the structure and its temperature-dependent fluctuations, with a QM excitonic model to determine the ECD. The excitonic model takes into account environmental effects through a polarizable embedding and uses a refined approach to calculate the electronic couplings in terms of full transition densities. Three NAs with either similar conformations but different base sequences or similar base sequences but different conformations have been investigated and the results were compared with experimental observations; a good agreement was seen in all cases. A detailed analysis of the nature of the ECD bands in terms of their excitonic composition was also carried out. Finally, a comparison between the QM and the DeVoe models clearly revealed the importance of including fluctuations of the excitonic parameters and of accurately determining the electronic couplings. This study demonstrates the feasibility of the ab initio simulation of the ECD spectra of NAs, that is, without the need of experimental structural or electronic data.
Collapse
Affiliation(s)
- Daniele Padula
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124, Pisa, Italy
| |
Collapse
|
137
|
Esposito V, Russo A, Amato T, Varra M, Vellecco V, Bucci M, Russo G, Virgilio A, Galeone A. Backbone modified TBA analogues endowed with antiproliferative activity. Biochim Biophys Acta Gen Subj 2016; 1861:1213-1221. [PMID: 27663232 DOI: 10.1016/j.bbagen.2016.09.019] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/13/2016] [Accepted: 09/16/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The thrombin binding aptamer (TBA) is endowed with antiproliferative properties but its potential development is counteracted by the concomitant anticoagulant activity. METHODS Five oligonucleotides (ODNs) based on TBA sequence (GGTTGGTGTGGTTGG) and containing l-residues or both l-residues and inversion of polarity sites have been investigated by NMR and CD techniques for their ability to form G-quadruplex structures. Furthermore, their anticoagulant (PT assay) and antiproliferative properties (MTT assay), and their resistance in fetal bovine serum have been tested. RESULTS CD and NMR data suggest that the investigated ODNs are able to form right- and left-handed G-quadruplex structures. All ODNs do not retain the anticoagulant activity characteristic of TBA but are endowed with a significant antiproliferative activity against two cancerous cell lines. Their resistance in biological environment after six days is variable, depending on the ODN. CONCLUSIONS A comparison between results and literature data suggests that the antiproliferative activity of the TBA analogues investigated could depends on two factors: a) biological pathways and targets different from those already identified or proposed for other antiproliferative G-quadruplex aptamers, and b) the contribution of the guanine-based degradation products. GENERAL SIGNIFICANCE Modified TBA analogues containing l-residues and inversion of polarity sites lose the anticoagulant activity but gain antiproliferative properties against two cancer cell lines. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
Collapse
Affiliation(s)
- Veronica Esposito
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Annapina Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Teresa Amato
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Michela Varra
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Valentina Vellecco
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Mariarosaria Bucci
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Giulia Russo
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy
| | - Antonella Virgilio
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| | - Aldo Galeone
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, I-80131 Naples, Italy.
| |
Collapse
|
138
|
Loco D, Jurinovich S, Di Bari L, Mennucci B. A fast but accurate excitonic simulation of the electronic circular dichroism of nucleic acids: how can it be achieved? Phys Chem Chem Phys 2016; 18:866-77. [PMID: 26646952 DOI: 10.1039/c5cp06341h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present and discuss a simple and fast computational approach to the calculation of electronic circular dichroism spectra of nucleic acids. It is based on a exciton model in which the couplings are obtained in terms of the full transition-charge distributions, as resulting from TDDFT methods applied on the individual nucleobases. We validated the method on two systems, a DNA G-quadruplex and a RNA β-hairpin whose solution structures have been accurately determined by means of NMR. We have shown that the different characteristics of composition and structure of the two systems can lead to quite important differences in the dependence of the accuracy of the simulation on the excitonic parameters. The accurate reproduction of the CD spectra together with their interpretation in terms of the excitonic composition suggest that this method may lend itself as a general computational tool to both predict the spectra of hypothetic structures and define clear relationships between structural and ECD properties.
Collapse
Affiliation(s)
- Daniele Loco
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Sandro Jurinovich
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Lorenzo Di Bari
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica Industriale, University of Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy.
| |
Collapse
|
139
|
Lin S, Long H, Zhou J, Yuan G. Study of G-quadruplexes in the STAT3 gene using electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30 Suppl 1:173-178. [PMID: 27539434 DOI: 10.1002/rcm.7640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
RATIONALE As a key signal transducer and transcription activator, STAT3 plays a very important role in many cell processes. We found that there were many G-rich sequences existing in the STAT3 gene including its promoter, intron, exon and 3'-flanking regions. These G-rich tracts can form G-quadruplexes under near physiological conditions. In this research, we systemically studied the G-quadruplexes in the STAT3 gene at a whole gene scale for the first time. METHODS In this research, the formation of G-quadruplexes in the STAT3 gene was probed by electrospray ionization mass spectrometry (ESI-MS) and circular dichroism (CD). Their structures were constructed and refined by a molecular modeling method. We also used ESI-MS to study the recognition of the G-quadruplexes in the promoter of the STAT3 gene by flexible molecules which do not have a planar core like the other common quadruplex ligands. RESULTS The results based on ESI-MS suggested that the G-quadruplexes in the promoter of the STAT3 gene formed and were further recognized by some small molecules. CONCLUSION Our research proved that the G-rich sequences in the STAT3 gene could form G-quadruplexes under near physiological conditions. This provides a promising target to study the regulation of cell signal transduction in vivo and drug design that aims to target STAT3 G-quadruplexes. Copyright © 2016 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Sen Lin
- 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, China
- Beijing National Day School, Beijing, 100871, China
| | - Haitao Long
- 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, China
| | - Jiang Zhou
- 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, 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, China
| |
Collapse
|
140
|
Fu B, Huang J, Chen Y, Wang Y, Xue T, Xu G, Wang S, Zhou X. Right-handed and left-handed G-quadruplexes have the same DNA sequence: distinct conformations induced by an organic small molecule and potassium. Chem Commun (Camb) 2016; 52:10052-5. [PMID: 27452654 DOI: 10.1039/c6cc04866h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Herein, we report two distinct G-quadruplex conformations of the same G-rich oligonucleotide, regulated by a small molecule. This is the first report in which both right- and left-handed G-quadruplex conformations have been obtained from the same sequence. We discriminated these two distinct conformations and investigated their kinetics and thermodynamics.
Collapse
Affiliation(s)
- Boshi Fu
- College of Chemistry and Molecular Sciences, Institute of Advanced Studies, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan, Hubei 430072, P. R. China.
| | | | | | | | | | | | | | | |
Collapse
|
141
|
Amato J, Morigi R, Pagano B, Pagano A, Ohnmacht S, De Magis A, Tiang YP, Capranico G, Locatelli A, Graziadio A, Leoni A, Rambaldi M, Novellino E, Neidle S, Randazzo A. Toward the Development of Specific G-Quadruplex Binders: Synthesis, Biophysical, and Biological Studies of New Hydrazone Derivatives. J Med Chem 2016; 59:5706-20. [PMID: 27223049 DOI: 10.1021/acs.jmedchem.6b00129] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
G-Quadruplex-binding compounds are currently perceived as possible anticancer therapeutics. Here, starting from a promising lead, a small series of novel hydrazone-based compounds were synthesized and evaluated as G-quadruplex binders. The in vitro G-quadruplex-binding properties of the synthesized compounds were investigated employing both human telomeric and oncogene promoter G-quadruplexes with different folding topologies as targets. The present investigation led to the identification of potent G-quadruplex stabilizers with high selectivity over duplex DNA and preference for one G-quadruplex topology over others. Among them, selected derivatives have been shown to trap G-quadruplex structures in the nucleus of cancer cells. Interestingly, this behavior correlates with efficient cytotoxic activity in human osteosarcoma and colon carcinoma cells.
Collapse
Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Alessia Pagano
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Stephan Ohnmacht
- UCL School of Pharmacy, University College London , London WC1N 1AX, U.K
| | - Alessio De Magis
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Yee-Peng Tiang
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alessandra Graziadio
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Mirella Rambaldi
- Department of Pharmacy and Biotechnology, University of Bologna , 40126 Bologna, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| | - Stephen Neidle
- UCL School of Pharmacy, University College London , London WC1N 1AX, U.K
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples "Federico II" , via D. Montesano 49, 80131 Napoli, Italy
| |
Collapse
|
142
|
Yang J, Zheng L, Wang Y, Li W, Zhang J, Gu J, Fu Y. Guanine-rich DNA-based peroxidase mimetics for colorimetric assays of alkaline phosphatase. Biosens Bioelectron 2016; 77:549-56. [DOI: 10.1016/j.bios.2015.10.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/23/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022]
|
143
|
Li H, Hai J, Zhou J, Yuan G. Exploration of binding affinity and selectivity of brucine with G-quadruplex in the c-myb proto-oncogene by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:407-414. [PMID: 26754134 DOI: 10.1002/rcm.7454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/07/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The c-myb gene is a potential therapeutic target for human tumors and leukemias. Active ingredients from natural products may be used as drugs in chemotherapy for human cancers. Here, electrospray ionization mass spectrometry (ESI-MS) was used to probe the formation and recognition of the G-quadruplex structure from the G-rich sequence that is found in the c-myb gene promoter, 5'-GGGCTGGGCTGGGCGGGG-3'. The aim of our study is to evaluate a potential binder for the c-myb gene from natural products, and thereby to modulate c-myb gene expression. METHODS ESI-MS, as an effective method, was utilized not only to characterize the formation of the G-quadruplex in the c-myb oncogene, but also as a tool to probe the binding characteristics of alkaloid molecules with the target G-quadruplex DNA. RESULTS ESI-MS results with the support of circular dichroism (CD) spectra demonstrated the formation of an intramolecular parallel-stranded G-quadruplex in the c-myb oncogene promoter. A screening of six alkaloid molecules showed that brucine (P1) had a strong binding affinity to the c-myb G-quadruplex DNA. It is notable that P1 can bind selectively to the c-myb G-quadruplex with respect to duplex DNAs, as well as to G-quadruplexes in other types of gene sequences. According to ESI-MS results, in which the stability was tested by capillary heating and collision-induced dissociation, the binding of P1 could thermally stabilize the c-myb G-quadruplex DNA. CONCLUSIONS In this work, brucine (P1), an alkaloid molecule, has been found to bind to the intramolecular parallel G-quadruplex in the c-myb oncogene promoter with high affinity and selectivity, and could thermally stabilize the c-myb G-quadruplex DNA, indicating that the binding of P1 has the potential to modulate c-myb gene expression. Copyright © 2015 John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jinhui Hai
- 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, China
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jiang Zhou
- 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, 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, China
| |
Collapse
|
144
|
Padula D, Santoro F, Pescitelli G. A simple dimeric model accounts for the vibronic ECD spectra of chiral polythiophenes in their aggregated states. RSC Adv 2016. [DOI: 10.1039/c6ra05500a] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aggregates of chiral polythiophenes (PTs) show exciton-coupled electronic circular dichroism (ECD) spectra with a unique vibronic structure, which can be reproduced by quantum dynamical simulations on the coupled states of small dimeric models.
Collapse
Affiliation(s)
- Daniele Padula
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche – CNR
- Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR)
- UOS di Pisa
- I-56124 Pisa
- Italy
| | - Gennaro Pescitelli
- Università di Pisa
- Dipartimento di Chimica e Chimica Industriale Via G. Moruzzi 13
- I-56124 Pisa
- Italy
| |
Collapse
|
145
|
Abstract
A G4-quartet based hydrogel formed by self-assembly of borate esters of 5′-deoxy-5′-iodoguanosine (5′-IG 2) undergoes in situ cyclization to give 5′-deoxy-N3,5′-cycloguanosine (5′-cG 3). Formation of 5′-cG 3 causes self-destruction of the gel. This intramolecular cyclization can be used to release nucleoside analogs that have been pre-incorporated into the gel network.
Collapse
Affiliation(s)
- Taylor N. Plank
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| | - Jeffery T. Davis
- Department of Chemistry & Biochemistry
- University of Maryland
- College Park
- USA
| |
Collapse
|
146
|
Peters GM, Skala LP, Davis JT. A Molecular Chaperone for G4-Quartet Hydrogels. J Am Chem Soc 2015; 138:134-9. [DOI: 10.1021/jacs.5b08769] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Gretchen Marie Peters
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Luke P. Skala
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Jeffery T. Davis
- Department of Chemistry and
Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
147
|
Luo Y, Xu J, Li Y, Gao H, Guo J, Shen F, Sun C. A novel colorimetric aptasensor using cysteamine-stabilized gold nanoparticles as probe for rapid and specific detection of tetracycline in raw milk. Food Control 2015. [DOI: 10.1016/j.foodcont.2015.01.005] [Citation(s) in RCA: 129] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
148
|
Bhowmik D, Fiorillo G, Lombardi P, Suresh Kumar G. Recognition of human telomeric G-quadruplex DNA by berberine analogs: effect of substitution at the 9 and 13 positions of the isoquinoline moiety. J Mol Recognit 2015; 28:722-30. [DOI: 10.1002/jmr.2486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/11/2015] [Accepted: 05/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gaetano Fiorillo
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - Paolo Lombardi
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - G. Suresh Kumar
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| |
Collapse
|
149
|
Li Y, Cheng M, Hao J, Wang C, Jia G, Li C. Terpyridine-Cu(ii) targeting human telomeric DNA to produce highly stereospecific G-quadruplex DNA metalloenzyme. Chem Sci 2015; 6:5578-5585. [PMID: 29861895 PMCID: PMC5949855 DOI: 10.1039/c5sc01381j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 06/23/2015] [Indexed: 11/21/2022] Open
Abstract
The cofactors commonly involved in natural enzymes have provided the inspiration for numerous advances in the creation of artificial metalloenzymes. Nevertheless, to design an appropriate cofactor for a given biomolecular scaffold or vice versa remains a challenge in developing efficient catalysts in biochemistry. Herein, we extend the idea of G-quadruplex-targeting anticancer drug design to construct a G-quadruplex DNA metalloenzyme. We found that a series of terpyridine-Cu(ii) complexes (CuLn) can serve as excellent cofactors to dock with human telemetric G-quadruplex DNA. The resulting G-quadruplex DNA metalloenzyme utilising CuL1 catalyzes an enantioselective Diels-Alder reaction with enantioselectivity of >99% enantiomeric excess and about 73-fold rate acceleration compared to CuL1 alone. The terpyridine-Cu(ii) complex cofactors demonstrate dual functions, both as an active site to perform catalysis and as a structural regulator to promote the folding of human telemetric G-quadruplex DNA towards excellent catalysts.
Collapse
Affiliation(s)
- Yinghao Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Mingpan Cheng
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Jingya Hao
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ; .,University of Chinese Academy of Sciences , No. 19A Yuquan Road , Beijing , 100049 , China
| | - Changhao Wang
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Guoqing Jia
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| | - Can Li
- State Key Laboratory of Catalysis , Dalian Institute of Chemical Physics , Chinese Academy of Sciences , Dalian 116023 , China . ;
| |
Collapse
|
150
|
Miller MC, Ohrenberg CJ, Kuttan A, Trent JO. Separation of Quadruplex Polymorphism in DNA Sequences by Reversed-Phase Chromatography. CURRENT PROTOCOLS IN NUCLEIC ACID CHEMISTRY 2015; 61:17.7.1-17.7.18. [PMID: 26344226 PMCID: PMC4561857 DOI: 10.1002/0471142700.nc1707s61] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
This unit describes a method for the separation of a mixture of quadruplex conformations formed from the same parent sequence via reversed-phase chromatography (RPC). Polymorphism is inherent to quadruplex formation and even relatively simple quadruplex-forming sequences can fold into a cornucopia of possible conformations and topologies. Isolation of a specific conformation for study can be problematic. This is especially true for conformations of the human telomere sequence d(GGG(TTAGGG)3). High performance liquid chromatography (HPLC), especially reversed-phase chromatography, has been a mainstay of nucleic acid research and purification for many decades. We have successfully applied this method to the problem of separating individual quadruplex species in the ensemble from the same parent sequence.
Collapse
Affiliation(s)
- M. Clarke Miller
- Department of Chemistry and Biochemistry, University of North Georgia, 3820 Mundy Mill Road, Oakwood, Georgia 30566
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
| | - Carl J. Ohrenberg
- Department of Chemistry and Biochemistry, University of North Georgia, 3820 Mundy Mill Road, Oakwood, Georgia 30566
| | - Ashani Kuttan
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
| | - John O. Trent
- James Graham Brown Cancer Center, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
- Department of Medicine, University of Louisville, Clinical Translational Research Building, University of Louisville, 505 South Hancock Street, Louisville, KY 40202
| |
Collapse
|