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Wickhorst PJ, Ihmels H. Selective, pH-Dependent Colorimetric and Fluorimetric Detection of Quadruplex DNA with 4-Dimethylamino(phenyl)-Substituted Berberine Derivatives. Chemistry 2021; 27:8580-8589. [PMID: 33855748 PMCID: PMC8252107 DOI: 10.1002/chem.202100297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Indexed: 12/20/2022]
Abstract
The 9- and 12-dimethylaminophenyl-substituted berberine derivatives 3 a and 3 b were readily synthesized by Suzuki-Miyaura reactions and shown to be useful fluorescent probes for the optical detection of quadruplex DNA (G4-DNA). Their association with the nucleic acids was investigated by spectrometric titrations, CD and LD spectroscopy, and with DNA-melting analysis. Both ligands bind to duplex DNA by intercalation and to G4-DNA by terminal π stacking. At neutral conditions, they bind with higher affinity (Kb =105 -106 M-1 ) to representative quadruplex forming oligonucleotides 22AG, c-myc, c-kit, and a2, than to duplex calf thymus (ct) DNA (Kb =5-7×104 M-1 ). At pH 5, however, the affinity of 3 a towards G4-DNA 22AG is higher (Kb =1.2×106 M-1 ), whereas the binding constant towards ct DNA is lower (Kb =3.9×103 M-1 ) than under neutral conditions. Notably, the association of the ligand with DNA results in characteristic changes of the absorption and emission properties under specific conditions, which may be used for optical DNA detection. Other than the parent berberine, the ligands do not show a noticeable increase of their very low intrinsic emission intensity upon association with DNA at neutral conditions. In contrast, a fluorescence light-up effect was observed upon association to duplex (Φfl =0.01) and quadruplex DNA (Φfl =0.04) at pH 5. This fluorimetric response to G4-DNA association in combination with the distinct, red-shifted absorption under these conditions provides a simple and conclusive optical detection of G4-DNA at lower pH.
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Affiliation(s)
- Peter Jonas Wickhorst
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
| | - Heiko Ihmels
- Department of Chemistry – BiologyUniversity of Siegen, andCenter of Micro- and Nanochemistry and Engineering (Cμ)Adolf-Reichwein-Str. 257068SiegenGermany
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52
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Krafčík D, Ištvánková E, Džatko Š, Víšková P, Foldynová-Trantírková S, Trantírek L. Towards Profiling of the G-Quadruplex Targeting Drugs in the Living Human Cells Using NMR Spectroscopy. Int J Mol Sci 2021; 22:6042. [PMID: 34205000 PMCID: PMC8199861 DOI: 10.3390/ijms22116042] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 05/26/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
Recently, the 1H-detected in-cell NMR spectroscopy has emerged as a unique tool allowing the characterization of interactions between nucleic acid-based targets and drug-like molecules in living human cells. Here, we assess the application potential of 1H and 19F-detected in-cell NMR spectroscopy to profile drugs/ligands targeting DNA G-quadruplexes, arguably the most studied class of anti-cancer drugs targeting nucleic acids. We show that the extension of the original in-cell NMR approach is not straightforward. The severe signal broadening and overlap of 1H in-cell NMR spectra of polymorphic G-quadruplexes and their complexes complicate their quantitative interpretation. Nevertheless, the 1H in-cell NMR can be used to identify drugs that, despite strong interaction in vitro, lose their ability to bind G-quadruplexes in the native environment. The in-cell NMR approach is adjusted to a recently developed 3,5-bis(trifluoromethyl)phenyl probe to monitor the intracellular interaction with ligands using 19F-detected in-cell NMR. The probe allows dissecting polymorphic mixture in terms of number and relative populations of individual G-quadruplex species, including ligand-bound and unbound forms in vitro and in cellulo. Despite the probe's discussed limitations, the 19F-detected in-cell NMR appears to be a promising strategy to profile G-quadruplex-ligand interactions in the complex environment of living cells.
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Affiliation(s)
- Daniel Krafčík
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Eva Ištvánková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Šimon Džatko
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Pavlína Víšková
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
- National Centre for Biomolecular Research, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | | | - Lukáš Trantírek
- Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic; (D.K.); (E.I.); (Š.D.); (P.V.)
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53
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Preferential interaction with c-MYC quadruplex DNA mediates the cytotoxic activity of a nitro-flavone derivative in A375 cells. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY 2021. [DOI: 10.1016/j.jpap.2021.100033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
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54
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Selective discrimination and classification of G-quadruplex structures with a host-guest sensing array. Nat Chem 2021; 13:488-495. [PMID: 33795843 DOI: 10.1038/s41557-021-00647-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 01/27/2021] [Indexed: 02/01/2023]
Abstract
The secondary structures of nucleic acids have an important influence on their cellular functions but can be difficult to identify and classify quickly. Here, we show that an arrayed suite of synthetic hosts and dyes is capable of fluorescence detection of oligonucleotide secondary structures. Multivariate analysis of different fluorescence enhancements-generated using cationic dyes that show affinity for both DNA G-quadruplexes and the synthetic hosts-enables discrimination between G-quadruplex structures of identical length and highly similar topological types. Different G-quadruplexes that display the same folding topology can also be easily differentiated by the number of G-quartets and sequence differences at the 3' or 5' ends. The array is capable of both differentiation and classification of the G-quadruplex structures at the same time. This simple non-invasive sensing method does not require the discovery and synthesis of specific G-quadruplex binding ligands, but employs a simple multicomponent approach to ensure wide applicability.
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55
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Chen K, He Z, Xiong W, Wang CJ, Zhou X. Enantioselective Diels–Alder reactions with left-handed G-quadruplex DNA-based catalysts. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2020.12.047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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56
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Sun R, Guo X, Yang D, Tang Y, Lu J, Sun H. c-Myc G-quadruplex is sensitively and specifically recognized by a fluorescent probe. Talanta 2021; 226:122125. [PMID: 33676679 DOI: 10.1016/j.talanta.2021.122125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/12/2021] [Accepted: 01/15/2021] [Indexed: 10/22/2022]
Abstract
The G-quadruplex structure formed by the c-myc gene sequence has attracted much attention due to its important physiological function in biology and wide application in nanotechnology. So far, probes capable of recognition of c-myc G-quadruplex with both high specificity and sensitivity are still scarce. This work presented a cyanine dye fluorescent probe named Cy-1, which has almost no fluorescence in aqueous solution, but showing more than 1000-fold fluorescence enhancement for recognizing c-myc G-quadruplex. Cy-1 also has good specificity and can selectively recognize c-myc G-quadruplex from other a variety of G-quadruplex and non-G-quadruplex structures. These properties make Cy-1 a promising probe for c-myc G-quadruplex recognition in nanotechnology or biology.
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Affiliation(s)
- Ranran Sun
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, PR China; Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China
| | - Xiaomeng Guo
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Dawei Yang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jie Lu
- School of Chemistry and Chemical Engineering, Shanghai University of Engineering Science, Shanghai, 201620, PR China.
| | - Hongxia Sun
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China.
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57
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Lousen B, Pedersen SK, Răsădean DM, Pantoş GD, Pittelkow M. Triggering G-Quadruplex Conformation Switching with [7]Helicenes. Chemistry 2021; 27:6064-6069. [PMID: 33326174 DOI: 10.1002/chem.202004990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/14/2022]
Abstract
The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.
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Affiliation(s)
- Bodil Lousen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Dora M Răsădean
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - G Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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58
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POT1 stability and binding measured by fluorescence thermal shift assays. PLoS One 2021; 16:e0245675. [PMID: 33784306 PMCID: PMC8009405 DOI: 10.1371/journal.pone.0245675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 03/03/2021] [Indexed: 11/19/2022] Open
Abstract
The protein POT1 (Protection of Telomeres 1) is an integral part of the shelterin complex that protects the ends of human chromosomes from degradation or end fusions. It is the only component of shelterin that binds single-stranded DNA. We describe here the application of two separate fluorescent thermal shift assays (FTSA) that provide quantitative biophysical characterization of POT1 stability and its interactions. The first assay uses Sypro Orange™ and monitors the thermal stability of POT1 and its binding under a variety of conditions. This assay is useful for the quality control of POT1 preparations, for biophysical characterization of its DNA binding and, potentially, as an efficient screening tool for binding of small molecule drug candidates. The second assay uses a FRET-labeled human telomeric G-quadruplex structure that reveals the effects of POT1 binding on thermal stability from the DNA frame of reference. These complementary assays provide efficient biophysical approaches for the quantitative characterization of multiple aspects of POT1 structure and function. The results from these assays provide thermodynamics details of POT1 folding, the sequence selectivity of its DNA binding and the thermodynamic profile for its binding to its preferred DNA binding sequence. Most significantly, results from these assays elucidate two mechanisms for the inhibition of POT1 -DNA interactions. The first is by competitive inhibition at the POT1 DNA binding site. The second is indirect and is by stabilization of G-quadruplex formation within the normal POT1 single-stranded DNA sequence to prevent POT1 binding.
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59
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Lejault P, Mitteaux J, Sperti FR, Monchaud D. How to untie G-quadruplex knots and why? Cell Chem Biol 2021; 28:436-455. [PMID: 33596431 DOI: 10.1016/j.chembiol.2021.01.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/08/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022]
Abstract
For over two decades, the prime objective of the chemical biology community studying G-quadruplexes (G4s) has been to use chemicals to interact with and stabilize G4s in cells to obtain mechanistic interpretations. This strategy has been undoubtedly successful, as demonstrated by recent advances. However, these insights have also led to a fundamental rethinking of G4-targeting strategies: due to the prevalence of G4s in the human genome, transcriptome, and ncRNAome (collectively referred to as the G4ome), and their involvement in human diseases, should we continue developing G4-stabilizing ligands or should we invest in designing molecular tools to unfold G4s? Here, we first focus on how, when, and where G4s fold in cells; then, we describe the enzymatic systems that have evolved to counteract G4 folding and how they have been used as tools to manipulate G4s in cells; finally, we present strategies currently being implemented to devise new molecular G4 unwinding agents.
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Affiliation(s)
- Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Jérémie Mitteaux
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon, France.
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60
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Zell J, Rota Sperti F, Britton S, Monchaud D. DNA folds threaten genetic stability and can be leveraged for chemotherapy. RSC Chem Biol 2021; 2:47-76. [PMID: 35340894 PMCID: PMC8885165 DOI: 10.1039/d0cb00151a] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/20/2020] [Indexed: 12/22/2022] Open
Abstract
Damaging DNA is a current and efficient strategy to fight against cancer cell proliferation. Numerous mechanisms exist to counteract DNA damage, collectively referred to as the DNA damage response (DDR) and which are commonly dysregulated in cancer cells. Precise knowledge of these mechanisms is necessary to optimise chemotherapeutic DNA targeting. New research on DDR has uncovered a series of promising therapeutic targets, proteins and nucleic acids, with application notably via an approach referred to as combination therapy or combinatorial synthetic lethality. In this review, we summarise the cornerstone discoveries which gave way to the DNA being considered as an anticancer target, and the manipulation of DDR pathways as a valuable anticancer strategy. We describe in detail the DDR signalling and repair pathways activated in response to DNA damage. We then summarise the current understanding of non-B DNA folds, such as G-quadruplexes and DNA junctions, when they are formed and why they can offer a more specific therapeutic target compared to that of canonical B-DNA. Finally, we merge these subjects to depict the new and highly promising chemotherapeutic strategy which combines enhanced-specificity DNA damaging and DDR targeting agents. This review thus highlights how chemical biology has given rise to significant scientific advances thanks to resolutely multidisciplinary research efforts combining molecular and cell biology, chemistry and biophysics. We aim to provide the non-specialist reader a gateway into this exciting field and the specialist reader with a new perspective on the latest results achieved and strategies devised.
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Affiliation(s)
- Joanna Zell
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Francesco Rota Sperti
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS Toulouse France
- Équipe Labellisée la Ligue Contre le Cancer 2018 Toulouse France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne, ICMUB CNRS UMR 6302, UBFC Dijon France
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61
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Andreeva DV, Tikhomirov AS, Shchekotikhin AE. Ligands of G-quadruplex nucleic acids. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4968] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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62
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Chaudhuri R, Bhattacharya S, Dash J, Bhattacharya S. Recent Update on Targeting c-MYC G-Quadruplexes by Small Molecules for Anticancer Therapeutics. J Med Chem 2020; 64:42-70. [PMID: 33355454 DOI: 10.1021/acs.jmedchem.0c01145] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Guanine-rich DNA sequences have the propensity to adopt four-stranded tetrahelical G-quadruplex (G4) structures that are overrepresented in gene promoters. The structural polymorphism and physicochemical properties of these non-Watson-Crick G4 structures make them important targets for drug development. The guanine-rich nuclease hypersensitivity element III1 present in the upstream of P1 promoter of c-MYC oncogene has the ability to form an intramolecular parallel G4 structure. The G4 structure that forms transiently in the c-MYC promoter functions as a transcriptional repressor element. The c-MYC oncogene is overexpressed in a wide variety of cancers and plays a key role in cancer progression. Till now, a large number of compounds that are capable of interacting and stabilizing thec-MYC G4 have been reported. In this review, we summarize various c-MYC G4 specific molecules and discuss their effects on c-MYC gene expression in vitro and in vivo.
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Affiliation(s)
- Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Semantee Bhattacharya
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Santanu Bhattacharya
- School of Applied & Interdisciplinary Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.,Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
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63
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Devereux SJ, Poynton FE, Baptista FR, Gunnlaugsson T, Cardin CJ, Sazanovich IV, Towrie M, Kelly JM, Quinn SJ. Caught in the Loop: Binding of the [Ru(phen) 2 (dppz)] 2+ Light-Switch Compound to Quadruplex DNA in Solution Informed by Time-Resolved Infrared Spectroscopy. Chemistry 2020; 26:17103-17109. [PMID: 32725823 DOI: 10.1002/chem.202002165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Indexed: 01/05/2023]
Abstract
Ultrafast time-resolved infrared (TRIR) is used to report on the binding site of the [Ru(phen)2 (dppz)]2+ "light-switch" complex with both bimolecular (Oxytricha nova telomere) and intramolecular (human telomere) guanine-quadruplex structures in both K+ and Na+ containing solutions. TRIR permits the simultaneous monitoring both of the "dark" and "bright" states of the complex and of the quadruplex nucleobase bases, the latter via a Stark effect induced by the excited state of the complex. These data are used to establish the contribution of guanine base stacking and loop interactions to the binding site of this biologically relevant DNA structure in solution. A particularly striking observation is the strong thymine signal observed for the Na+ form of the human telomere sequence, which is expected to be in the anti-parallel conformation.
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Affiliation(s)
| | - Fergus E Poynton
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | | | - Thorfinnur Gunnlaugsson
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland.,Trinity Biomedical Sciences Institute (TBSI), Trinity College Dublin, Dublin, 2, Ireland
| | - Christine J Cardin
- Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK
| | | | - Michael Towrie
- Rutherford Appleton Laboratory, STFC, Harwell Campus, OX11 0FA, UK
| | - John M Kelly
- School of Chemistry, Trinity College Dublin, Dublin, 2, Ireland
| | - Susan J Quinn
- School of Chemistry, University College Dublin, Dublin, 4, Ireland
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64
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Cai Q, Meng J, Ge Y, Gao Y, Zeng Y, Li H, Sun Y. Fishing antitumor ingredients by G-quadruplex affinity from herbal extract on a three-phase-laminar-flow microfluidic chip. Talanta 2020; 220:121368. [DOI: 10.1016/j.talanta.2020.121368] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/28/2020] [Accepted: 06/30/2020] [Indexed: 12/28/2022]
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65
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Zhang JT, Wang LX, Yang FM, Yang L, Liu Y, Tang YL. Selective recognition of DNA parallel G-quadruplexes by 3,8a-disubstituted indolizinones. Bioorg Med Chem 2020; 29:115848. [PMID: 33189508 DOI: 10.1016/j.bmc.2020.115848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 11/25/2022]
Abstract
Owing to its potential biological relevance, DNA G-quadruplex has been considered as a prospective anti-cancer target. Some known G-quadruplex-interactive N-containing compounds with low cytotoxicity have become prospective anticancer drugs. Here we reported a new type of N-containing alkaloids 3,8a-disubstituted indolizinones, and investigated their substituent effects at 3- and 8a-positions in targeting to DNA c-myc G-quadruplex. And then we used 3-naphtyl-8a-(pyridin-2-yl) substrate I8 as an example, and investigated its ability in targeting to DNA parallel G-quadruplexes in vitro.
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Affiliation(s)
- Jing-Tao Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; Key Laboratory for Environmentally Friendly Chemistry and Application, Department of Chemistry, Xiangtan University, Hunan 411105, PR China
| | - Li-Xia Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Feng-Min Yang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Luo Yang
- Key Laboratory for Environmentally Friendly Chemistry and Application, Department of Chemistry, Xiangtan University, Hunan 411105, PR China
| | - Yan Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China
| | - Ya-Lin Tang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Center for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, PR China; University of the Chinese Academy of Sciences, Beijing 100049, PR China.
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67
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Gillard M, Weynand J, Bonnet H, Loiseau F, Decottignies A, Dejeu J, Defrancq E, Elias B. Flexible Ru
II
Schiff Base Complexes: G‐Quadruplex DNA Binding and Photo‐Induced Cancer Cell Death. Chemistry 2020; 26:13849-13860. [DOI: 10.1002/chem.202001409] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 05/28/2020] [Indexed: 12/20/2022]
Affiliation(s)
- Martin Gillard
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Hugues Bonnet
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Frédérique Loiseau
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Eric Defrancq
- Département de Chimie Moléculaire UMR CNRS 5250 Université Grenoble Alpes (UGA) CS 40700-38058 Grenoble France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN) Molecular Chemistry, Materials and Catalysis (MOST) Université catholique de Louvain (UCLouvain) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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68
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Human MYC G-quadruplex: From discovery to a cancer therapeutic target. Biochim Biophys Acta Rev Cancer 2020; 1874:188410. [PMID: 32827579 DOI: 10.1016/j.bbcan.2020.188410] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/21/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Overexpression of the MYC oncogene is a molecular hallmark of both cancer initiation and progression. Targeting MYC is a logical and effective cancer therapeutic strategy. A special DNA secondary structure, the G-quadruplex (G4), is formed within the nuclease hypersensitivity element III1 (NHE III1) region, located upstream of the MYC gene's P1 promoter that drives the majority of its transcription. Targeting such G4 structures has been a focus of anticancer therapies in recent decades. Thus, a comprehensive review of the MYC G4 structure and its role as a potential therapeutic target is timely. In this review, we first outline the discovery of the MYC G4 structure and evidence of its formation in vitro and in cells. Then, we describe the functional role of G4 in regulating MYC gene expression. We also summarize three types of MYC G4-interacting proteins that can promote, stabilize and unwind G4 structures. Finally, we discuss G4-binding molecules and the anticancer activities of G4-stabilizing ligands, including small molecular compounds and peptides, and assess their potential as novel anticancer therapeutics.
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69
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Lee C, Choi YK, Lee S, Han SY. Hydrogen bonding influences collision-induced dissociation of Na + -bound guanine tetrads. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 56:e4582. [PMID: 33085179 DOI: 10.1002/jms.4582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/25/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Na+ -bound guanine (G)-tetrads possess square planar structures formed solely by noncovalent interactions including multiple hydrogen bonds. Unlike G-tetrads facilitated by other alkali metal ions, an intriguing behavior in collision-induced dissociation (CID) has been observed in Na+ -bound G-tetrads, which features a preferential, simultaneous loss of two G ligands in the low energy regime. To understand this unique behavior, we investigated the CID of Na+ -bound G-tetrads with mixed ligands of G and 9-methylguanine (9mG), [Na·Gm ·9mGn ]+ (m + n = 4), and [Li·9mG4 ]+ for comparison. In the CID experiments, the simultaneous losses of two ligands were by far more pronounced than the loss of a single ligand for all five Na+ -bound G-tetrads. However, it appeared that the CID of [Li·9mG4 ]+ prefers to lose single ligands sequentially. An analysis of the fragment abundances suggested that the generation of Na+ -bound dimeric fragments might have occurred with two adjacent ligands. This theoretical study predicted for [Li·9mG4 ]+ that the loss of a single ligand is more energetically favorable than the production of neutral hydrogen-bonded fragments by 35.5 kJ/mol (ΔG). This contradicts our previous calculations for [Na·9mG4 ]+ that a neutral loss of hydrogen-bonded dimers provides the lowest energy product state of Na+ -bound dimeric fragments, which is lower than that of Na+ -bound trimeric fragments by 15.6 kJ/mol. From the results, this comparative study suggests that the pronounced generation of Na+ -bound dimeric fragments in CID of the G-tetrads is likely promoted by the dissociation pathway associated with neutral loss of hydrogen-bonded dimers. It thus demonstrates that multiple hydrogen bonding participating in formation of Na+ -bound G-tetrads may also strongly influence the fate of dissociating complexes of G-tetrads.
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Affiliation(s)
- Chaewon Lee
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Yoon Kyung Choi
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Sanghun Lee
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
| | - Sang Yun Han
- Department of Chemistry, Gachon University, Seongnam-si, Republic of Korea
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70
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Di Fonzo S, Amato J, D'Aria F, Caterino M, D'Amico F, Gessini A, Brady JW, Cesàro A, Pagano B, Giancola C. Ligand binding to G-quadruplex DNA: new insights from ultraviolet resonance Raman spectroscopy. Phys Chem Chem Phys 2020; 22:8128-8140. [PMID: 32246758 DOI: 10.1039/d0cp01022g] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
G-Quadruplexes (G4s) are noncanonical nucleic acid structures involved in the regulation of several biological processes of many organisms. The rational design of G4-targeting molecules developed as potential anticancer and antiviral therapeutics is a complex problem intrinsically due to the structural polymorphism of these peculiar DNA structures. The aim of the present work is to show how Ultraviolet Resonance Raman (UVRR) spectroscopy can complement other techniques in providing valuable information about ligand/G4 interactions in solution. Here, the binding of BRACO-19 and Pyridostatin - two of the most potent ligands - to selected biologically relevant G4s was investigated by polarized UVRR scattering at 266 nm. The results give new insights into the binding mode of these ligands to G4s having different sequences and topologies by performing an accurate analysis of peaks assigned to specific groups and their changes upon binding. Indeed, the UVRR data not only show that BRACO-19 and Pyridostatin interact with different G4 sites, but also shed light on the ligand and G4 chemical groups really involved in the interaction. In addition, UVRR results complemented by circular dichroism data clearly indicate that the binding mode of a ligand can also depend on the conformation(s) of the target G4. Overall, these findings demonstrate the utility of using UVRR spectroscopy in the investigation of G4s and G4-ligand interactions in solution.
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Affiliation(s)
- Silvia Di Fonzo
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Jussara Amato
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Federica D'Aria
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Marco Caterino
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Francesco D'Amico
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy.
| | - John W Brady
- Department of Food Science, Cornell University, Ithaca, New York, NY 14853, USA
| | - Attilio Cesàro
- Elettra-Sincrotrone Trieste S. C. p. A., Science Park, Trieste, I-34149, Italy. and Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, I-34127, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
| | - Concetta Giancola
- Department of Pharmacy, University of Naples Federico II, Naples, I-80131, Italy.
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71
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Self‐Assembly of DNA and RNA Building Blocks Explored by Nitrogen‐14 NMR Crystallography: Structure and Dynamics. Chemphyschem 2020; 21:1044-1051. [DOI: 10.1002/cphc.201901214] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/18/2020] [Indexed: 12/20/2022]
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72
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Effects of Molecular Crowding on G-Quadruplex-hemin Mediated Peroxidase Activity. Chem Res Chin Univ 2020. [DOI: 10.1007/s40242-020-0018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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73
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Tang W, Niu K, Yu G, Jin Y, Zhang X, Peng Y, Chen S, Deng H, Li S, Wang J, Song Q, Feng Q. In vivo visualization of the i-motif DNA secondary structure in the Bombyx mori testis. Epigenetics Chromatin 2020; 13:12. [PMID: 32138783 PMCID: PMC7059380 DOI: 10.1186/s13072-020-00334-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 02/19/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND A large number of in vitro experiments have confirmed that DNA molecules can form i-motif advanced structure when multiple cytosines exist in the sequence. However, whether these structures are present in vivo environment still lacks sufficient experimental evidence. RESULTS In this paper, we report the in vivo visualization of i-motif structures in the nuclei and chromosomes of the testis of the invertebrate Bombyx mori using immunofluorescence staining with an antibody specifically recognizing the endogenous transcription factor BmILF, which binds i-motif structure with high specificity. The number of i-motif structures observed in the genome increased when the pH was changed from basic to acidic and decreased under treatment with an i-motif inhibitor, the porphyrin compound TMPyP4. The pH change affected the transcription of genes that contain i-motif sequences. Moreover, there were more i-motif structures observed in the testis cells in interphase than in any other cell cycle stage. CONCLUSIONS In this study, the i-motif structures in invertebrates were detected for the first time at the cell and organ levels. The formation of the structures depended on cell cycle and pH and affected gene expression.
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Affiliation(s)
- Wenhuan Tang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Kangkang Niu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Guoxing Yu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ying Jin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Xian Zhang
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yuling Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shuna Chen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Huimin Deng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Jian Wang
- Department of Entomology, University of Maryland, College Park, MD, 20742, USA
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. .,Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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74
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Perenon M, Bonnet H, Lavergne T, Dejeu J, Defrancq E. Surface plasmon resonance study of the interaction of N-methyl mesoporphyrin IX with G-quadruplex DNA. Phys Chem Chem Phys 2020; 22:4158-4164. [PMID: 32039427 DOI: 10.1039/c9cp06321h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Surface plasmon resonance (SPR) was used to investigate the interaction between N-methyl mesoporphyrin IX (NMM) and different G-quadruplex (G4) topologies. The study was associated with circular dichroism analysis (CD) to assess the topology of the G4s when they interacted with NMM. We demonstrate the high selectivity of NMM for the parallel G4 structure with a dissociation constant at least ten times lower than those of other G4 topologies. We also confirm the ability of NMM to shift the G4 conformation from both the hybrid and antiparallel topologies toward the parallel structure.
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Affiliation(s)
- M Perenon
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - H Bonnet
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - T Lavergne
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - J Dejeu
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
| | - E Defrancq
- Univ. Grenoble Alpes, CNRS, DCM UMR-5250, F-38000 Grenoble, France.
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75
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Molecular dynamics simulations of G-quadruplexes: The basic principles and their application to folding and ligand binding. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2020. [DOI: 10.1016/bs.armc.2020.04.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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76
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Singh A, Joshi S, Kukreti S. Cationic porphyrins as destabilizer of a G-quadruplex located at the promoter of human MYH7 β gene. J Biomol Struct Dyn 2019; 38:4801-4816. [PMID: 31809672 DOI: 10.1080/07391102.2019.1689850] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
G-quadruplex (GQ) architecture is adopted by guanine rich sequences, present throughout the eukaryotic genome including promoter locations and telomeric ends. The in vivo presence indicates their involvement and role in various biological processes. Various small ligands have been developed to interact and stabilize/destabilize G-quadruplex structures. Cationic porphyrins are among the most studied ligands, reported to bind and stabilize G-quadruplexes. Herein, we report the recognition and destabilization of a parallel G-quadruplex by porphyrins (TMPyP3 and TMPyP4). This G-quadruplex forming 23-nt G-rich sequence is in the promoter region of Human Myosin Heavy Chain β gene (MYH7β). Presence of various putative regulatory sequence elements (TATA Box, CCAAT, SP-1) located in the vicinity of this quadruplex motif, highlight its regulatory implications. Biophysical methods as Circular Dichroism Spectroscopy, UV-Absorption Spectroscopy, UV-Thermal Denaturation and Fluorescence Spectroscopy (steady as well as Time Resolved) have been used for studying the interaction and binding parameters. It is proposed that porphyrins have a destabilizing effect on the G-quadruplexes with parallel topology and a stronger binding specifically via intercalation mode is needed to cause destabilization. The study deals with better understanding and insights of DNA-Drug interactions in biological systems.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Anju Singh
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Savita Joshi
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
| | - Shrikant Kukreti
- Nucleic Acids Research Laboratory, Department of Chemistry, University of Delhi (North Campus), Delhi, India
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77
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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78
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Renard I, Grandmougin M, Roux A, Yang SY, Lejault P, Pirrotta M, Wong JMY, Monchaud D. Small-molecule affinity capture of DNA/RNA quadruplexes and their identification in vitro and in vivo through the G4RP protocol. Nucleic Acids Res 2019; 47:5502-5510. [PMID: 30949698 PMCID: PMC6582334 DOI: 10.1093/nar/gkz215] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/12/2019] [Accepted: 03/18/2019] [Indexed: 01/25/2023] Open
Abstract
Guanine-rich DNA and RNA sequences can fold into higher-order structures known as G-quadruplexes (or G4-DNA and G4-RNA, respectively). The prevalence of the G4 landscapes in the human genome, transcriptome and ncRNAome (non-coding RNA), collectively known as G4ome, is strongly suggestive of biological relevance at multiple levels (gene expression, replication). Small-molecules can be used to track G4s in living cells for the functional characterization of G4s in both normal and disease-associated changes in cell biology. Here, we describe biotinylated biomimetic ligands referred to as BioTASQ and their use as molecular tools that allow for isolating G4s through affinity pull-down protocols. We demonstrate the general applicability of the method by purifying biologically relevant G4s from nucleic acid mixtures in vitro and from human cells through the G4RP-RT-qPCR protocol. Overall, the results presented here represent a step towards the optimization of G4-RNAs identification, a key step in studying G4s in cell biology and human diseases.
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Affiliation(s)
- Isaline Renard
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
| | | | - Apolline Roux
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
| | - Sunny Y Yang
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada
| | - Pauline Lejault
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
| | - Marc Pirrotta
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
| | - Judy M Y Wong
- Faculty of Pharmaceutical Sciences, The University of British Columbia, Vancouver, Canada
| | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC Dijon, France
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79
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Benabou S, Mazzini S, Aviñó A, Eritja R, Gargallo R. A pH-dependent bolt involving cytosine bases located in the lateral loops of antiparallel G-quadruplex structures within the SMARCA4 gene promotor. Sci Rep 2019; 9:15807. [PMID: 31676783 PMCID: PMC6825181 DOI: 10.1038/s41598-019-52311-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 10/15/2019] [Indexed: 01/01/2023] Open
Abstract
Some lung and ovarian tumors are connected to the loss of expression of SMARCA4 gene. In its promoter region, a 44-nucleotides long guanine sequence prone to form G-quadruplex structures has been studied by means of spectroscopic techniques (circular dichroism, molecular absorption and nuclear magnetic resonance), size exclusion chromatography and multivariate analysis. The results have shown that the central 21-nucleotides long sequence comprising four guanine tracts of disparate length is able to fold into a pH-dependent ensemble of G-quadruplex structures. Based on acid-base titrations and melting experiments of wild and mutated sequences, the formation of a C·C+ base pair between cytosine bases present at the two lateral loops is shown to promote a reduction in conformational heterogeneity, as well as an increase in thermal stability. The formation of this base pair is characterized by a pKa value of 7.1 ± 0.2 at 20 °C and 150 mM KCl. This value, higher than those usually found in i-motif structures, is related to the additional stability provided by guanine tetrads in the G-quadruplex. To our knowledge, this is the first thermodynamic description of this base pair in loops of antiparallel G-quadruplex structures.
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Affiliation(s)
- Sanae Benabou
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain
| | - Stefania Mazzini
- Department of Food, Environmental and Nutritional Sciences (DEFENS), University of Milan, Milan, Italy
| | - Anna Aviñó
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Ramon Eritja
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Networking Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Raimundo Gargallo
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Barcelona, Spain.
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80
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Bazoobandi M, Bozorgmehr MR, Mahmoudi A, Morsali A. The Effect of Temperature on the Interaction of Phenanthroline-based Ligands with G-quadruplex: In Silico Viewpoint. Comb Chem High Throughput Screen 2019; 22:546-554. [PMID: 31642773 DOI: 10.2174/1386207322666191022142629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/02/2019] [Accepted: 08/09/2019] [Indexed: 11/22/2022]
Abstract
AIM AND OBJECTIVE The stability of the G-quadruplex structure can increase its activity in telomerase inhibiting cancer cells. In this study, a molecular dynamics simulation method was used to study the effect of three phenanthroline-based ligands on the structure of G-quadruplex at the temperatures of 20, 40, 60 and 80°C. MATERIALS AND METHODS RMSD values and frequency of calculated RMSD in the presence and absence of ligands show that ligands cause the relative stability of the G-quadruplex, particularly at low temperatures. The calculation of hydrogen bonds in Guanine-tetrads in three different quadruplex sheets shows that the effect of ligands on the sheets is not the same so that the bottom sheet of G-quadruplex is most affected by the ligands at high temperatures, and the Guaninetetrads in this sheet are far away. Conformation factor was calculated as a measure of ligands binding affinity for each of the G-quadruplex residues. RESULTS The results show that the studied ligands interact more with the G-quadruplex than loop areas, although with increasing temperature, the binding area also includes the G-quadruplex sheets. The contribution of each of the residues involved in the G-quadruplex binding area with ligands was also calculated. CONCLUSION The calculations performed are consistent with the previous experimental observations that can help to understand the molecular mechanism of the interaction of phenanthroline and its derivatives with quadruplex.
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Affiliation(s)
- Mohadeseh Bazoobandi
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
| | | | - Ali Mahmoudi
- Faculty of Chemistry, Islamic Azad University, North Tehran Branch, Hakimiyeh, Tehran, Iran
| | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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81
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Weynand J, Bonnet H, Loiseau F, Ravanat JL, Dejeu J, Defrancq E, Elias B. Targeting G-Rich DNA Structures with Photoreactive Bis-Cyclometallated Iridium(III) Complexes. Chemistry 2019; 25:12730-12739. [PMID: 31290208 DOI: 10.1002/chem.201902183] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 07/02/2019] [Indexed: 01/19/2023]
Abstract
The synthesis and characterisation of three novel iridium(III) bis-cyclometallated complexes is reported. Their photophysics have been fully characterised by classical methods and revealed charge-transfer (CT) and ligand-centred (LC) transitions. Their ability to selectively interact with G-quadruplex telomeric DNA over duplex DNA has been studied by circular dichroism (CD), bio-layer interferometry (BLI) and surface plasmon resonance (SPR) analyses. Interestingly, one of the complexes was able to promote photoinduced electron transfer (PET) with the guanine DNA base, which in turn led to oxidative damage (such as the formation of 8-oxoguanine) to the telomeric sequence. To the best of our knowledge, this is the first study of highly photo-oxidising bis-cyclometallated iridium(III) complexes with G-quadruplex telomeric DNA.
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Affiliation(s)
- Justin Weynand
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium.,CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Hughes Bonnet
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | | | - Jean-Luc Ravanat
- CEA, CNRS, INAC-SyMMES, Université Grenoble Alpes, 17 rue des martyrs, 38054, Grenoble CEDEX 9, France
| | - Jérôme Dejeu
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Eric Defrancq
- CNRS, DCM UMR5250, Université Grenoble Alpes, 38000, Grenoble, France
| | - Benjamin Elias
- Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST), Université catholique de Louvain (UCLouvain), Place Louis Pasteur 1, bte L4.01.02, 1348, Louvain-la-Neuve, Belgium
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82
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Krafcikova M, Dzatko S, Caron C, Granzhan A, Fiala R, Loja T, Teulade-Fichou MP, Fessl T, Hänsel-Hertsch R, Mergny JL, Foldynova-Trantirkova S, Trantirek L. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc 2019; 141:13281-13285. [PMID: 31394899 DOI: 10.1021/jacs.9b03031] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Studies on DNA-ligand interactions in the cellular environment are problematic due to the lack of suitable biophysical tools. To address this need, we developed an in-cell NMR-based approach for monitoring DNA-ligand interactions inside the nuclei of living human cells. Our method relies on the acquisition of NMR data from cells electroporated with preformed DNA-ligand complexes. The impact of the intracellular environment on the integrity of the complexes is assessed based on in-cell NMR signals from unbound and ligand-bound forms of a given DNA target. This technique was tested on complexes of two model DNA fragments and four ligands, namely, a representative DNA minor-groove binder (netropsin) and ligands binding DNA base-pairing defects (naphthalenophanes). In the latter case, we demonstrate that two of the three in vitro-validated ligands retain their ability to form stable interactions with their model target DNA in cellulo, whereas the third one loses this ability due to off-target interactions with genomic DNA and cellular metabolites. Collectively, our data suggest that direct evaluation of the behavior of drug-like molecules in the intracellular environment provides important insights into the development of DNA-binding ligands with desirable biological activity and minimal side effects resulting from off-target binding.
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Affiliation(s)
- Michaela Krafcikova
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | - Simon Dzatko
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Coralie Caron
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Radovan Fiala
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Tomas Loja
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France
| | - Tomas Fessl
- Faculty of Science , University of South Bohemia , Ceske Budejovice CZ-370 05 , Czech Republic
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute , University of Cambridge , Cambridge CB2 0RE , United Kingdom
| | - Jean-Louis Mergny
- CNRS UMR9187, INSERM U1196, Institut Curie , PSL Research University , Orsay 91405 , France.,CNRS UMR9187, INSERM U1196, Université Paris Sud , Université Paris Saclay , Orsay 91405 , France.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
| | | | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University , Brno 62500 , Czech Republic.,Institute of Biophysics , v.v.i., ASCR, Brno 62500 , Czech Republic
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83
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Das AK, Ihmels H, Kölsch S. Diphenylaminostyryl-substituted quinolizinium derivatives as fluorescent light-up probes for duplex and quadruplex DNA. Photochem Photobiol Sci 2019; 18:1373-1381. [PMID: 30916703 DOI: 10.1039/c9pp00096h] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
(E)-2-[1'-((Diphenylamino)styryl)quinolizinium (3a) and 2,2'-{(phenylimino)-bis[(E)-1'',1'''-styryl]}-bis[quinolizinium] (3b) were synthesized, and their interactions with duplex DNA and quadruplex DNA were investigated with a particular focus on their ability to operate as DNA-sensitive fluorescent probes. Due to the significantly different size and steric demand of these quinolizinium derivatives they exhibit different binding modes. Thus, 3a intercalates into duplex DNA and binds through π stacking to quadruplex DNA, whereas 3b favours groove binding to both DNA forms. The emission intensity of these compounds is very low in aqueous solution, but it increases drastically upon association with duplex DNA by a factor of 11 (3a) and >100 (3b) and with quadruplex DNA by a factor of >100 (3a) and 10 (3b), with emission bands between 600 and 750 nm.
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Affiliation(s)
- Avijit Kumar Das
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and Engineering, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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84
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Guyon L, Pirrotta M, Duskova K, Granzhan A, Teulade-Fichou MP, Monchaud D. TWJ-Screen: an isothermal screening assay to assess ligand/DNA junction interactions in vitro. Nucleic Acids Res 2019; 46:e16. [PMID: 29149299 PMCID: PMC5815093 DOI: 10.1093/nar/gkx1118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022] Open
Abstract
The quest for chemicals able to operate at selected genomic loci in a spatiotemporally controlled manner is desirable to create manageable DNA damages. Mounting evidence now shows that alternative DNA structures, including G-quadruplexes and branched DNA (or DNA junctions), might hamper proper progression of replication fork, thus triggering DNA damages and genomic instability. Therefore, small molecules that stabilize these DNA structures are currently scrutinized as a promising way to create genomic defects that cannot be dealt with properly by cancer cells. While much emphasis has been recently given to G-quadruplexes and related ligands, we report herein on three-way DNA junctions (TWJ) and related ligands. We first highlight the biological implications of TWJ and their strategic relevance as triggers for replicative stress. Then, we describe a new in vitro high-throughput screening assay, TWJ-Screen, which allows for identifying TWJ ligands with both high affinity and selectivity for TWJ over other DNA structures (duplexes and quadruplexes), in a convenient and unbiased manner as demonstrated by the screening of a library of 25 compounds from different chemical families. TWJ-Screen thus represents a reliable mean to uncover molecular tools able to foster replicative stress through an innovative approach, thus providing new strategic opportunities to combat cancers.
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Affiliation(s)
- Ludivine Guyon
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Marc Pirrotta
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Katerina Duskova
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
| | - Anton Granzhan
- Institut Curie, PSL Research University, CNRS UMR9187, INSERM U1196, 91405 Orsay, France
| | | | - David Monchaud
- Institut de Chimie Moléculaire, ICMUB CNRS UMR6302, UBFC, 21078 Dijon, France
- To whom correspondence should be addressed. Tel: +33 380 399 043; Fax: 33 380 396 117;
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85
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Ihmels H, Karbasiyoun M, Löhl K, Stremmel C. Structural flexibility versus rigidity of the aromatic unit of DNA ligands: binding of aza- and azoniastilbene derivatives to duplex and quadruplex DNA. Org Biomol Chem 2019; 17:6404-6413. [PMID: 31225566 DOI: 10.1039/c9ob00809h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The known azastilbene (E)-1,2-di(quinolin-3-yl)ethane (2a) and the novel azoniastilbene derivatives (E)-2-(2-(naphthalen-2-yl)vinyl)quinolizinium (2b) and (E)-3,3'-(ethane-1,2-diyl)bis(1-methylquinolinin-1-ium) (2c) were synthesized. Their interactions with duplex and quadruplex DNA (G4-DNA) were studied by photometric, fluorimetric, polarimetric and flow-LD analysis, and by thermal DNA denaturation studies, as well as by 1H-NMR spectroscopy. The main goal of this study was a comparison of these conformationally flexible compounds with the known G4-DNA-binding diazoniadibenzo[b,k]chrysenes, that have a comparable π-system extent, but a rigid structure. We have observed that the aza- and azoniastilbene derivatives 2a-c, i.e. compounds with almost the same spatial dimensions and steric demand, bind to DNA with an affinity and selectivity that depends significantly on the number of positive charges. Whereas the charge neutral derivative 2a binds unspecifically to the DNA backbone of duplex DNA, the ionic compounds 2b and 2c are typical DNA intercalators. Notably, the bis-quinolinium derivative 2c binds to G4-DNA with moderate affinity (Kb = 4.8 × 105 M-1) and also stabilizes the G4-DNA towards thermal denaturation (ΔTm = 11 °C at ligand-DNA ratio = 5.0). Strikingly, the corresponding rigid counterpart, 4a,12a-diazonia-8,16-dimethyldibenzo[b,k]chrysene, stabilizes the G4-DNA to an even greater extent under identical conditions (ΔTm = 27 °C). These results indicate that the increased flexibility of a G4-DNA ligand does not necessarily lead to stronger interactions with the G4-DNA as compared with rigid ligands that have essentially the same size and π system extent.
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Affiliation(s)
- H Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - M Karbasiyoun
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - K Löhl
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - C Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
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86
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Li F, Guo D, Kang L. Study on the recognition of G-quadruplexes by two stereoisomers of alkaloids. Anal Bioanal Chem 2019; 411:5555-5561. [PMID: 31197422 DOI: 10.1007/s00216-019-01937-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022]
Abstract
G-quadruplexes have been widely researched as new targets for cancer treatment owing to their non-canonical structure and crucial role in biological processes. Although attention has been paid to the development of selective G-quadruplex ligands, few studies have focused on the binding affinity of stereoisomers towards G-quadruplex, which will be conducive to support the optimal design of G-quadruplex ligands in future studies. Here, tetrandrine and isotetrandrine were used to study the binding affinity and difference of stereoisomers towards G-quadruplex structures. The results showed that tetrandrine had a high possibility of binding to the N-myc and Bcl-2 G-quadruplexes through hydrogen bonding, whereas the possibility of binding of isotetrandrine was low and it seemed to have no possibility of forming hydrogen bonds. Our study shows that optical isomerism of ligand molecules has an important effect on G-quadruplex recognition, which is helpful for the design of G-quadruplex ligands in future studies. Graphical abstract.
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Affiliation(s)
- Fangyuan Li
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Dan Guo
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lin Kang
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
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87
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Zhou K, Liu J, Xiong X, Cheng M, Hu X, Narva S, Zhao X, Wu Y, Zhang W. Design, synthesis of 4,5-diazafluorene derivatives and their anticancer activity via targeting telomeric DNA G-quadruplex. Eur J Med Chem 2019; 178:484-499. [PMID: 31202994 DOI: 10.1016/j.ejmech.2019.06.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/02/2019] [Accepted: 06/03/2019] [Indexed: 01/19/2023]
Abstract
In our work, 19 novel 4,5-diazafluorene derivatives (11a-d, 12a-d, 13a-d, 14a-c, 15c, 16a-c) bearing a 1,3-disubstituted pyrazol/thioxothiazolidinone or thioxothiazolidinone-oxadiazole moieties were designed, synthesized, preliminarily explored for their antitumor activities and in vitro mechanism. All compounds showed different values of antiproliferative activity against A549, AGS, HepG2 and MCF-7 cell lines through CCK-8. Especially, the compound 14c exhibited the strongest activity and best selectivity against A549 cells with an IC50 1.13 μM and an SI value of 7.01 relative to MRC-5 cells, which was better than cisplatin (SI = 1.80) as a positive control. Experimental results at extracellular level demonstrated that compounds 14a-c could strongly interact with the G-quadruplex(es) formed in a 26 nt telomeric G-rich DNA, in particular, the 14c exhibits quite strong binding affinity with an association equilibrium constant (KA) of 7.04(±0.16) × 107 M-1 and more than 1000-fold specificity to G4-DNA over ds-DNA and Mut-DNA at the compound/G4-DNA ratio of 1:1. Further trap assay ascertained that compounds 14a-c owned strong inhibitory ability of telomerase activity in A549 cells, suggesting that these compounds have great possibility to target telomeric G-quadruplexes and consequently indirectly inhibit the telomerase activity. In addition, it is worthy of note that the remarkable inhibitory effects of 14a-c on the mobility of tested cancer cells were observed by wound healing assays. Furthermore, molecular docking and UV-Vis spectral results unclose the rationale for the interaction of compounds with such G-quadruplex(es). These results indicate that the growth and metastasis inhibition of cancer cells mediated by these 4,5-diazafluorene derivatives possibly result from their interaction with telomeric G-quadruplexes, suggesting that 4,5-diazafluorene derivatives, especially 14c, possess potential as anticancer drugs.
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Affiliation(s)
- Kang Zhou
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Jiachun Liu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xuqiong Xiong
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Mei Cheng
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaolin Hu
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Suresh Narva
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Xiaoyin Zhao
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yanling Wu
- Lab of Molecular Immunology, Virus Inspection Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Wen Zhang
- Lab of Chemical Biology and Molecular Drug Design, College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, 310014, China; Lab of Chemical Biology and Molecular Drug Design, Institute of Drug Development & Chemical Biology, Zhejiang University of Technology, Hangzhou, 310014, China.
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88
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Panda D, Saha P, Chaudhuri R, Prasanth T, Ravichandiran V, Dash J. A Competitive Pull-Down Assay Using G-quadruplex DNA Linked Magnetic Nanoparticles To Determine Specificity of G-quadruplex Ligands. Anal Chem 2019; 91:7705-7711. [DOI: 10.1021/acs.analchem.9b00889] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Deepanjan Panda
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Puja Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ritapa Chaudhuri
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Thumpati Prasanth
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
- National Institute of Pharmaceutical Education and Research, Jadavpur, Kolkata 700032, India
| | | | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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89
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Evaluation of the selectivity of G-quadruplex ligands in living cells with a small molecule fluorescent probe. Anal Chim Acta X 2019; 2:100017. [PMID: 33117978 PMCID: PMC7587023 DOI: 10.1016/j.acax.2019.100017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 04/17/2019] [Indexed: 11/22/2022] Open
Abstract
G-quadruplex has been an emerging target for drug design due to its physiologically important roles in oncology. A number of quadruplex-interactive ligands have been developed by synthetic and medicinal chemists over the past decades. However, the great challenge still remains that the method for detecting the specific targeting of these ligands to the G-quadruplex structures in cells is still lacking. Herein, a detection system for directly identifying the specific targeting of a ligand to DNA G-quadruplexes in cells was constructed by using a small-molecular fluorescent probe (IMT) as a fluorescent indicator. Four typical ligands have been successfully evaluated, demonstrating the promising application of this detection system in the screening and evaluation of quadruplex-specific therapeutic agents.
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90
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Practical Microwave Synthesis of Carbazole Aldehydes for the Development of DNA-Binding Ligands. Molecules 2019; 24:molecules24050965. [PMID: 30857275 PMCID: PMC6429063 DOI: 10.3390/molecules24050965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 01/28/2023] Open
Abstract
Microwave formylation of carbazole derivatives was investigated and 3-monoaldehydes were obtained in high yield. A potential DNA-binding ligand, 3-[(3-ethyl)-2-vinylbenzothiazolium]-9-N-ethyl carbazole iodide, was synthesized and characterized including spectral properties (UV-Vis absorption and fluorescence spectra). The binding selectivity and affinity of three carbazole ligands for double-stranded and G-quadruplex DNA structures were studied using a competitive dialysis method in sodium- and potassium-containing buffer solutions.
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91
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Ramos CIV, Almeida SP, Lourenço LMO, Pereira PMR, Fernandes R, Faustino MAF, Tomé JPC, Carvalho J, Cruz C, Neves MGPMS. Multicharged Phthalocyanines as Selective Ligands for G-Quadruplex DNA Structures. Molecules 2019; 24:E733. [PMID: 30781675 PMCID: PMC6412362 DOI: 10.3390/molecules24040733] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/12/2019] [Accepted: 02/13/2019] [Indexed: 01/21/2023] Open
Abstract
The stabilization of G-Quadruplex DNA structures by ligands is a promising strategy for telomerase inhibition in cancer therapy since this enzyme is responsible for the unlimited proliferation of cancer cells. To assess the potential of a compound as a telomerase inhibitor, selectivity for quadruplex over duplex DNA is a fundamental attribute, as the drug must be able to recognize quadruplex DNA in the presence of a large amount of duplex DNA, in the cellular nucleus. By using different spectroscopic techniques, such as ultraviolet-visible, fluorescence and circular dichroism, this work evaluates the potential of a series of multicharged phthalocyanines, bearing four or eight positive charges, as G-Quadruplex stabilizing ligands. This work led us to conclude that the existence of a balance between the number and position of the positive charges in the phthalocyanine structure is a fundamental attribute for its selectivity for G-Quadruplex structures over duplex DNA structures. Two of the studied phthalocyanines, one with four peripheral positive charges (ZnPc1) and the other with less exposed eight positive charges (ZnPc4) showed high selectivity and affinity for G-Quadruplex over duplex DNA structures and were able to accumulate in the nucleus of UM-UC-3 bladder cancer cells.
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Affiliation(s)
- Catarina I V Ramos
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Susana P Almeida
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Leandro M O Lourenço
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Patrícia M R Pereira
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal.
- CNC.IBILI Consortium, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - Rosa Fernandes
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal.
- CNC.IBILI Consortium, University of Coimbra, 3000-548 Coimbra, Portugal.
| | - M Amparo F Faustino
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - João P C Tomé
- CQE & Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, n1, 1049-001 Lisboa, Portugal.
| | - Josué Carvalho
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - Carla Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Av. Infante D. Henrique, 6200-506 Covilhã, Portugal.
| | - M Graça P M S Neves
- QOPNA & LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal.
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92
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Saha P, Panda D, Dash J. The application of click chemistry for targeting quadruplex nucleic acids. Chem Commun (Camb) 2019; 55:731-750. [PMID: 30489575 DOI: 10.1039/c8cc07107a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Cu(i)-catalyzed azide and alkyne 1,3-dipolar cycloaddition (CuAAC), commonly known as the "click reaction", has emerged as a powerful and versatile synthetic tool that finds a broad spectrum of applications in chemistry, biology and materials science. The efficiency, selectivity and versatility of the CuAAC reactions have enabled the preparation of vast arrays of triazole compounds with biological and pharmaceutical applications. In this feature article, we outline the applications and future prospects of click chemistry in the synthesis and development of small molecules that target G-quadruplex nucleic acids and show promising biological activities. Furthermore, this article highlights the template-assisted in situ click chemistry for developing G-quadruplex specific ligands and the use of click chemistry for enhancing drug specificity as well as designing imaging and sensor systems to elucidate the biological functions of G-quadruplex nucleic acids in live cells.
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Affiliation(s)
- Puja Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India.
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93
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Xu X, Wang S, Mi Y, Zhao H, Zheng Z, Zhao X. A hydroxyquinoline-appended ruthenium(II)-polypyridyl complex that induces and stabilizes G-quadruplex DNA. J COORD CHEM 2019. [DOI: 10.1080/00958972.2018.1548703] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- Xuexue Xu
- College of Chemistry and Environmental Science, Hebei University, Baoding, P.R. China
| | - Shuang Wang
- College of Chemistry and Environmental Science, Hebei University, Baoding, P.R. China
| | - Yaxuan Mi
- College of Chemistry and Environmental Science, Hebei University, Baoding, P.R. China
| | - Huaqian Zhao
- College of Chemistry and Environmental Science, Hebei University, Baoding, P.R. China
| | - Zebao Zheng
- College of Chemistry and Chemical Engineering, Taishan University, Taian, P.R. China
| | - Xiaolong Zhao
- College of Chemistry and Environmental Science, Hebei University, Baoding, P.R. China
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94
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Weynand J, Diman A, Abraham M, Marcélis L, Jamet H, Decottignies A, Dejeu J, Defrancq E, Elias B. Towards the Development of Photo‐Reactive Ruthenium(II) Complexes Targeting Telomeric G‐Quadruplex DNA. Chemistry 2018; 24:19216-19227. [DOI: 10.1002/chem.201804771] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 10/22/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Justin Weynand
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Aurélie Diman
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Michaël Abraham
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Lionel Marcélis
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
| | - Hélène Jamet
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Anabelle Decottignies
- Université catholique de Louvain (UCLouvain) de Duve Institute Avenue Hippocrate 75 1200 Brussels Belgium
| | - Jérôme Dejeu
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Eric Defrancq
- Université Grenoble-Alpes (UGA)Département de Chimie Moléculaire, UMR CNRS 5250, CS 40700 38058 Grenoble France
| | - Benjamin Elias
- Université catholique de Louvain (UCLouvain)Institut de la Matière Condensée et des Nanosciences (IMCN), Molecular Chemistry, Materials and Catalysis (MOST) Place Louis Pasteur 1, bte L4.01.02 1348 Louvain-la-Neuve Belgium
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95
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Kudrev AG. Scheme of the Complex Formation of DNA Telomeric Sequence with TMPyP4 Porphyrine. RUSS J GEN CHEM+ 2018. [DOI: 10.1134/s1070363218120198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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96
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Prado E, Bonnat L, Bonnet H, Lavergne T, Van der Heyden A, Pratviel G, Dejeu J, Defrancq E. Influence of the SPR Experimental Conditions on the G-Quadruplex DNA Recognition by Porphyrin Derivatives. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:13057-13064. [PMID: 30293430 DOI: 10.1021/acs.langmuir.8b02942] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful technique to study the interactions of ligands with analytes and therefore a number of biosensor surfaces and injection methods have been developed so far. However, many experimental parameters can affect the interactions and consequently the affinity measurements. In particular, the interactions of positively charged analytes (often used for anionic nucleic acids targets) can be influenced by the sensing surfaces (e.g., negatively charged), leading to significant nonspecific interactions as well as regeneration problems. The aim of the present work is to investigate the effect of different parameters, including ionic strength, SPR biosensor (i.e., nature of the surfaces), and the injection method on the recognition of porphyrin G-quadruplex ligands. We demonstrate that the injection method does not influence the affinity whereas the ionic strength and the nature of the surface impact the recognition properties of the porphyrin for the G-quadruplex DNA. We also found that self-assembled monolayer coating surface presents many advantages in comparison with carboxymethylated dextran surface for SPR studies of G-quadruplex DNA/ligand interactions: (i) the electrostatic interaction with charged analytes is less important, (ii) its structure/composition is less sensitive to the ionic concentration and less prone to unspecific adsorption, (iii) it is easily homemade, and (iv) the cost is approximately 10 times cheaper.
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Affiliation(s)
- E Prado
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - L Bonnat
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - H Bonnet
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - T Lavergne
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | | | - G Pratviel
- CNRS, Laboratoire de Chimie de Coordination , 205 route de Narbonne, BP44099 , F-31077 Toulouse Cedex 4, France
- Université de Toulouse, UPS, INPT , Toulouse , France
| | - J Dejeu
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
| | - E Defrancq
- Univ. Grenoble Alpes, CNRS, DCM , 38000 Grenoble , France
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97
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Flusberg DA, Rizvi NF, Kutilek V, Andrews C, Saradjian P, Chamberlin C, Curran P, Swalm B, Kattar S, Smith GF, Dandliker P, Nickbarg EB, O'Neil J. Identification of G-Quadruplex-Binding Inhibitors of Myc Expression through Affinity Selection-Mass Spectrometry. SLAS DISCOVERY 2018; 24:142-157. [PMID: 30204533 DOI: 10.1177/2472555218796656] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Myc oncogene is overexpressed in many cancers, yet targeting it for cancer therapy has remained elusive. One strategy for inhibition of Myc expression is through stabilization of the G-quadruplex (G4), a G-rich DNA secondary structure found within the Myc promoter; stabilization of G4s has been shown to halt transcription of downstream gene products. Here we used the Automated Ligand Identification System (ALIS), an affinity selection-mass spectrometry method, to identify compounds that bind to the Myc G4 out of a pool of compounds that had previously been shown to inhibit Myc expression in a reporter screen. Using an ALIS-based screen, we identified hits that bound to the Myc G4, a small subset of which bound preferentially relative to G4s from the promoters of five other genes. To determine functionality and specificity of the Myc G4-binding compounds in cell-based assays, we compared inhibition of Myc expression in cells with and without Myc G4 regulation. Several compounds inhibited Myc expression only in the Myc G4-containing line, and one compound was verified to function through Myc G4 binding. Our study demonstrates that ALIS can be used to identify selective nucleic acid-binding compounds from phenotypic screen hits, increasing the pool of drug targets beyond proteins.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Sam Kattar
- 3 Chemistry, Merck & Co., Inc., Boston, MA, USA
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98
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Liu W, Sun T, Zhang P, Li L, Lv J, Li B. [Application of atomic force microscopy-based single molecule force spectroscopy in G-quadruplex studies]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2018; 38:1107-1114. [PMID: 30377115 DOI: 10.12122/j.issn.1673-4254.2018.09.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Telomere plays a crucial role in the physiological and pathological processes of cells. At the end of the telomere, the single-stranded DNA repeat sequence rich in guanine (G) folds in the presence of monovalent metal ions such as Na+ or K+ to form a G-quadruplex structure. This structure can not be extended by telomerase and inhibits the activity of telomerase, thus becoming a potential anticancer target. Stabilizing the formation of DNA G-quadruplex structures by small molecule ligands has become a new strategy for designing many anticancer drugs, and studying the interaction strength of these small molecule ligands with G-quadruplex is thus of particular importance for screening highly effective anticancer drugs. Single molecule force spectroscopy enables direct measurement of the interaction between small molecule ligands and G-quadruplexes. This review highlights the advances of single-molecule force spectroscopy based on atomic force microscopy in the study of the G quadruplex structure and its interaction with small molecule ligands, and summarizes the application and development trend of single molecule force spectrum technology in G quadruplex.
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Affiliation(s)
- Wenjing Liu
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tong Sun
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhang
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lin Li
- School of Science, Ningbo University, Ningbo 315211, China
| | - Junhong Lv
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Bin Li
- Laboratory of Physical Biology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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99
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Deng L, Wu Y, Xu S, Tang Y, Zhang X, Wu P. Improving the Signal-to-Background Ratio during Catalytic Hairpin Assembly through Both-End-Blocked DNAzyme. ACS Sens 2018; 3:1190-1195. [PMID: 29855182 DOI: 10.1021/acssensors.8b00243] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Catalyzed hairpin assembly (CHA) is an important DNA engineering tool for a variety of applications such as DNA nanotechnology and biosensing. Here we report a hairpin-type of both-end-blocked DNAzyme to improve the signal-to-background ratio during the CHA process. In the design, the DNAzyme activity can be blocked efficiently via locking both ends of the G-rich DNAzyme sequence in the loop and stem (blocking efficiency = 96%) and can be easily recovered during the CHA process (activation efficiency = 94%). The both-end-blocked DNAzyme is by far the most sensitive optical detection mode for monitoring the CHA process that can be used for determination of 0.05 fmol miRNA-21. The fabricated CHA-DNAzyme sensing system was also able to discriminate miRNA-21 from single-/three-base mismatch miRNA-21. The feasibility of real application was also tested via detection of miRNA-21 levels in tumor cell samples. Therefore, the sensing system with the advantages of convenience, high sensitivity, and selectivity is an appealing strategy for miRNA detection.
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Affiliation(s)
- Li Deng
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yuanheng Wu
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Shuxia Xu
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Yurong Tang
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Xinfeng Zhang
- College of Materials and Chemistry and Chemical Engineering, Chengdu University of Technology, Chengdu 610059, China
| | - Peng Wu
- Analytical and Testing Center, Sichuan University, 29 Wangjiang Road, Chengdu 610064, China
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100
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Platella C, Musumeci D, Arciello A, Doria F, Freccero M, Randazzo A, Amato J, Pagano B, Montesarchio D. Controlled Pore Glass-based oligonucleotide affinity support: towards High Throughput Screening methods for the identification of conformation-selective G-quadruplex ligands. Anal Chim Acta 2018; 1030:133-141. [PMID: 30032762 DOI: 10.1016/j.aca.2018.04.071] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/27/2018] [Accepted: 04/30/2018] [Indexed: 10/17/2022]
Abstract
Target selectivity is one of the main challenges in the search for small molecules able to act as effective and non-toxic anticancer and/or antiviral drugs. To achieve this goal, handy, rapid and reliable High Throughput Screening methodologies are needed. We here describe a novel functionalization for the solid phase synthesis of oligonucleotides on Controlled Pore Glass, including a flexible hexaethylene glycol spacer linking the first nucleoside through the nucleobase via a covalent bond stable to the final deprotection step. This allowed us preparing fully deprotected oligonucleotides still covalently attached to their supports. In detail, on this support we performed both the on-line synthesis of different secondary structure-forming oligonucleotides and the affinity chromatography-based screenings of conformation-selective G-quadruplex ligands. By using a fluorescent core-extended naphthalene diimide with different emitting response upon binding to sequences folding into G-quadruplexes of different topologies, we have been able to discriminate not only G-quadruplex vs. duplex DNA structures, but also different G-quadruplex conformations on the glass beads by confocal microscopy.
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Affiliation(s)
- Chiara Platella
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia, Viale Taramelli 12, 27100, Pavia, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131, Naples, Italy
| | - Jussara Amato
- 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
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, via Cintia 21, 80126, Naples, Italy.
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