1
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Roy S, Majee P, Sudhakar S, Mishra S, Kalia J, Pradeepkumar PI, Srivatsan SG. Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsive 19F-labeled nucleoside probes. Chem Sci 2024; 15:7982-7991. [PMID: 38817587 PMCID: PMC11134374 DOI: 10.1039/d4sc01755b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 04/23/2024] [Indexed: 06/01/2024] Open
Abstract
Understanding the structure and recognition of highly conserved regulatory segments of the integrated viral DNA genome that forms unique topologies can greatly aid in devising novel therapeutic strategies to counter chronic infections. In this study, we configured a probe system using highly environment-sensitive nucleoside analogs, 5-fluoro-2'-deoxyuridine (FdU) and 5-fluorobenzofuran-2'-deoxyuridine (FBFdU), to investigate the structural polymorphism of HIV-1 long terminal repeat (LTR) G-quadruplexes (GQs) by fluorescence and 19F NMR. FdU and FBFdU, serving as hairpin and GQ sensors, produced distinct spectral signatures for different GQ topologies adopted by LTR G-rich oligonucleotides. Importantly, systematic 19F NMR analysis in Xenopus laevis oocytes gave unprecedented information on the structure adopted by the LTR G-rich region in the cellular environment. The results indicate that it forms a unique GQ-hairpin hybrid architecture, a potent hotspot for selective targeting. Furthermore, structural models generated using MD simulations provided insights on how the probe system senses different GQs. Using the responsiveness of the probes and Taq DNA polymerase stop assay, we monitored GQ- and hairpin-specific ligand interactions and their synergistic inhibitory effect on the replication process. Our findings suggest that targeting GQ and hairpin motifs simultaneously using bimodal ligands could be a new strategy to selectively block the viral replication.
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Affiliation(s)
- Sarupa Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
| | - Priyasha Majee
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Satyajit Mishra
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - Jeet Kalia
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal Bhopal Bypass Road, Bhauri Bhopal 462066 India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay Mumbai 400076 India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune Dr Homi Bhabha Road Pune 411008 India
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2
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Krause NM, Bains JK, Blechar J, Richter C, Bessi I, Grote P, Leisegang MS, Brandes RP, Schwalbe H. Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr. Chembiochem 2024; 25:e202400049. [PMID: 38456652 DOI: 10.1002/cbic.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators of gene expression and can associate with DNA as RNA : DNA heteroduplexes or RNA ⋅ DNA : DNA triple helix structures. Here, we review in vitro biochemical and biophysical experiments including electromobility shift assays (EMSA), circular dichroism (CD) spectroscopy, thermal melting analysis, microscale thermophoresis (MST), single-molecule Förster resonance energy transfer (smFRET) and nuclear magnetic resonance (NMR) spectroscopy to investigate RNA ⋅ DNA : DNA triple helix and RNA : DNA heteroduplex formation. We present the investigations of the antiparallel triplex-forming lncRNA MEG3 targeting the gene TGFB2 and the parallel triplex-forming lncRNA Fendrr with its target gene Emp2. The thermodynamic properties of these oligonucleotides lead to concentration-dependent heterogeneous mixtures, where a DNA duplex, an RNA : DNA heteroduplex and an RNA ⋅ DNA : DNA triplex coexist and their relative populations are modulated in a temperature-dependent manner. The in vitro data provide a reliable readout of triplex structures, as RNA ⋅ DNA : DNA triplexes show distinct features compared to DNA duplexes and RNA : DNA heteroduplexes. Our experimental results can be used to validate computationally predicted triple helix formation between novel disease-relevant lncRNAs and their DNA target genes.
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Affiliation(s)
- Nina M Krause
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Jasleen K Bains
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Julius Blechar
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
- Institute for Organic Chemistry, Julius-Maximilians-University, Würzburg, Bavaria, 97074, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Frankfurt am Main, Hesse, 60590, Germany
- Georg-Speyer-Haus, Frankfurt am Main, Hesse, 60590, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
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3
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Sato K, Knipscheer P. G-quadruplex resolution: From molecular mechanisms to physiological relevance. DNA Repair (Amst) 2023; 130:103552. [PMID: 37572578 DOI: 10.1016/j.dnarep.2023.103552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/29/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
Guanine-rich DNA sequences can fold into stable four-stranded structures called G-quadruplexes or G4s. Research in the past decade demonstrated that G4 structures are widespread in the genome and prevalent in regulatory regions of actively transcribed genes. The formation of G4s has been tightly linked to important biological processes including regulation of gene expression and genome maintenance. However, they can also pose a serious threat to genome integrity especially by impeding DNA replication, and G4-associated somatic mutations have been found accumulated in the cancer genomes. Specialised DNA helicases and single stranded DNA binding proteins that can resolve G4 structures play a crucial role in preventing genome instability. The large variety of G4 unfolding proteins suggest the presence of multiple G4 resolution mechanisms in cells. Recently, there has been considerable progress in our detailed understanding of how G4s are resolved, especially during DNA replication. In this review, we first discuss the current knowledge of the genomic G4 landscapes and the impact of G4 structures on DNA replication and genome integrity. We then describe the recent progress on the mechanisms that resolve G4 structures and their physiological relevance. Finally, we discuss therapeutic opportunities to target G4 structures.
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Affiliation(s)
- Koichi Sato
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Puck Knipscheer
- Oncode Institute, Hubrecht Institute-KNAW & University Medical Center Utrecht, Utrecht, the Netherlands; Department of Human Genetics, Leiden University Medical Center, Leiden, the Netherlands.
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4
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Prescott TAK, Anaissi-Afonso L, Fox KR, Maxwell A, Panaretou B, Machín F. A simplified and easy-to-use HIP HOP assay provides insights into chalcone antifungal mechanisms of action. FEBS Lett 2022; 596:3087-3102. [PMID: 36053795 PMCID: PMC10087691 DOI: 10.1002/1873-3468.14483] [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: 05/09/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/14/2022]
Abstract
Elucidating the mechanism of action of an antifungal or cytotoxic compound is a time-consuming process. Yeast chemogenomic profiling provides a compelling solution to the problem but is experimentally complex. Here, we demonstrate the use of a highly simplified yeast chemical genetic assay comprising just 89 yeast deletion strains, each diagnostic for a specific mechanism of action. We use the assay to investigate the mechanism of action of two antifungal chalcone compounds, trans-chalcone and 4'-hydroxychalcone, and narrow down the mechanism to transcriptional stress. Crucially, the assay eliminates mechanisms of action such as topoisomerase I inhibition and membrane disruption that have been suggested for related chalcone compounds. We propose this simplified assay as a useful tool to rapidly identify common off-target mechanisms.
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Affiliation(s)
| | - Laura Anaissi-Afonso
- Unidad de Investigación, Hospital Universitario Ntra Sra de Candelaria, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de la Laguna, Tenerife, Spain
| | - Keith R Fox
- School of Biological Sciences, University of Southampton, UK
| | - Anthony Maxwell
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK
| | - Barry Panaretou
- School of Cancer and Pharmaceutical Sciences, King's College London, UK
| | - Félix Machín
- Unidad de Investigación, Hospital Universitario Ntra Sra de Candelaria, Santa Cruz de Tenerife, Spain.,Instituto de Tecnologías Biomédicas, Universidad de la Laguna, Tenerife, Spain.,Facultad de Ciencias de la Salud, Universidad Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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5
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Fleming AM, Xiao S, Chabot MB, Burrows CJ. Fluorophore-mediated Photooxidation of the Guanine Heterocycle. J PHYS ORG CHEM 2022; 35:e4325. [PMID: 36388261 PMCID: PMC9642976 DOI: 10.1002/poc.4325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 11/09/2022]
Abstract
Fluorescent dyes are routinely used to visualize DNA or RNA in various experiments, and some dyes also act as photosensitizers capable of catalyzing oxidation reactions. The present studies explored whether the common labeling dyes fluorescein, rhodamine, BODIPY, or cyanine3 (Cy3) can function as photosensitizers to oxidize nucleic acid polymers. Photoirradiation of each dye in the presence of the guanine (G) heterocycle, which is the most sensitive toward oxidation, identified slow rates of nucleobase oxidation in the nucleoside and DNA contexts. For all four fluorophores studied, the only product detected was spiroiminodihydantoin (Sp) suggesting the dyes functioned as Type II photosensitizers and generate singlet oxygen (1O2). The nucleoside reactions were then conducted in D2O solutions, known to increase the lifetime of 1O2, which resulted in a ~6-fold increase in the Sp yield, further supporting the classification of these dyes as Type II photosensitizers. Lastly, we inspected the pattern of G reactivity with the dyes upon photoirradiation in the context of a parallel-stranded G-quadruplex. The G nucleotides in the two exterior G-tetrads were found to be oxidation prone, providing the third line of evidence that the dyes are Type II photooxidants. The present work found that the common dyes fluorescein, rhodamine, BODIPY, or Cy3 can drive G oxidation but with a slow rate and low overall yield. This will likely not impact many experiments using dyes to study nucleic acids except for those that have long exposures with high-intensity lights, such as sequencing-by-synthesis experiments using fluorescence as the readout.
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Affiliation(s)
- Aaron M. Fleming
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Songjun Xiao
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Michael B. Chabot
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
| | - Cynthia J. Burrows
- 315 South 1400 East, Dept. of Chemistry, University of Utah, Salt Lake City, UT 84112-0850
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6
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Monsen RC, Maguire JM, DeLeeuw LW, Chaires JB, Trent JO. Drug discovery of small molecules targeting the higher-order hTERT promoter G-quadruplex. PLoS One 2022; 17:e0270165. [PMID: 35709230 PMCID: PMC9202945 DOI: 10.1371/journal.pone.0270165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/03/2022] [Indexed: 12/15/2022] Open
Abstract
DNA G-quadruplexes (G4s) are now widely accepted as viable targets in the pursuit of anticancer therapeutics. To date, few small molecules have been identified that exhibit selectivity for G4s over alternative forms of DNA, such as the ubiquitous duplex. We posit that the lack of current ligand specificity arises for multiple reasons: G4 atomic models are often small, monomeric, single quadruplex structures with few or no druggable pockets; targeting G-tetrad faces frequently results in the enrichment of extended electron-deficient polyaromatic end-pasting scaffolds; and virtual drug discovery efforts often under-sample chemical search space. We show that by addressing these issues we can enrich for non-standard molecular templates that exhibit high selectivity towards G4s over other forms of DNA. We performed an extensive virtual screen against the higher-order hTERT core promoter G4 that we have previously characterized, targeting 12 of its unique loop and groove pockets using libraries containing 40 million drug-like compounds for each screen. Using our drug discovery funnel approach, which utilizes high-throughput fluorescence thermal shift assay (FTSA) screens, microscale thermophoresis (MST), and orthogonal biophysical methods, we have identified multiple unique G4 binding scaffolds. We subsequently used two rounds of catalogue-based SAR to increase the affinity of a disubstituted 2-aminoethyl-quinazoline that stabilizes the higher-order hTERT G-quadruplex by binding across its G4 junctional sites. We show selectivity of its binding affinity towards hTERT is virtually unaffected in the presence of near-physiological levels of duplex DNA, and that this molecule downregulates hTERT transcription in breast cancer cells.
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Affiliation(s)
- Robert C. Monsen
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Jon M. Maguire
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Lynn W. DeLeeuw
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (JBC); (JOT)
| | - John O. Trent
- UofL Health Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (JBC); (JOT)
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7
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Ongaro A, Desiderati G, Oselladore E, Auricchio D, Memo M, Ribaudo G, Sissi C, Gianoncelli A. Amino-Acid-Anthraquinone Click Chemistry Conjugates Selectively Target Human Telomeric G-Quadruplexes. ChemMedChem 2021; 17:e202100665. [PMID: 34882992 DOI: 10.1002/cmdc.202100665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/07/2021] [Indexed: 11/06/2022]
Abstract
Guanine-rich sequences are known to fold into G-quadruplex (G4) arrangements, which are present in oncogenes and in the telomeric regions of chromosomes. In particular, G4s represent an obstacle to functioning of telomerase, an enzyme overexpressed in cancer cells causing their immortalization. Therefore, G4 stabilization using small molecules represents an appealing strategy for the medicinal chemist. Ligands based on an anthraquinone scaffold, to which peptidic side chains were attached by an amide bond, were previously reported. We envisioned improving this ligand concept leveraging the click chemistry approach, which, besides representing a flexible, high yielding synthetic strategy, allows an elongation of the side chains and an increase of π-π stacking and H-bond interactions with the nucleobases through the triazole ring. Compounds were tested for their ability to interact with G4 DNA with a multiple analytical approach, demonstrating an elevated aptitude to stabilize the G4 and high selectivity over double stranded DNA.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Desiderati
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Davide Auricchio
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
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8
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Rusling DA. Triplex-forming properties and enzymatic incorporation of a base-modified nucleotide capable of duplex DNA recognition at neutral pH. Nucleic Acids Res 2021; 49:7256-7266. [PMID: 34233006 PMCID: PMC8287925 DOI: 10.1093/nar/gkab572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/31/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
The sequence-specific recognition of duplex DNA by unmodified parallel triplex-forming oligonucleotides is restricted to low pH conditions due to a necessity for cytosine protonation in the third strand. This has severely restricted their use as gene-targeting agents, as well as for the detection and/or functionalisation of synthetic or genomic DNA. Here I report that the nucleobase 6-amino-5-nitropyridin-2-one (Z) finally overcomes this constraint by acting as an uncharged mimic of protonated cytosine. Synthetic TFOs containing the nucleobase enabled stable and selective triplex formation at oligopurine-oligopyrimidine sequences containing multiple isolated or contiguous GC base pairs at neutral pH and above. Moreover, I demonstrate a universal strategy for the enzymatic assembly of Z-containing TFOs using its commercially available deoxyribonucleotide triphosphate. These findings seek to improve not only the recognition properties of TFOs but also the cost and/or expertise associated with their chemical syntheses.
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Affiliation(s)
- David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
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9
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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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10
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Oliveira LM, Long AS, Brown T, Fox KR, Weber G. Melting temperature measurement and mesoscopic evaluation of single, double and triple DNA mismatches. Chem Sci 2020; 11:8273-8287. [PMID: 34094181 PMCID: PMC8163305 DOI: 10.1039/d0sc01700k] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Unlike the canonical base pairs AT and GC, the molecular properties of mismatches such as hydrogen bonding and stacking interactions are strongly dependent on the identity of the neighbouring base pairs. As a result, due to the sheer number of possible combinations of mismatches and flanking base pairs, only a fraction of these have been studied in varying experiments or theoretical models. Here, we report on the melting temperature measurement and mesoscopic analysis of contiguous DNA mismatches in nearest-neighbours and next-nearest neighbour contexts. A total of 4032 different mismatch combinations, including single, double and triple mismatches were covered. These were compared with 64 sequences containing all combinations of canonical base pairs in the same location under the same conditions. For a substantial number of single mismatch configurations, 15%, the measured melting temperatures were higher than the least stable AT base pair. The mesoscopic calculation, using the Peyrard-Bishop model, was performed on the set of 4096 sequences, and resulted in estimates of on-site and nearest-neighbour interactions that can be correlated to hydrogen bonding and base stacking. Our results confirm many of the known properties of mismatches, including the peculiar sheared stacking of tandem GA mismatches. More intriguingly, it also reveals that a number of mismatches present strong hydrogen bonding when flanked on both sites by other mismatches. To highlight the applicability of our results, we discuss a number of practical situations such as enzyme binding affinities, thymine DNA glycosylase repair activity, and trinucleotide repeat expansions.
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Affiliation(s)
- Luciana M Oliveira
- Departamento de Física, Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil +55 31 3409 5600 +55 31 3409 6616
| | - Adam S Long
- School of Biological Sciences, University of Southampton Life Sciences Building 85 Southampton SO17 1BJ UK
| | - Tom Brown
- Department of Chemistry, University of Oxford Oxford UK
| | - Keith R Fox
- School of Biological Sciences, University of Southampton Life Sciences Building 85 Southampton SO17 1BJ UK
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais 31270-901 Belo Horizonte MG Brazil +55 31 3409 5600 +55 31 3409 6616
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11
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Koike K, Nagano M, Ebihara M, Hirayama T, Tsuji M, Suga H, Nagasawa H. Design, Synthesis, and Conformation-Activity Study of Unnatural Bridged Bicyclic Depsipeptides as Highly Potent Hypoxia Inducible Factor-1 Inhibitors and Antitumor Agents. J Med Chem 2020; 63:4022-4046. [PMID: 32202785 DOI: 10.1021/acs.jmedchem.9b02039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
By carrying out structural modifications based on the bicyclic peptide structure of echinomycin, we successfully synthesized various powerful antitumor derivatives. The ring conformation in the obtained compounds was restricted by cross-linking with an unnatural bond. The prepared derivatives were demonstrated to strongly suppress the hypoxia inducible factor (HIF)-1 transcriptional activation and hypoxia induction of HIF-1 protein expression. Particularly, alkene-bridged derivative 12 exhibited remarkably potent cytotoxicity (IC50 = 0.22 nM on the MCF-7 cell line) and HIF-1 inhibition (IC50 = 0.09 nM), which considerably exceeded those of echinomycin. Conformational analyses and molecular modeling studies revealed that the biological activities were enhanced following restriction of the conformation by cross-linking through a metabolically stable and rigid bridge bond. In addition, we proposed a new globular conformation stabilized by intramolecular π stacking that can contribute to the biological effects of bicyclic depsipeptides. The developments presented in the current study serve as a useful guide to expand the chemical space of peptides in drug discovery.
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Affiliation(s)
- Kota Koike
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Masanobu Nagano
- Department of Chemistry, The University of Tokyo, Bunkyoku, Tokyo 113-0033, Japan
| | - Masahiro Ebihara
- Department of Chemistry and Biomolecular Science, Faculty of Engineering, Gifu University, Gifu-city, Gifu 501-1193, Japan
| | - Tasuku Hirayama
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Mieko Tsuji
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
| | - Hiroaki Suga
- Department of Chemistry, The University of Tokyo, Bunkyoku, Tokyo 113-0033, Japan
| | - Hideko Nagasawa
- Laboratory of Pharmaceutical and Medicinal Chemistry, Gifu Pharmaceutical University, Gifu-city, Gifu 501-1196, Japan
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12
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Nuthanakanti A, Ahmed I, Khatik SY, Saikrishnan K, Srivatsan SG. Probing G-quadruplex topologies and recognition concurrently in real time and 3D using a dual-app nucleoside probe. Nucleic Acids Res 2020; 47:6059-6072. [PMID: 31106340 PMCID: PMC6614846 DOI: 10.1093/nar/gkz419] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves as a common probe to detect and correlate different GQ structures and ligand binding under equilibrium conditions and in 3D by fluorescence and X-ray crystallography techniques. The probe (SedU) is composed of a microenvironment-sensitive fluorophore and an excellent anomalous X-ray scatterer (Se), which is assembled by attaching a selenophene ring at 5-position of 2'-deoxyuridine. SedU incorporated into the loop region of human telomeric DNA repeat fluorescently distinguished subtle differences in GQ topologies and enabled quantify ligand binding to different topologies. Importantly, anomalous X-ray dispersion signal from Se could be used to determine the structure of GQs. As the probe is minimally perturbing, a direct comparison of fluorescence data and crystal structures provided structural insights on how the probe senses different GQ conformations without affecting the native fold. Taken together, our dual-app probe represents a new class of tool that opens up new experimental strategies to concurrently investigate nucleic acid structure and recognition in real time and 3D.
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Affiliation(s)
- Ashok Nuthanakanti
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Ishtiyaq Ahmed
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Saddam Y Khatik
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
| | - Kayarat Saikrishnan
- Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- Correspondence may also be addressed to Kayarat Saikrishnan.
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr. Homi Bhabha Road, Pune 411008, India
- To whom correspondence should be addressed. Tel: +91 2025908086;
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13
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Del Mundo IMA, Cho EJ, Dalby KN, Vasquez KM. A 'light-up' intercalator displacement assay for detection of triplex DNA stabilizers. Chem Commun (Camb) 2020; 56:1996-1999. [PMID: 31960843 PMCID: PMC7323859 DOI: 10.1039/c9cc08817b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here, we developed a coralyne-based, 'light-up' intercalator displacement assay to identify molecular stabilizers of triplex DNA using a sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. Its potential to identify triplex DNA ligands was demonstrated using BePI and doxorubicin. Identification of triplex-interacting ligands may allow the regulation of genetic instability in human genomes.
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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, USA.
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14
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Sayoh I, Rusling DA, Brown T, Fox KR. DNA Structural Changes Induced by Intermolecular Triple Helix Formation. ACS OMEGA 2020; 5:1679-1687. [PMID: 32010842 PMCID: PMC6990630 DOI: 10.1021/acsomega.9b03776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/20/2019] [Indexed: 06/10/2023]
Abstract
DNase I footprints of intermolecular DNA triplexes are often accompanied by enhanced cleavage at the 3'-end of the target site at the triplex-duplex junction. We have systematically studied the sequence dependence of this effect by examining oligonucleotide binding to sites flanked by each base in turn. For complexes with a terminal T.AT triplet, the greatest enhancement is seen with ApC, followed by ApG and ApT, with the weakest enhancement at ApA. Similar DNase I enhancements were observed for a triplex with a terminal C+.GC triplet, though with little difference between the different GpN sites. Enhanced reactivity to diethylpyrocarbonate was observed at As that flank the triplex-duplex junction at AAA or AAC but not AAG or AAT. Fluorescence melting experiments demonstrated that the flanking base affected the stability with a 4 °C difference in T m between a flanking C and G. Sequences that produced the strongest enhancement correlated with those having the lower thermal stability. These results are interpreted in terms of oligonucleotide-induced changes in DNA structure and/or flexibility.
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Affiliation(s)
- Ibrahim Sayoh
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
| | - David A. Rusling
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
| | - Tom Brown
- Department
of Chemistry, University of Oxford, Oxford OX1 3TA, U.K.
| | - Keith R. Fox
- School
of Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, U.K.
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15
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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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16
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Carter MLJ, Rusling DA, Gurr S, Brown T, Fox KR. Stability of the different arms of a DNA tetrahedron and its interaction with a minor groove ligand. Biophys Chem 2019; 256:106270. [PMID: 31706136 DOI: 10.1016/j.bpc.2019.106270] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 10/02/2019] [Accepted: 10/02/2019] [Indexed: 11/27/2022]
Abstract
DNA strands can be designed to assemble into stable three-dimensional structures, based on Watson-Crick base pairing rules. The simplest of these is the DNA tetrahedron that is composed of four oligonucleotides. We have re-designed the sequence of a DNA tetrahedron so that it contains a single (AATT) binding site for the minor groove binding ligand Hoechst 33258. We examined the stability of this structure by placing fluorescent groups within each of its edges and have shown that all the edges melt at the same temperature in the absence of the ligand. The minor groove ligand still binds to its recognition sequence within the tetrahedron and increases the melting temperature of the folded complex. This ligand-induced stabilisation is propagated into the adjacent helical arms and the tetrahedron melts as a single entity in a cooperative fashion.
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Affiliation(s)
- Michael L J Carter
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - David A Rusling
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Steven Gurr
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom
| | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Keith R Fox
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, United Kingdom.
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17
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Ageeli AA, McGovern-Gooch KR, Kaminska MM, Baird NJ. Finely tuned conformational dynamics regulate the protective function of the lncRNA MALAT1 triple helix. Nucleic Acids Res 2019; 47:1468-1481. [PMID: 30462290 PMCID: PMC6379651 DOI: 10.1093/nar/gky1171] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 10/28/2018] [Accepted: 11/03/2018] [Indexed: 12/21/2022] Open
Abstract
Nucleic acid triplexes may regulate many important biological processes. Persistent accumulation of the oncogenic 7-kb long noncoding RNA MALAT1 is dependent on an unusually long intramolecular triple helix. This triplex structure is positioned within a conserved ENE (element for nuclear expression) motif at the lncRNA 3′ terminus and protects the entire transcript from degradation in a polyA-independent manner. A requisite 3′ maturation step leads to triplex formation though the precise mechanism of triplex folding remains unclear. Furthermore, the contributions of several peripheral structural elements to triplex formation and protective function have not been determined. We evaluated the stability, conformational fluctuations, and function of this MALAT1 ENE triple helix (M1TH) protective element using in vitro mutational analyses coupled with biochemical and biophysical characterizations. Using fluorescence and UV melts, FRET, and an exonucleolytic decay assay we define a concerted mechanism for triplex formation and uncover a metastable, dynamic triplex population under near-physiological conditions. Structural elements surrounding the triplex regulate the dynamic M1TH conformational variability, but increased triplex dynamics lead to M1TH degradation. Taken together, we suggest that finely tuned dynamics may be a general mechanism regulating triplex-mediated functions.
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Affiliation(s)
- Abeer A Ageeli
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
| | | | - Magdalena M Kaminska
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
| | - Nathan J Baird
- Department of Chemistry & Biochemistry, University of the Sciences, Philadelphia, PA 19143, USA
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18
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Thiazole orange – Spermine conjugate: A potent human telomerase inhibitor comparable to BRACO-19. Eur J Med Chem 2019; 175:20-33. [DOI: 10.1016/j.ejmech.2019.04.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/31/2019] [Accepted: 04/14/2019] [Indexed: 11/17/2022]
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19
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del Mundo IMA, Cho EJ, Dalby KN, Vasquez KM. A tunable assay for modulators of genome-destabilizing DNA structures. Nucleic Acids Res 2019; 47:e73. [PMID: 30949695 PMCID: PMC6648359 DOI: 10.1093/nar/gkz237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 03/21/2019] [Accepted: 03/25/2019] [Indexed: 11/24/2022] Open
Abstract
Regions of genomic instability are not random and often co-localize with DNA sequences that can adopt alternative DNA structures (i.e. non-B DNA, such as H-DNA). Non-B DNA-forming sequences are highly enriched at translocation breakpoints in human cancer genomes, representing an endogenous source of genetic instability. However, a further understanding of the mechanisms involved in non-B DNA-induced genetic instability is needed. Small molecules that can modulate the formation/stability of non-B DNA structures, and therefore the subsequent mutagenic outcome, represent valuable tools to study DNA structure-induced genetic instability. To this end, we have developed a tunable Förster resonance energy transfer (FRET)-based assay to detect triplex/H-DNA-destabilizing and -stabilizing ligands. The assay was designed by incorporating a fluorophore-quencher pair in a naturally-occurring H-DNA-forming sequence from a chromosomal breakpoint hotspot in the human c-MYC oncogene. By tuning triplex stability via buffer composition, the assay functions as a dual-reporter that can identify stabilizers and destabilizers, simultaneously. The assay principle was demonstrated using known triplex stabilizers, BePI and coralyne, and a complementary oligonucleotide to mimic a destabilizer, MCRa2. The potential of the assay was validated in a 384-well plate with 320 custom-assembled compounds. The discovery of novel triplex stabilizers/destabilizers may allow the regulation of genetic instability in human genomes.
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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, USA
| | - Eun Jeong Cho
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, USA
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin, Austin, TX, 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, USA
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20
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Bösch CD, Abay E, Langenegger SM, Nazari M, Cannizzo A, Feurer T, Häner R. DNA‐Organized Light‐Harvesting Antennae: Energy Transfer in Polyaromatic Stacks Proceeds through Interposed Nucleobase Pairs. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Caroline D. Bösch
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern, Switzerland
| | - Elif Abay
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern, Switzerland
| | - Simon M. Langenegger
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern, Switzerland
| | - Maryam Nazari
- Institute for Applied PhysicsUniversity of Bern Sidlerstrasse 5 CH-3012 Bern
| | - Andrea Cannizzo
- Institute for Applied PhysicsUniversity of Bern Sidlerstrasse 5 CH-3012 Bern
| | - Thomas Feurer
- Institute for Applied PhysicsUniversity of Bern Sidlerstrasse 5 CH-3012 Bern
| | - Robert Häner
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern, Switzerland
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21
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Walsh S, El-Sagheer AH, Brown T. Fluorogenic thiazole orange TOTFO probes stabilise parallel DNA triplexes at pH 7 and above. Chem Sci 2018; 9:7681-7687. [PMID: 30393529 PMCID: PMC6182420 DOI: 10.1039/c8sc02418a] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 07/30/2018] [Indexed: 12/20/2022] Open
Abstract
The instability of DNA triplexes particularly at neutral pH and above severely limits their applications. Here, we demonstrate that the introduction of a thiazole orange (TO) intercalator onto a thymine nucleobase in triplex forming oligonucleotides (TFOs) resolves this problem. The stabilising effects are additive; multiple TO units produce nanomolar duplex binding and triplex stability can surpass that of the underlying duplex. In one example, a TFO containing three TO units increased the triplex melting temperature at pH 7 by a remarkable 50 °C relative to the unmodified triplex. Notably, TO intercalation promotes TFO binding to target sequences other than pure polypurine tracts by the use of 5-(1-propynyl)cytosine (pC) against C:G inversions. By overcoming the instability of triplexes across a broad range of pH and sequence contexts, these very simple 'TOTFO' probes could expand triplex applications into many areas including diagnostics and cell imaging.
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Affiliation(s)
- Sarah Walsh
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- ATDBio Ltd. , Oxford Science Park , Oxford , UK
| | - Afaf Helmy El-Sagheer
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
- Chemistry Branch , Department of Science and Mathematics , Faculty of Petroleum and Mining Engineering , Suez University , Suez 43721 , Egypt
| | - Tom Brown
- Department of Chemistry , University of Oxford , Oxford , OX1 3TA , UK .
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22
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Marchand A, Rosu F, Zenobi R, Gabelica V. Thermal Denaturation of DNA G-Quadruplexes and Their Complexes with Ligands: Thermodynamic Analysis of the Multiple States Revealed by Mass Spectrometry. J Am Chem Soc 2018; 140:12553-12565. [PMID: 30183275 DOI: 10.1021/jacs.8b07302] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Designing ligands targeting G-quadruplex nucleic acid structures and affecting cellular processes is complicated because there are multiple target sequences and some are polymorphic. Further, structure alone does not reveal the driving forces for ligand binding. To know why a ligand binds, the thermodynamics of binding must be characterized. Electrospray mass spectrometry enables one to detect and quantify each specific stoichiometry (number of strands, cations, and ligands) and thus to simultaneously determine the equilibrium constants for each complex. Using a temperature-controlled nanoelectrospray source, we determined the temperature dependence of the equilibrium constants, and thus the enthalpic and entropic contributions to the formation of each stoichiometry. Enthalpy drives the formation of each quartet-K+-quartet unit, whereas entropy drives the formation of quartet-K+-triplet units. Consequently, slip-stranded structures can become more abundant as the temperature increases. In the presence of ligands (Phen-DC3, TrisQ, TMPyP4, Cu-ttpy), we observed that, even when only a 1:1 (ligand/quadruplex) complex is observed at room temperature, new states are populated at intermediate temperatures, including 2:1 complexes. In most cases, ligand-G4-quadruplex binding is entropically driven, and we discuss that this may have resulted from biases when ranking ligand potency using melting experiments. Other thermodynamic profiles could be linked to topology changes in terms of number of G-quartets (reflected in the number of specific K+ ions in the complex). The thermodynamics of ligand binding to each form, one ligand at a time, provides unprecedented detail on the interplay between ligand binding and topology changes in terms of number of G-quartets.
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Affiliation(s)
- Adrien Marchand
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Frédéric Rosu
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences , ETH Zurich , CH-8093 Zurich , Switzerland
| | - Valérie Gabelica
- Université de Bordeaux, INSERM U1212, CNRS UMR 5320, ARNA Laboratory, IECB, F-33600 Pessac , France
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23
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Basher MA, Rahman KM, Jackson PJM, Thurston DE, Fox KR. Sequence-selective binding of C8-conjugated pyrrolobenzodiazepines (PBDs) to DNA. Biophys Chem 2017; 230:53-61. [PMID: 28941814 DOI: 10.1016/j.bpc.2017.08.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 08/18/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
DNA footprinting and melting experiments have been used to examine the sequence-specific binding of C8-conjugates of pyrrolobenzodiazepines (PBDs) and benzofused rings including benzothiophene and benzofuran, which are attached using pyrrole- or imidazole-containing linkers. The conjugates modulate the covalent attachment points of the PBDs, so that they bind best to guanines flanked by A/T-rich sequences on either the 5'- or 3'-side. The linker affects the binding, and pyrrole produces larger changes than imidazole. Melting studies with 14-mer oligonucleotide duplexes confirm covalent attachment of the conjugates, which show a different selectivity to anthramycin and reveal that more than one ligand molecule can bind to each duplex.
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Affiliation(s)
- Mohammad A Basher
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - Paul J M Jackson
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - David E Thurston
- Institute of Pharmaceutical Science, King's College London, Franklin-Wilkins Building, Stamford Street, London SE1 9NH, UK
| | - Keith R Fox
- Biological Sciences, Life Sciences Building 85, University of Southampton, Southampton SO17 1BJ, UK.
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24
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Yeo QY, Loh IY, Tee SR, Chiang YH, Cheng J, Liu MH, Wang ZS. A DNA bipedal nanowalker with a piston-like expulsion stroke. NANOSCALE 2017; 9:12142-12149. [PMID: 28805877 DOI: 10.1039/c7nr03809g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Artificial molecular walkers beyond burn-bridge designs are important for nanotechnology, but their systematic development remains difficult. Herein, we have reported a new rationally designed DNA walker-track system and experimentally verified a previously proposed general expulsion regime for implementing non-burn-bridge nanowalkers. The DNA walker has an optically powered engine motif that reversibly extends and contracts the walker via a quadruplex-duplex conformational change. The walker's extension is an energy-absorbing and force-generating process, which drives the walker's leg dissociation off-track in a piston-like expulsion stroke. The unzipping-shearing asymmetry provides the expulsion stroke a bias, which decides the direction of the walker. Moreover, three candidate walkers of different sizes were fabricated. Fluorescence motility experiments indicated two of them as successful walkers and revealed a distinctive size dependence that was expected for these expulsive walkers, but was not observed in previously reported walkers. This study identifies unique technical requirements for expulsive nanowalkers. The present DNA design is readily adapted for making similar walkers from other molecules since the unzipping-shearing asymmetry is common.
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Affiliation(s)
- Q Y Yeo
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - I Y Loh
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - S R Tee
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - Y H Chiang
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - J Cheng
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - M H Liu
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.
| | - Z S Wang
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542. and NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore
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25
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Manna S, Panse CH, Sontakke VA, Sangamesh S, Srivatsan SG. Probing Human Telomeric DNA and RNA Topology and Ligand Binding in a Cellular Model by Using Responsive Fluorescent Nucleoside Probes. Chembiochem 2017; 18:1604-1615. [PMID: 28569423 PMCID: PMC5724660 DOI: 10.1002/cbic.201700283] [Citation(s) in RCA: 12] [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: 05/29/2017] [Indexed: 01/03/2023]
Abstract
The development of biophysical systems that enable an understanding of the structure and ligand-binding properties of G-quadruplex (GQ)-forming nucleic acid sequences in cells or models that mimic the cellular environment would be highly beneficial in advancing GQ-directed therapeutic strategies. Herein, the establishment of a biophysical platform to investigate the structure and recognition properties of human telomeric (H-Telo) DNA and RNA repeats in a cell-like confined environment by using conformation-sensitive fluorescent nucleoside probes and a widely used cellular model, bis(2-ethylhexyl) sodium sulfosuccinate reverse micelles (RMs), is described. The 2'-deoxy and ribonucleoside probes, composed of a 5-benzofuran uracil base analogue, faithfully report the aqueous micellar core through changes in their fluorescence properties. The nucleoside probes incorporated into different loops of H-Telo DNA and RNA oligonucleotide repeats are minimally perturbing and photophysically signal the formation of respective GQ structures in both aqueous buffer and RMs. Furthermore, these sensors enable a direct comparison of the binding affinity of a ligand to H-Telo DNA and RNA GQ structures in the bulk and confined environment of RMs. These results demonstrate that this combination of a GQ nucleoside probe and easy-to-handle RMs could provide new opportunities to study and devise screening-compatible assays in a cell-like environment to discover GQ binders of clinical potential.
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Affiliation(s)
- Sudeshna Manna
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Cornelia H. Panse
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Vyankat A. Sontakke
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Sarangamath Sangamesh
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
| | - Seergazhi G. Srivatsan
- Department of ChemistryIndian Institute of Science Education and Research (IISER)Dr. Homi Bhabha RoadPune411008India
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26
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Liu W, Wang S, Dotsenko IA, Samoshin VV, Xue L. Arylsulfanyl groups - Suitable side chains for 5-substituted 1,10-phenanthroline and nickel complexes as G4 ligands and telomerase inhibitors. J Inorg Biochem 2017; 173:12-20. [PMID: 28476011 DOI: 10.1016/j.jinorgbio.2017.04.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 04/14/2017] [Accepted: 04/21/2017] [Indexed: 01/03/2023]
Abstract
Guanine-rich DNA sequences can undergo self-assembly into unique G-quadruplex structures that interfere with the binding of proteins to the same DNA region. The formation of DNA G-quadruplexes requires monovalent cations (Na+ and K+) or small molecules known as G-quadruplex (G4) ligands. Phenanthroline is a type of G4 ligand scaffold known for its coordination with metal ions to form complexes with a large aromatic surface area, which aptly stack with G-quartets. In this report, we have investigated the side chain effect on G-quadruplex recognition by evaluating a series of 5-substituted phenanthroline-based metal complexes (Phen-Ni) binding to telomeric G-quadruplex DNA. Results from biophysical methods including fluorescence and circular dichroism (CD) thermal denaturation, CD titration, and the fluorescent intercalator displacement (FID) assay suggest that several Phen-Ni complexes bind to G-quadruplex DNA with submicromolar G4DC50 values. Arylsulfanyl groups at the 5 position of 1,10-phenanthroline are the best side chains regarding binding affinity and selectivity towards G-quadruplex DNA. Most of the G-quadruplex binding Phen-Ni complexes can inhibit telomerase activity in vitro as indicated by the telomeric repeat amplification protocol (TRAP) assay and such inhibition is clearly concentration dependent. Our results here provide a guidance of utilizing 5-substituted phenanthroline derivatives as a viable and facile approach to design novel G4 ligands.
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Affiliation(s)
- Wanbo Liu
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Siwen Wang
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Irina A Dotsenko
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Vyacheslav V Samoshin
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States
| | - Liang Xue
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, United States.
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27
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Munzar JD, Ng A, Corrado M, Juncker D. Complementary oligonucleotides regulate induced fit ligand binding in duplexed aptamers. Chem Sci 2017; 8:2251-2256. [PMID: 28507681 PMCID: PMC5408566 DOI: 10.1039/c6sc03993f] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1.8 to 0.7). To validate these unexpected findings, we developed a non-equilibrium surface-based assay that only signals induced fit binding, and corroborated the results from the solution-based assay. Our findings indicate that ACEs regulate ATP DA ligand binding dynamics, opening new avenues for the study and design of ligand-responsive nucleic acids.
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Affiliation(s)
- Jeffrey D Munzar
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Andy Ng
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - Mario Corrado
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
| | - David Juncker
- McGill University and Genome Quebec Innovation Centre , 740 Dr. Penfield Avenue , Montreal , Quebec H3A 0G1 , Canada .
- Department of Biomedical Engineering , McGill University , 3775 Rue University , Montreal , Quebec H3A 2B4 , Canada
- Department of Neurology and Neurosurgery , McGill University , 3801 Rue University , Montreal , Quebec H3A 2B4 , Canada
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28
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Saleh MM, Laughton CA, Bradshaw TD, Moody CJ. Development of a series of bis-triazoles as G-quadruplex ligands. RSC Adv 2017. [DOI: 10.1039/c7ra07257k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Maintenance of telomeres – specialized complexes that protect the ends of chromosomes – is provided by the enzyme complex telomerase, which is a key factor that is activated in more than 80% of cancer cells, but absent in most normal cells.
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Affiliation(s)
- Maysaa M. Saleh
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
| | - Charles A. Laughton
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
| | - Tracey D. Bradshaw
- School of Pharmacy
- Centre of Bimolecular Science
- University of Nottingham
- University Park
- Nottingham NG7 2RD
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29
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Chen Z, Zhang H, Ma X, Lin Z, Zhang L, Chen G. A novel fluorescent reagent for recognition of triplex DNA with high specificity and selectivity. Analyst 2016; 140:7742-7. [PMID: 26456316 DOI: 10.1039/c5an01852h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A fluorescent agent (DMT) was screened for recognizing triplex DNA with a specific and selective characteristic, which was embedded into the triplex DNA structure. The triplex DNA was firstly formed by a complementary target sequence through two distinct and sequential events. The conditions including pH and hybridization time, fluorescent agent concentration and embedding time were optimized in the experiment. Under the optimum conditions, the fluorescence signal was enhanced up to 9-fold in comparison with the DMT embedding into the ssDNA, dsDNA and G-quadruplexes. Under the same fluorescence conditions, the changes of the fluorescence signal were also investigated by several kinds of base mismatched DNAs in the experiment. The results showed that our biosensor provided excellent discrimination efficiency toward the perfectly mismatched target DNA with no formation of triplex DNA. We preliminarily deduced the mechanism of the fluorescent reagent for recognizing triplex DNA with high specificity and selectivity.
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Affiliation(s)
- Zongbao Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China. and Key Laboratory of Applied Organic Chemistry, College of Jiangxi Province Department of Chemistry, Shangrao Normal University, 334001, Jiangxi, China
| | - Huimi Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Xiaoming Ma
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Lan Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350002, China.
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30
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Kaserer T, Rigo R, Schuster P, Alcaro S, Sissi C, Schuster D. Optimized Virtual Screening Workflow for the Identification of Novel G-Quadruplex Ligands. J Chem Inf Model 2016; 56:484-500. [PMID: 26841201 DOI: 10.1021/acs.jcim.5b00658] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
G-quadruplexes, alternative DNA secondary structures present in telomeres, emerge as promising targets for the treatment of cancer, because they prevent telomere elongation and accordingly cell proliferation. Within this study, theoretically validated pharmacophore- and shape-based models as well as a theoretically validated docking protocol were generated and applied in parallel for virtual screening and the identification of novel G-quadruplex ligands. Top-ranked hits retrieved with all methods independently and in addition in a consensus approach were selected for biological testing. Of the 32 tested virtual hits seven selectively stabilized G-quadruplexes over duplex DNA in the fluorescence melting assay. For the five most active compounds, chemically closely related analogues were collected and subjected to in vitro analysis. Thereby, seven further novel G-quadruplex ligands could be identified. These molecules do not only represent novel scaffolds, but some of them are in addition even more potent G-quadruplex stabilizers than the established reference compound berberine. This study proposes an optimized in silico workflow for the identification of novel G-quadruplex stabilizers, which can also be applied in future studies. In addition, structurally novel and promising lead candidates with strong and selective G-quadruplex stabilizing properties are reported.
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Affiliation(s)
- Teresa Kaserer
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
| | - Riccardo Rigo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , via Marzolo 5, 35131 Padova, Italy
| | - Philipp Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università "Magna Graecia" di Catanzaro , Campus "S. Venuta", Viale Europa, 88100 Catanzaro, Italy
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova , via Marzolo 5, 35131 Padova, Italy
| | - Daniela Schuster
- Computer-Aided Molecular Design Group, Institute of Pharmacy/Pharmaceutical Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck , Innrain 80-82, 6020 Innsbruck, Austria
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31
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Chauhan A, Paladhi S, Debnath M, Dash J. Selective recognition of c-MYC G-quadruplex DNA using prolinamide derivatives. Org Biomol Chem 2016; 14:5761-7. [DOI: 10.1039/c6ob00177g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein we report the design, synthesis, biophysical and biological evaluation of triazole containing prolinamide derivatives as selectivec-MYCG-quadruplex binding ligands.
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Affiliation(s)
- Ajay Chauhan
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
| | - Sushovan Paladhi
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
| | - Manish Debnath
- Department of Organic Chemistry
- Indian Association for the Cultivation of Science
- Kolkata-700032
- India
| | - Jyotirmayee Dash
- Department of Chemical Sciences
- Indian Institute of Science Education and Research Kolkata
- Mohanpur
- India
- Department of Organic Chemistry
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32
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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33
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Castillo-González D, Mergny JL, De Rache A, Pérez-Machado G, Cabrera-Pérez MA, Nicolotti O, Introcaso A, Mangiatordi GF, Guédin A, Bourdoncle A, Garrigues T, Pallardó F, Cordeiro MNDS, Paz-y-Miño C, Tejera E, Borges F, Cruz-Monteagudo M. Harmonization of QSAR Best Practices and Molecular Docking Provides an Efficient Virtual Screening Tool for Discovering New G-Quadruplex Ligands. J Chem Inf Model 2015; 55:2094-110. [DOI: 10.1021/acs.jcim.5b00415] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daimel Castillo-González
- ARNA Laboratory, IECB, University of Bordeaux, F-33600 Pessac, France
- ARNA Laboratory,
INSERM, U869, F-33000 Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, IECB, University of Bordeaux, F-33600 Pessac, France
- ARNA Laboratory,
INSERM, U869, F-33000 Bordeaux, France
| | - Aurore De Rache
- ARNA Laboratory, IECB, University of Bordeaux, F-33600 Pessac, France
- ARNA Laboratory,
INSERM, U869, F-33000 Bordeaux, France
| | - Gisselle Pérez-Machado
- Molecular Simulation and
Drug Design Group, Centro de Bioactivos Químicos (CBQ), Central University of Las Villas, Santa Clara, Villa Clara 54830, Cuba
- Department of Physiology,
Faculty of Medicine, University of Valencia, Valencia 46010, Valencia, Spain
- Department
of Pharmacy and Pharmaceutical Technology, University of Valencia, Burjassot 46100, Valencia, Spain
| | - Miguel Angel Cabrera-Pérez
- Molecular Simulation and
Drug Design Group, Centro de Bioactivos Químicos (CBQ), Central University of Las Villas, Santa Clara, Villa Clara 54830, Cuba
- Department
of Pharmacy and Pharmaceutical Technology, University of Valencia, Burjassot 46100, Valencia, Spain
- Department of Engineering, Area of Pharmacy and Pharmaceutical
Technology, Miguel Hernández University, 03550 Sant Joan d’Alacant, Alicante, Alicante, Spain
| | - Orazio Nicolotti
- Dipartimento
di Farmacia-Scienze, Università degli Studi di Bari “Aldo Moro″, Via Orabona 4, 70125 Bari, Bari, Italy
| | - Antonellina Introcaso
- Dipartimento
di Farmacia-Scienze, Università degli Studi di Bari “Aldo Moro″, Via Orabona 4, 70125 Bari, Bari, Italy
| | - Giuseppe Felice Mangiatordi
- Dipartimento
di Farmacia-Scienze, Università degli Studi di Bari “Aldo Moro″, Via Orabona 4, 70125 Bari, Bari, Italy
| | - Aurore Guédin
- ARNA Laboratory, IECB, University of Bordeaux, F-33600 Pessac, France
- ARNA Laboratory,
INSERM, U869, F-33000 Bordeaux, France
| | - Anne Bourdoncle
- ARNA Laboratory, IECB, University of Bordeaux, F-33600 Pessac, France
- ARNA Laboratory,
INSERM, U869, F-33000 Bordeaux, France
| | - Teresa Garrigues
- Department
of Pharmacy and Pharmaceutical Technology, University of Valencia, Burjassot 46100, Valencia, Spain
| | - Federico Pallardó
- Department of Physiology,
Faculty of Medicine, University of Valencia, Valencia 46010, Valencia, Spain
| | | | - Cesar Paz-y-Miño
- Instituto de Investigaciones
Biomédicas (IIB), Universidad de Las Américas, 170513 Quito, Pichincha, Ecuador
| | - Eduardo Tejera
- Instituto de Investigaciones
Biomédicas (IIB), Universidad de Las Américas, 170513 Quito, Pichincha, Ecuador
| | | | - Maykel Cruz-Monteagudo
- Instituto de Investigaciones
Biomédicas (IIB), Universidad de Las Américas, 170513 Quito, Pichincha, Ecuador
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34
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Panda D, Debnath M, Mandal S, Bessi I, Schwalbe H, Dash J. A Nucleus-Imaging Probe That Selectively Stabilizes a Minor Conformation of c-MYC G-quadruplex and Down-regulates c-MYC Transcription in Human Cancer Cells. Sci Rep 2015; 5:13183. [PMID: 26286633 PMCID: PMC4541407 DOI: 10.1038/srep13183] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 07/17/2015] [Indexed: 12/27/2022] Open
Abstract
The c-MYC proto-oncogene is a regulator of fundamental cellular processes such as cell cycle progression and apoptosis. The development of novel c-MYC inhibitors that can act by targeting the c-MYC DNA G-quadruplex at the level of transcription would provide potential insight into structure-based design of small molecules and lead to a promising arena for cancer therapy. Herein we report our finding that two simple bis-triazolylcarbazole derivatives can inhibit c-MYC transcription, possibly by stabilizing the c-MYC G-quadruplex. These compounds are prepared using a facile and modular approach based on Cu(I) catalysed azide and alkyne cycloaddition. A carbazole ligand with carboxamide side chains is found to be microenvironment-sensitive and highly selective for "turn-on" detection of c-MYC quadruplex over duplex DNA. This fluorescent probe is applicable to visualize the cellular nucleus in living cells. Interestingly, the ligand binds to c-MYC in an asymmetric fashion and selects the minor-populated conformer via conformational selection.
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Affiliation(s)
- Deepanjan Panda
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Manish Debnath
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Samir Mandal
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
| | - Irene Bessi
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Harald Schwalbe
- Institute of Organic Chemistry and Chemical Biology, Goethe University Frankfurt and Centre for Biomolecular, Magnetic Resonance, Max-von-Laue Strasse 7, 60438, Frankfurt am Main, Germany
| | - Jyotirmayee Dash
- Department of Organic Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata-700032, India
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35
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Tanpure AA, Srivatsan SG. Conformation-sensitive nucleoside analogues as topology-specific fluorescence turn-on probes for DNA and RNA G-quadruplexes. Nucleic Acids Res 2015. [PMID: 26202965 PMCID: PMC4678839 DOI: 10.1093/nar/gkv743] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Development of probes that can discriminate G-quadruplex (GQ) structures and indentify efficient GQ binders on the basis of topology and nucleic acid type is highly desired to advance GQ-directed therapeutic strategies. In this context, we describe the development of minimally perturbing and environment-sensitive pyrimidine nucleoside analogues, based on a 5-(benzofuran-2-yl)uracil core, as topology-specific fluorescence turn-on probes for human telomeric DNA and RNA GQs. The pyrimidine residues of one of the loop regions (TTA) of telomeric DNA and RNA GQ oligonucleotide (ON) sequences were replaced with 5-benzofuran-modified 2′-deoxyuridine and uridine analogues. Depending on the position of modification the fluorescent nucleoside analogues distinguish antiparallel, mixed parallel-antiparallel and parallel stranded DNA and RNA GQ topologies from corresponding duplexes with significant enhancement in fluorescence intensity and quantum yield. Further, these GQ sensors enabled the development of a simple fluorescence binding assay to quantify topology- and nucleic acid-specific binding of small molecule ligands to GQ structures. Together, our results demonstrate that these nucleoside analogues are useful GQ probes, which are anticipated to provide new opportunities to study and discover efficient G-quadruplex binders of therapeutic potential.
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Affiliation(s)
- Arun A Tanpure
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India
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36
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Suzuki Y, Yokoyama K. Development of Functional Fluorescent Molecular Probes for the Detection of Biological Substances. BIOSENSORS 2015; 5:337-63. [PMID: 26095660 PMCID: PMC4493553 DOI: 10.3390/bios5020337] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 06/08/2015] [Accepted: 06/09/2015] [Indexed: 01/27/2023]
Abstract
This review is confined to sensors that use fluorescence to transmit biochemical information. Fluorescence is, by far, the most frequently exploited phenomenon for chemical sensors and biosensors. Parameters that define the application of such sensors include intensity, decay time, anisotropy, quenching efficiency, and luminescence energy transfer. To achieve selective (bio)molecular recognition based on these fluorescence phenomena, various fluorescent elements such as small organic molecules, enzymes, antibodies, and oligonucleotides have been designed and synthesized over the past decades. This review describes the immense variety of fluorescent probes that have been designed for the recognitions of ions, small and large molecules, and their biological applications in terms of intracellular fluorescent imaging techniques.
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Affiliation(s)
- Yoshio Suzuki
- Health Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, 1-1-1 Higashi, Tsukuba 305-8566, Japan.
| | - Kenji Yokoyama
- School of Bioscience and Biotechnology, Tokyo University of Technology, 1404-1 Katakura, Hachioji, Tokyo 192-0982, Japan.
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37
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Silvers R, Keller H, Schwalbe H, Hengesbach M. Differential Scanning Fluorimetry for Monitoring RNA Stability. Chembiochem 2015; 16:1109-14. [DOI: 10.1002/cbic.201500046] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Indexed: 11/05/2022]
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38
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Böttcher A, Kowerko D, Sigel RKO. Explicit analytic equations for multimolecular thermal melting curves. Biophys Chem 2015; 202:32-9. [PMID: 25910861 DOI: 10.1016/j.bpc.2015.04.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 11/19/2022]
Abstract
The analysis of thermal melting curves requires the knowledge of equations for the temperature dependence of the relative fraction of folded and unfolded components. To implement these equations as standard tools for curve fitting, they should be as explicit as possible. From the van't Hoff formalism it is known that the equilibrium constant and hence the folded fraction is a function of the absolute temperature, the van't Hoff transition enthalpy, and the melting temperature. The work presented here is devoted to the mathematically self-contained derivation and the listing of explicit equations for the folded fraction as a function of the thermodynamic parameters in the case of arbitrary molecularities. Part of the results are known, others are new. It is in particular shown for the first time that the folded fraction is the composition of a universal function which depends solely on the molecularity and a dimensionless function which is governed by the concrete thermodynamic regime but is independent of the molecularity. The results will prove useful for extracting the thermodynamic parameters from experimental data on the basis of regression analysis. As supporting information, open-source Matlab scripts for the computer implementation of the equations are provided.
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Affiliation(s)
- Albrecht Böttcher
- Chemnitz University of Technology, Department of Mathematics, 09107 Chemnitz, Germany.
| | - Danny Kowerko
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
| | - Roland K O Sigel
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, 8057 Zurich, Switzerland.
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39
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Das RN, Debnath M, Gaurav A, Dash J. Environment-Sensitive Probes Containing a 2,6-Diethynylpyridine Motif for Fluorescence Turn-On Detection and Induction of Nanoarchitectures of Human Telomeric Quadruplex. Chemistry 2014; 20:16688-93. [DOI: 10.1002/chem.201404795] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2014] [Indexed: 12/24/2022]
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40
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Ribeiro MM, Teixeira GS, Martins L, Marques MR, de Souza AP, Line SRP. G-quadruplex formation enhances splicing efficiency of PAX9 intron 1. Hum Genet 2014; 134:37-44. [PMID: 25204874 DOI: 10.1007/s00439-014-1485-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 08/25/2014] [Indexed: 11/25/2022]
Abstract
G-quadruplexes are secondary structures present in DNA and RNA molecules, which are formed by stacking of G-quartets (i.e., interaction of four guanines (G-tracts) bounded by Hoogsteen hydrogen bonding). Human PAX9 intron 1 has a putative G-quadruplex-forming region located near exon 1, which is present in all known sequenced placental mammals. Using circular dichroism (CD) analysis and CD melting, we showed that these sequences are able to form highly stable quadruplex structures. Due to the proximity of the quadruplex structure to exon-intron boundary, we used a validated double-reporter splicing assay and qPCR to analyze its role on splicing efficiency. The human quadruplex was shown to have a key role on splicing efficiency of PAX9 intron 1, as a mutation that abolished quadruplex formation decreased dramatically the splicing efficiency of human PAX9 intron 1. The less stable, rat quadruplex had a less efficient splicing when compared to human sequences. Additionally, the treatment with 360A, a strong ligand that stabilizes quadruplex structures, further increased splicing efficiency of human PAX9 intron 1. Altogether, these results provide evidences that G-quadruplex structures are involved in splicing efficiency of PAX9 intron 1.
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Affiliation(s)
- Mariana Martins Ribeiro
- Department of Morphology, Piracicaba Dental School, University of Campinas-UNICAMP, Piracicaba, SP, 13414-903, Brazil,
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41
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Rahman KM, Corcoran DB, Bui TTT, Jackson PJM, Thurston DE. Pyrrolobenzodiazepines (PBDs) do not bind to DNA G-quadruplexes. PLoS One 2014; 9:e105021. [PMID: 25133504 PMCID: PMC4136862 DOI: 10.1371/journal.pone.0105021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Accepted: 07/15/2014] [Indexed: 12/11/2022] Open
Abstract
The pyrrolo[2,1-c][1,4] benzodiazepines (PBDs) are a family of sequence-selective, minor-groove binding DNA-interactive agents that covalently attach to guanine residues. A recent publication in this journal (Raju et al, PloS One, 2012, 7, 4, e35920) reported that two PBD molecules were observed to bind with high affinity to the telomeric quadruplex of Tetrahymena glaucoma based on Electrospray Ionisation Mass Spectrometry (ESI-MS), Circular Dichroism, UV-Visible and Fluorescence spectroscopy data. This was a surprising result given the close 3-dimensional shape match between the structure of all PBD molecules and the minor groove of duplex DNA, and the completely different 3-dimensional structure of quadruplex DNA. Therefore, we evaluated the interaction of eight PBD molecules of diverse structure with a range of parallel, antiparallel and mixed DNA quadruplexes using DNA Thermal Denaturation, Circular Dichroism and Molecular Dynamics Simulations. Those PBD molecules without large C8-substitutents had an insignificant affinity for the eight quadruplex types, although those with large π-system-containing C8-substituents (as with the compounds evaluated by Raju and co-workers) were found to interact to some extent. Our molecular dynamics simulations support the likelihood that molecules of this type, including those examined by Raju and co-workers, interact with quadruplex DNA through their C8-substituents rather than the PBD moiety itself. It is important for the literature to be clear on this matter, as the mechanism of action of these agents will be under close scrutiny in the near future due to the growing number of PBD-based agents entering the clinic as both single-agents and as components of antibody-drug conjugates (ADCs).
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Affiliation(s)
- Khondaker M. Rahman
- Department of Pharmacy, Institute of Pharmaceutical Science, King's College London, London, United Kingdom
- * E-mail: (KMR); (DET)
| | - David B. Corcoran
- Department of Pharmacy, Institute of Pharmaceutical Science, King's College London, London, United Kingdom
| | - Tam T. T. Bui
- Department of Pharmacy, Institute of Pharmaceutical Science, King's College London, London, United Kingdom
| | - Paul J. M. Jackson
- Department of Pharmacy, Institute of Pharmaceutical Science, King's College London, London, United Kingdom
| | - David E. Thurston
- Department of Pharmacy, Institute of Pharmaceutical Science, King's College London, London, United Kingdom
- * E-mail: (KMR); (DET)
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42
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Chauhan A, Paladhi S, Debnath M, Mandal S, Das RN, Bhowmik S, Dash J. A small molecule peptidomimetic that binds to c-KIT1 G-quadruplex and exhibits antiproliferative properties in cancer cells. Bioorg Med Chem 2014; 22:4422-9. [DOI: 10.1016/j.bmc.2014.05.060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2014] [Revised: 05/19/2014] [Accepted: 05/28/2014] [Indexed: 10/25/2022]
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Su YC, Wang CH, Chang WH, Chen TY, Lee GB. Rapid and amplification-free detection of fish pathogens by utilizing a molecular beacon-based microfluidic system. Biosens Bioelectron 2014; 63:196-203. [PMID: 25089817 DOI: 10.1016/j.bios.2014.07.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 11/26/2022]
Abstract
Nervous necrosis virus (NNV) and iridovirus are highly infectious pathogens that can cause lethal diseases in various species of fish. These infectious diseases have no effective treatments and the mortality rate is over 80%, which could cause dramatic economic losses in the aquaculture industry. Conventional diagnostic methods of NNV or iridovirus infected fishes, such as virus culture, enzyme-linked immunosorbent assays and nucleic acid assays usually require time-consuming and complex procedures performed by specialized technicians with delicate laboratory facilities. Rapid, simple, accurate and on-site detection of NNV and iridovirus infections would enable timely preventive measures such as immediate sacrifice of infected fishes, and is therefore critically needed for the aquaculture industry. In this study, a microfluidic-based assay that employ magnetic beads conjugated with viral deoxyribonucleic acid (DNA) capturing probes and fluorescent DNA molecular beacons were developed to rapidly detect NNV and iridovirus. Importantly, this new assay was realized in an integrated microfluidic system with a custom-made control system. With this approach, direct and automated NNV and iridovirus detection from infected fishes can be achieved in less than 30 min. Therefore, this molecular-beacon based microfluidic system presents a potentially promising tool for rapid diagnosis of fish pathogens in the field in the future.
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Affiliation(s)
- Yi-Chih Su
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Wen-Hsin Chang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Tzong-Yueh Chen
- Institute of Biotechnology, National Cheng Kung University, Tainan 70101, Taiwan.
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Biomedical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of NanoEngineering and Microsystems, National Tsing Hua University, Hsinchu 30013, Taiwan.
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44
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Rusling DA, Fox KR. Sequence-specific recognition of DNA nanostructures. Methods 2014; 67:123-33. [PMID: 24583116 DOI: 10.1016/j.ymeth.2014.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 02/04/2014] [Accepted: 02/20/2014] [Indexed: 01/02/2023] Open
Abstract
DNA is the most exploited biopolymer for the programmed self-assembly of objects and devices that exhibit nanoscale-sized features. One of the most useful properties of DNA nanostructures is their ability to be functionalized with additional non-nucleic acid components. The introduction of such a component is often achieved by attaching it to an oligonucleotide that is part of the nanostructure, or hybridizing it to single-stranded overhangs that extend beyond or above the nanostructure surface. However, restrictions in nanostructure design and/or the self-assembly process can limit the suitability of these procedures. An alternative strategy is to couple the component to a DNA recognition agent that is capable of binding to duplex sequences within the nanostructure. This offers the advantage that it requires little, if any, alteration to the nanostructure and can be achieved after structure assembly. In addition, since the molecular recognition of DNA can be controlled by varying pH and ionic conditions, such systems offer tunable properties that are distinct from simple Watson-Crick hybridization. Here, we describe methodology that has been used to exploit and characterize the sequence-specific recognition of DNA nanostructures, with the aim of generating functional assemblies for bionanotechnology and synthetic biology applications.
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Affiliation(s)
- David A Rusling
- Centre for Biological Sciences and Institute for Life Sciences, Life Sciences Building 85, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
| | - Keith R Fox
- Centre for Biological Sciences and Institute for Life Sciences, Life Sciences Building 85, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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45
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Hégarat N, Novopashina D, Fokina AA, Boutorine AS, Venyaminova AG, Praseuth D, François JC. Monitoring DNA triplex formation using multicolor fluorescence and application to insulin-like growth factor I promoter downregulation. FEBS J 2014; 281:1417-1431. [DOI: 10.1111/febs.12714] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 12/30/2013] [Accepted: 01/08/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Nadia Hégarat
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Darya Novopashina
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Alesya A. Fokina
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Alexandre S. Boutorine
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Alya G. Venyaminova
- Laboratory of RNA Chemistry; Institute of Chemical Biology and Fundamental Medicine; Siberian Division of Russian Academy of Sciences; Novosibirsk Russia
| | - Danièle Praseuth
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
| | - Jean-Christophe François
- Acides nucléiques: dynamique, ciblage et fonctions biologiques; INSERM U565; Paris France
- Département Régulations, développement et diversité moléculaire; MNHN - CNRS UMR7196; Paris France
- Sorbonne Universités; UPMC Univ Paris 06; UMR_S 938; CDR Saint Antoine; Paris France
- Faculté de Médecine and Hôpital Saint Antoine; INSERM; UMR_S 938; CDR Saint Antoine; Paris France
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46
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Zamudio-Vázquez R, Albericio F, Tulla-Puche J, Fox KR. Thioester Bonds of Thiocoraline Can Be Replaced with NMe-Amide Bridges without Affecting Its DNA-Binding Properties. ACS Med Chem Lett 2014; 5:45-50. [PMID: 24900772 DOI: 10.1021/ml400323x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Accepted: 11/04/2013] [Indexed: 11/30/2022] Open
Abstract
In the search for new drug candidates for DNA recognition, affinity and sequence selectivity are two of the most important features. NMe-azathiocoraline, a synthetic antitumor bisintercalator derived from the natural marine product thiocoraline, shows similar potency to the parent compound, as well as possessing enhanced stability. Analysis of the DNA-binding selectivity of NMe-azathiocoraline by DNase I footprinting using universal substrates with all 136 tetranucleotides and all possible symmetrical hexanucleotide sequences revealed that, although this ligand binds to all CpG steps with lower affinities than thiocoraline, it displays additional binding to AT-rich sites. Moreover, fluorescence melting studies showed a strong interaction of the synthetic molecule with CACGTG and weaker binding to ACATGT and AGATCT. These findings demonstrate that NMe-azathiocoraline has the same mode of action as thiocoraline, mimicking its DNA-binding selectivity despite the substitution of its thioester bonds by NMe-amide bridges.
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Affiliation(s)
- Rubí Zamudio-Vázquez
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Fernando Albericio
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
- Department of Organic
Chemistry, Faculty of Chemistry, University of Barcelona, Martí
i Franquès 1-11, 08028 Barcelona, Spain
- School of Chemistry, University of KwaZulu-Natal, 4001 Durban, South Africa
| | - Judit Tulla-Puche
- Institute for Research in Biomedicine, Barcelona Science Park, Baldiri Reixac 10-12, 08028 Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Keith R. Fox
- Centre for Biological Sciences, Life Sciences Building
85, University of Southampton, Southampton SO17 1BJ, U.K
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47
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Percivalle C, Sissi C, Greco ML, Musetti C, Mariani A, Artese A, Costa G, Perrore ML, Alcaro S, Freccero M. Aryl ethynyl anthraquinones: a useful platform for targeting telomeric G-quadruplex structures. Org Biomol Chem 2014; 12:3744-54. [DOI: 10.1039/c4ob00220b] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
2,7-Diaryl ethynyl anthraquinones have been synthesized by Sonogashira cross-coupling and evaluated as telomeric G-quadruplex ligands, with good G-quadruplex/duplex selectivity.
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Affiliation(s)
| | - Claudia Sissi
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova, Italy
| | - Maria Laura Greco
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova, Italy
| | - Caterina Musetti
- Department of Pharmaceutical and Pharmacological Sciences
- 35131 Padova, Italy
| | | | - Anna Artese
- Dipartimento di Scienze della Salute
- Universitá di Catanzaro
- 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute
- Universitá di Catanzaro
- 88100 Catanzaro, Italy
| | | | - Stefano Alcaro
- Dipartimento di Scienze della Salute
- Universitá di Catanzaro
- 88100 Catanzaro, Italy
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48
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Yang Y, Endo M, Suzuki Y, Hidaka K, Sugiyama H. Direct observation of the dual-switching behaviors corresponding to the state transition in a DNA nanoframe. Chem Commun (Camb) 2014; 50:4211-3. [DOI: 10.1039/c4cc00489b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The dual-switching behaviors of photoresponsive DNAs and the G-quadruplex in the DNA nanoframe were successfully visualized by high-speed atomic force microscopy.
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Affiliation(s)
- Yangyang Yang
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
| | - Masayuki Endo
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501, Japan
- CREST
- Japan Science and Technology Corporation (JST)
| | - Yuki Suzuki
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
- CREST
| | - Kumi Hidaka
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry
- Graduate School of Science
- Kyoto University
- Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)
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49
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Kumar YP, Bhowmik S, Das RN, Bessi I, Paladhi S, Ghosh R, Schwalbe H, Dash J. A Fluorescent Guanosine Dinucleoside as a Selective Switch-On Sensor forc-mycG-Quadruplex DNA with Potent Anticancer Activities. Chemistry 2013; 19:11502-6. [DOI: 10.1002/chem.201302107] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Indexed: 02/01/2023]
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50
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Ikeda S, Yanagisawa H, Yuki M, Okamoto A. Fluorescent triplex-forming DNA oligonucleotides labeled with a thiazole orange dimer unit. ARTIFICIAL DNA, PNA & XNA 2013; 4:19-27. [PMID: 23445822 DOI: 10.4161/adna.24102] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescent probes for the detection of a double-stranded DNA were prepared by labeling a triplex-forming DNA oligonucleotide with a thiazole orange (TO) dimer unit. They belong to ECHO (exciton-controlled hybridization-sensitive fluorescent oligonucleotide) probes which we have previously reported. The excitonic interaction between the two TO molecules was expected to effectively suppress the background fluorescence of the probes. The applicability of the ECHO probes for the detection of double-stranded DNA was confirmed by examining the thermal stability and photophysical and kinetic properties of the DNA triplexes formed by the ECHO probes.
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Affiliation(s)
- Shuji Ikeda
- Advanced Science Institute, RIKEN, Saitama, Japan.
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