Relevant bibliographies by topics / G quadruplex binding ligand

Academic literature on the topic 'G quadruplex binding ligand'

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Published: 10 December 2022
Last updated: 29 January 2023

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Journal articles on the topic "G quadruplex binding ligand"

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Neidle, Stephen. "Structured Waters Mediate Small Molecule Binding to G-Quadruplex Nucleic Acids." Pharmaceuticals 15, no. 1 (December 22, 2021): 7. http://dx.doi.org/10.3390/ph15010007.

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The role of G-quadruplexes in human cancers is increasingly well-defined. Accordingly, G-quadruplexes can be suitable drug targets and many small molecules have been identified to date as G-quadruplex binders, some using computer-based design methods and co-crystal structures. The role of bound water molecules in the crystal structures of G-quadruplex-small molecule complexes has been analyzed in this study, focusing on the water arrangements in several G-quadruplex ligand complexes. One is the complex between the tetrasubstituted naphthalene diimide compound MM41 and a human intramolecular telomeric DNA G-quadruplex, and the others are in substituted acridine bimolecular G-quadruplex complexes. Bridging water molecules form most of the hydrogen-bond contacts between ligands and DNA in the parallel G-quadruplex structures examined here. Clusters of structured water molecules play essential roles in mediating between ligand side chain groups/chromophore core and G-quadruplex. These clusters tend to be conserved between complex and native G-quadruplex structures, suggesting that they more generally serve as platforms for ligand binding, and should be taken into account in docking and in silico studies.
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Oblak, Domen, San Hadži, Črtomir Podlipnik, and Jurij Lah. "Binding-Induced Diversity of a Human Telomeric G-Quadruplex Stability Phase Space." Pharmaceuticals 15, no. 9 (September 15, 2022): 1150. http://dx.doi.org/10.3390/ph15091150.

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The structural polymorphism of G-quadruplex nucleic acids is an important factor in their recognition by proteins and small-molecule ligands. However, it is not clear why the binding of several ligands alters G-quadruplex topology. We addressed this question by following the (un)folding and binding of the human telomeric fragment 5′-(GGGTTA)3GGGT-3′ (22GT) by calorimetry (DSC, ITC) and spectroscopy (CD). A thermodynamic analysis of the obtained data led to a detailed description of the topological phase space of stability (phase diagram) of 22GT and shows how it changes in the presence of a specific bisquinolinium ligand (360A). Various 1:1 and 2:1 ligand–quadruplex complexes were observed. With increasing temperature, the 1:1 complexes transformed into 2:1 complexes, which is attributed to the preferential binding of the ligand to the folding intermediates. Overall, the dissection of the thermodynamic parameters in combination with molecular modelling clarified the driving forces of the topological quadruplex transformations in a wide range of ligand concentrations and temperatures.
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Santos, Tiago, Gilmar F. Salgado, Eurico J. Cabrita, and Carla Cruz. "G-Quadruplexes and Their Ligands: Biophysical Methods to Unravel G-Quadruplex/Ligand Interactions." Pharmaceuticals 14, no. 8 (August 5, 2021): 769. http://dx.doi.org/10.3390/ph14080769.

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Progress in the design of G-quadruplex (G4) binding ligands relies on the availability of approaches that assess the binding mode and nature of the interactions between G4 forming sequences and their putative ligands. The experimental approaches used to characterize G4/ligand interactions can be categorized into structure-based methods (circular dichroism (CD), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography), affinity and apparent affinity-based methods (surface plasmon resonance (SPR), isothermal titration calorimetry (ITC) and mass spectrometry (MS)), and high-throughput methods (fluorescence resonance energy transfer (FRET)-melting, G4-fluorescent intercalator displacement assay (G4-FID), affinity chromatography and microarrays. Each method has unique advantages and drawbacks, which makes it essential to select the ideal strategies for the biological question being addressed. The structural- and affinity and apparent affinity-based methods are in several cases complex and/or time-consuming and can be combined with fast and cheap high-throughput approaches to improve the design and development of new potential G4 ligands. In recent years, the joint use of these techniques permitted the discovery of a huge number of G4 ligands investigated for diagnostic and therapeutic purposes. Overall, this review article highlights in detail the most commonly used approaches to characterize the G4/ligand interactions, as well as the applications and types of information that can be obtained from the use of each technique.
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Nowak-Karnowska, Joanna, Agata Głuszyńska, Joanna Kosman, Grażyna Neunert, and Anna Dembska. "Interaction of 9-Methoxyluminarine with Different G-Quadruplex Topologies: Fluorescence and Circular Dichroism Studies." International Journal of Molecular Sciences 22, no. 19 (September 27, 2021): 10399. http://dx.doi.org/10.3390/ijms221910399.

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The interactions of G–quadruplexes of different topologies with highly fluorescent 9-methoxyluminarine ligand 9-MeLM were investigated by fluorescence and circular dichroism spectroscopy. The results showed that 9-methoxyluminarine was able to interact and did not destabilize any investigated molecular targets. The studied compound was selectively quenched by parallel c-MYC G-quadruplex DNA, whereas hybrid and antiparallel G4 topology caused only a negligible decrease in the fluorescence of the ligand. A high decrease of fluorescence of the ligand after binding with c-MYC G-quadruplex suggests that this molecule can be used as a selective probe for parallel G-quadruplexes.
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Hasegawa, Hijiri, Ikkei Sasaki, Kaori Tsukakoshi, Yue Ma, Kazuo Nagasawa, Shusuke Numata, Yuuki Inoue, Yeji Kim, and Kazunori Ikebukuro. "Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands." International Journal of Molecular Sciences 22, no. 23 (December 6, 2021): 13159. http://dx.doi.org/10.3390/ijms222313159.

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Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.
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Głuszyńska, Agata, Bernard Juskowiak, and Błażej Rubiś. "Binding Study of the Fluorescent Carbazole Derivative with Human Telomeric G-Quadruplexes." Molecules 23, no. 12 (November 30, 2018): 3154. http://dx.doi.org/10.3390/molecules23123154.

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The carbazole ligand 3 was synthesized, characterized and its binding interactions with human telomeric (22HT) G-quadruplex DNA in Na+ and K+-containing buffer were investigated by ultraviolet-visible (UV-Vis) spectrophotometry, fluorescence, circular dichroism (CD) spectroscopy, and DNA melting. The results showed that the studied carbazole ligand interacted and stabilized the intramolecular G-quadruplexes formed by the telomeric sequence in the presence of sodium and potassium ions. In the UV-Vis titration experiments a two-step complex formation between ligand and G-quadruplex was observed. Very low fluorescence intensity of the carbazole derivative in Tris HCl buffer in the presence of the NaCl or KCl increased significantly after addition of the 22HT G4 DNA. Binding stoichiometry of the ligand/G-quadruplex was investigated with absorbance-based Job plots. Carbazole ligand binds 22HT with about 2:1 stoichiometry in the presence of sodium and potassium ions. The binding mode appeared to be end-stacking with comparable binding constants of ~105 M−1 as determined from UV-Vis and fluorescence titrations data. The carbazole ligand is able to induce formation of G4 structure of 22HT in the absence of salt, which was proved by CD spectroscopy and melting studies. The derivative of carbazole 3 shows significantly higher cytotoxicity against breast cancer cells then for non-tumorigenic breast epithelial cells. The cytotoxic activity of ligand seems to be not associated with telomerase inhibition.
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Tsukakoshi, Kaori, Yuri Ikuta, Koichi Abe, Wataru Yoshida, Keisuke Iida, Yue Ma, Kazuo Nagasawa, Koji Sode, and Kazunori Ikebukuro. "Structural regulation by a G-quadruplex ligand increases binding abilities of G-quadruplex-forming aptamers." Chemical Communications 52, no. 85 (2016): 12646–49. http://dx.doi.org/10.1039/c6cc07552e.

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Bhadane, Rajendra, Rupali Bhadane, and Dhananjay Meshram. "Insights of potential G-quadruplex sequences in telomeres and proto-oncogenes." Archive of Oncology 21, no. 3-4 (2013): 118–24. http://dx.doi.org/10.2298/aoo1304118b.

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Guanine rich sequences have the ability to fold into stable 4 stranded structures called G-quadruplex under physiological concentrations of Na+ or K+. G-quadruplexes are found in telomeres, being stable structures under the control of telomerase binding proteins. They are also identified throughout the genome and are enriched in promoter regions of protein coding genes, upstream and downstream of the transcription initiation sites. A number of these promoter quadruplexes have been investigated for several proto-oncogenes. The formation of these quadruplexes can lead to chemical intervention of gene expression using a G-quadruplex binding ligand. We review location, configuration, and stabilization of these quadruplexes in some of the important promoters with regards to their potential as anticancer target.
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Moreira, David, Daniela Leitão, Jéssica Lopes-Nunes, Tiago Santos, Joana Figueiredo, André Miranda, Daniela Alexandre, Cândida Tomaz, Jean-Louis Mergny, and Carla Cruz. "G-Quadruplex Aptamer-Ligand Characterization." Molecules 27, no. 20 (October 11, 2022): 6781. http://dx.doi.org/10.3390/molecules27206781.

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In this work we explore the structure of a G-rich DNA aptamer termed AT11-L2 (TGGTGGTGGTTGTTGTTGGTGGTGGTGGT; derivative of AT11) by evaluating the formation and stability of G-quadruplex (G4) conformation under different experimental conditions such as KCl concentration, temperature, and upon binding with a variety of G4 ligands (360A, BRACO-19, PDS, PhenDC3, TMPyP4). We also determined whether nucleolin (NCL) can be a target of AT11-L2 G4. Firstly, we assessed by circular dichroism, UV and NMR spectroscopies the formation of G4 by AT11-L2. We observed that, for KCl concentrations of 65 mM or less, AT11-L2 adopts hybrid or multiple topologies. In contrast, a parallel topology predominates for buffer containing 100 mM of KCl. The Tm of AT11-L2 in 100 mM of KCl is 38.9 °C, proving the weak stability of this sequence. We also found that upon titration with two molar equivalents of 360A, BRACO-19 and PhenDC3, the G4 is strongly stabilized and its topology is maintained, while the addition of 3.5 molar equivalents of TMPyP4 promotes the disruption of G4. The KD values between AT11-L2 G4, ligands and NCL were obtained by fluorescence titrations and are in the range of µM for ligand complexes and nM when adding NCL. In silico studies suggest that four ligands bind to the AT11-L2 G4 structure by stacking interactions, while the RBD1,2 domains of NCL interact preferentially with the thymines of AT11-L2 G4. Finally, AT11-L2 G4 co-localized with NCL in NCL-positive tongue squamous cell carcinoma cell line.
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Desai, Nakshi, Viraj Shah, and Bhaskar Datta. "Assessing G4-Binding Ligands In Vitro and in Cellulo Using Dimeric Carbocyanine Dye Displacement Assay." Molecules 26, no. 5 (March 5, 2021): 1400. http://dx.doi.org/10.3390/molecules26051400.

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G-quadruplexes (G4) are the most actively studied non-canonical secondary structures formed by contiguous repeats of guanines in DNA or RNA strands. Small molecule mediated targeting of G-quadruplexes has emerged as an attractive tool for visualization and stabilization of these structures inside the cell. Limited number of DNA and RNA G4-selective assays have been reported for primary ligand screening. A combination of fluorescence spectroscopy, AFM, CD, PAGE, and confocal microscopy have been used to assess a dimeric carbocyanine dye B6,5 for screening G4-binding ligands in vitro and in cellulo. The dye B6,5 interacts with physiologically relevant DNA and RNA G4 structures, resulting in fluorescence enhancement of the molecule as an in vitro readout for G4 selectivity. Interaction of the dye with G4 is accompanied by quadruplex stabilization that extends its use in primary screening of G4 specific ligands. The molecule is cell permeable and enables visualization of quadruplex dominated cellular regions of nucleoli using confocal microscopy. The dye is displaced by quarfloxin in live cells. The dye B6,5 shows remarkable duplex to quadruplex selectivity in vitro along with ligand-like stabilization of DNA G4 structures. Cell permeability and response to RNA G4 structures project the dye with interesting theranostic potential. Our results validate that B6,5 can serve the dual purpose of visualization of DNA and RNA G4 structures and screening of G4 specific ligands, and adds to the limited number of probes with such potential.
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Dissertations / Theses on the topic "G quadruplex binding ligand"

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Marchand, Adrien. "Mass Spectrometry Study of G-Quadruplex Nucleic Acids : folding Pathways and Ligand Binding Modes." Thesis, Bordeaux, 2016. http://www.theses.fr/2016BORD0196/document.

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Un G-quadruplex (G4) est une structure non-canonique d’acides nucléiques formée par des séquences riches en guanines. Certains G4s sont polymorphiques, une même séquence peut former desG4s de différentes topologies. Les G4s sont proposés comme régulateurs de processus biologiques car ils sont trouvés dans des régions génomiques clés telles que dans des promoteurs de gènes et au niveau des télomères. Stabiliser ces G4s par rapport à la forme duplexe est une stratégie proposée pour combattre le cancer. Pour ce faire, des ligands spécifiques et affins sont utilisés. Le design de ces ligands implique habituellement de larges plans aromatiques, optimisés pour se lier par des interactions π-π sur les Gquartets extérieurs. Cependant, si ce type d’interaction était le seul mode de liaison, tous les ligands auraient des affinités similaires pour tous les G4s.Afin de caractériser les structures ciblées et de quelle manière les ligands vont interagir avec celles-ci, nous avons utilisé la spectrométrie de masse de type native (MS). D’abord, nous avons développé une méthode de préparation d’échantillons en conditions KCl pour former les G4s dans des conditions biologiquement pertinentes. Ensuite, nous avons caractérisé les équilibres de liaison du K+ aux G4s et caractérisé leur mécanisme de repliement. Ce mécanisme implique la présence d’une impasse constituée de G4s antiparallèles à 1- et 2-K+ qui sont formés rapidement. Enfin, nos études de liaison de ligands ont montré que certains des ligands les plus affins pouvaient influencer la structure des G4s comme observé par le nombre d’ions potassium liés. Les ligands Phen-DC3, 360A et PDS sont capables de déplacer les équilibres vers la forme à 1-K+ antiparallèle. La structure antiparallèle à 2-K+ est favorisée par la liaison coopérative de deux ligands Cu-ttpy. Ces résultats démontrent l’importance de la caractérisation des stoechiométries de complexes ternaires (G4:ligand:K+), obtenue par la spectrométrie de masse native
A G-quadruplex (G4) is a non-canonical nucleic acids structure formed by guanine-rich sequences. Some G4s are polymorphic, a given sequence can form G4s of different topologies. G4s are proposed to be biological regulators because they are found in key regions of the genome, for example, ingene promoters or at the telomeres. Stabilizing G4s formed in those regions as compared to the duplex form is a strategy to fight cancer. To do so, specific and affine ligands are used. Ligand design usually implies the optimization of large aromatic planes to π-π stack on external G-quartets. However, if this was the only binding mode, all ligands would bind with similar affinities to all G4s.To characterize which structures should be targeted and how the ligands interact with these structures, we used native mass spectrometry (MS).First, we developed a MS-compatible sample preparation method in KCl conditions in which G4s are folded with similar topologies as compared to those obtained in biologically relevant conditions. Then, we characterized the K+ binding equilibria and G4s folding pathways. This folding pathway involves the presence of a dead-end constituted by antiparallel G4s with either 1- or 2-K+ cations that are folded first. Finally, our ligand binding studies showed that some of the most affine ligands can influence G4’sstructures, as probed by the number of K+ ions bound. Ligands Phen-DC3, 360A and PDS are able to shift the equilibria towards the 1-K+ antiparallel G4s. The formation of antiparallel with 2-K+ complexes is induced by the cooperative binding of two Cu-ttpy ligands. Our results demonstrate the importance to characterize ternary complex stoichiometries (G4:ligand:K+) as obtained from native mass spectrometry
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Bai, Liping. "The noncovalent binding of benzophenathridine alkaloids to double-stranded, bulged and G-quadruplex DNA." HKBU Institutional Repository, 2008. http://repository.hkbu.edu.hk/etd_ra/910.

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Bright, Lois Eleanor. "Ligands and complexes for non-covalent binding to G-quadruplex DNA structures." Thesis, University of Birmingham, 2017. http://etheses.bham.ac.uk//id/eprint/7457/.

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The structure, occurrence and biological relevance of G-quadruplex DNA structures has been reviewed, along with a review of several notable G-quadruplex binding compounds published in the literature to date. The synthetic route towards two G-quadruplex DNA binders previously developed within the Hannon group has been modified and improved. Electrospray ionisation mass spectrometry studies have been carried out to evaluate nucleotide binding. The in vitro biological activities of these compounds have been validated against the human ovarian carcinoma cell line A2780 via MTT and comet assays, flow cytometry and inductively coupled plasma mass spectrometry. Both compounds and the corresponding metal-free ligand exhibited higher drug efficiencies than cisplatin against A2780 cells. Both compounds display mild genotoxicity and induce G2/M phase cell cycle arrest. The overall cellular uptake and nuclear localisation demonstrated by both complexes exceeds that of cisplatin. A new class of palladium and platinum(II) complexes have been synthesised from methylthio-substituted terpyridine ligands. In addition to assessing their stability in solution via UV-Vis spectroscopy, initial DNA binding studies with both duplex and quadruplex-forming sequences of DNA have been carried out via circular dichroism and gel electrophoresis. The design and synthesis of alternative ligand systems proffering a range of desirable characteristics to aid future ligand and complex development has been investigated.
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Pipier, Angélique. "Etudes des G-quadruplexes : impact de la stabilisation par des ligands en tant qu'agents anti-cancéreux et identification des protéines associées régulant leur métabolisme." Thesis, Toulouse 3, 2020. http://www.theses.fr/2020TOU30118.

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Les G-quadruplexes (ou G4) sont des structures non canoniques des acides nucléiques formées à partir de séquences riches en guanines. Les G4 sont des structures stables, présentes sur l'ensemble du génome et qui peuvent adopter différentes conformations. La formation des G4 peut réguler, de façon positive ou négative, différents processus cellulaires tels que la transcription, la réplication, les transactions des ARN et les mécanismes mitochondriaux. L'ensemble de ces processus nécessite le recrutement de protéines capables de moduler la formation de ces structures. Certaines protéines, telles que les hélicases BLM, WRN ou DHX36, sont capables de dérouler les G4 alors que d'autres, comme la nucléoline (NCL), se lient aux G4 et les stabilisent. Enfin, des molécules capables de stabiliser les G4 appelées ligands de G4, peuvent impacter divers processus dans lesquels sont impliqués les G4 ; en particulier, ils peuvent entrainer la répression de l'expression d'oncogènes et mener à de l'instabilité génomique. Ainsi, les ligands de G4 sont considérés comme de potentiels agents anti-cancéreux. Mes travaux de thèses s'articulent autour de plusieurs problématiques concernant les G4 : 1/ l'amélioration des ligands de G4 et leur caractérisation ; 2/ le décryptage des mécanismes induisant de l'instabilité génomique suite à la stabilisation des G4 par des ligands ; 3/ l'identification des protéines capables de se lier aux G4 (ou GBP pour " G4 Binding Proteins "). Par des expériences biochimiques et biophysiques, j'ai participé à la caractérisation de ligands dérivés de porphyrine. Dans le cas du ligand AuMA, j'ai montré une augmentation à la fois de la capacité de stabilisation des G4 et de la spécificité envers les G4, par rapport à d'autres molécules dérivées de porphyrine. Cette molécule représente donc un meilleur potentiel thérapeutique que le TMPyP4, ligand largement étudié, dont elle est dérivée. J'ai également étudié l'instabilité génomique due à la stabilisation des G4 grâce à l'utilisation du ligand pyridostatine et du ligand CX5461, actuellement en phase II d'un essai clinique. Ces ligands induisent des cassures double brin de l'ADN (ou CDB) dépendantes de la transcription par l'ARN polymérase II et partiellement dues à la pause transcriptionnelle. Les CDB sont initiées par l'activité des Topoisomérases II, enzymes impliquées dans la résolution des stress topologiques de l'ADN dus à la transcription et à la réplication. Ces résultats montrent le rôle important de la transcription dans l'induction de l'instabilité génomique et ouvrent de nouvelles pistes thérapeutiques, dans le traitement de cancers dans lesquels ces protéines sont surexprimées ou par la combinaison avec d'autres chimiothérapies telles que l'étoposide afin d'en augmenter le potentiel cytotoxique. J'ai étudié les protéines se liant aux G4 grâce à des structures contraintes, bloquées dans une conformation particulière, en mettant au point un protocole de détection des GBP par des expériences de "Pull-Down" suivie d'une analyse par spectrométrie de masse. Ces résultats, validés par la liaison aux G4 de protéines déjà identifiées et caractérisées telles que WRN, DHX36 ou encore CNBP, ont permis l'identification de 425 GBP. Ainsi, j'ai mis en évidence de nouvelles GBP impliquées dans divers processus cellulaires tels que la réplication, la réparation de l'ADN, la transcription et le métabolisme des ARN. De façon annexe, l'étude de la protéine CNBP dans un modèle animal a permis de montrer que la régulation des G4 in vivo impacte la transcription et le développement embryonnaire, renforçant le rôle des G4 dans des organismes vivants. Mes travaux contribuent à étendre les connaissances sur les G4 et leurs ligands, particulièrement celles portant sur les mécanismes d'action des G4 pendant la transcription, et ouvrent de nouvelles perspectives thérapeutiques
G-quadruplexes (or G4) are non-canonical structures of nucleic acid formed from guanine-rich sequences. G4 are stable structures, present throughout the genome and could be folded into different conformations. G4 formation can regulate, positively or negatively, different cellular processes such as transcription, replication, RNA transactions and mitochondrial mechanisms. All these processes require the recruitment of proteins able to modulate the formation of these structures. Indeed, some proteins, such as BLM, WRN or DHX36 helicases, are able to unwind G4 while others, like nucleolin (NCL), bind to and stabilize G4. Finally, G4 ligands, small molecules stabilizing G4, can impact various processes in which G4 are involved; in particular, they can cause repression of oncogene expression and lead to genomic instability. Thus, G4 ligands are considered to be potential anti-cancer agents. My thesis work focuses on several issues concerning G4: 1/ the improvement of G4 ligands and their characterization; 2/ the deciphering of the mechanisms inducing genomic instability following G4 stabilization by ligands; 3/ the identification of proteins able to bind to G4 (or GBPs for "G4 Binding Proteins"). Through biochemical and biophysical experiments, I have participated in the characterization of porphyrin-derived ligands. In the case of the AuMA ligand, I showed an increase in both G4 stabilization capacity and G4 specificity, compared to other porphyrin-derived molecules. This molecule therefore represents a better therapeutic potential than TMPyP4, a widely characterized ligand from which it is derived. I have also studied the genomic instability due to G4 stabilization using the pyridostatin ligand and the CX5461 ligand, currently in Phase II of a clinical trial. These ligands induce DNA double-strand breaks (or DSBs) dependent on transcription by RNA polymerase II and partly due to the transcriptional pausing. DSBs are initiated by the activity of Topoisomerases II, enzymes involved in the resolution of DNA topological stresses due to transcription and replication. These results show the significant role of transcription in the induction of genomic instability and open up new therapeutic approaches in the treatment of cancers in which these proteins are overexpressed or by combining them with other chemotherapies such as etoposide to increase their cytotoxic potential. I have studied G4-binding proteins using constrained structures, blocked in a particular conformation, by developing a protocol for the detection of GBPs through Pull-Down experiments followed by mass spectrometry analysis. These results, validated by the binding to G4 of proteins already identified and characterized such as WRN, DHX36 or CNBP, allow the identification of 425 GBP. Thus, I have highlighted new GBPs involved in various cellular processes such as replication, DNA repair, transcription and RNA metabolism. Aside, the study of CNBP protein in a zebrafish model has shown that the regulation of G4 in vivo affects transcription and embryonic development, reinforcing the role of G4 in whole living organisms. My work contributes to extend the knowledge of G4 and their ligands, particularly the mechanisms of action of G4 during transcription, and is opening up new therapeutic perspectives
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Schouten, James Alexander. "Probing selective G-quadruplex binding using peptide motifs." Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620018.

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Kerkour, Abdelaziz. "Study of DNA G-quadruplex structures by Nuclear Magnetic Resonance (NMR)." Thesis, Bordeaux, 2014. http://www.theses.fr/2014BORD0292/document.

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Les G-quadruplexes (G4) sont des structures d'acides nucléiques non-canoniques formées par des séquences riches en Guanines (G) principalement localisées dans les telomères et les régions promotrices des oncogènes. Elles sont constituées de l'empilement de plusieurs tétrades de G en présence de cations. En utilisant la spectroscopie par RMN, nous avons caractérisé l'interaction entre le ligand TAP et le G4 télomérique humain constituée de la séquence d(AG3(T2AG3)3). CD et RMN 1D 1H ont été utilisés pour suivre l'interaction entre les deux partenaires. RMN 2D a été utilisé pour attribuer sans ambiguïté toutes les résonances de 1H dans le complexe et d'explorer le site d'interaction. Un modèle illustrant l'interaction de TAP avec 22AG au niveau des sillons et boucles a été généré. Une autre partie de ce travail consiste en l'étude du G4 tétra-moléculaire formé par TG4T et son interaction avec des ligands G4 par la RMN dans les cellules. Des spectres 1H-15N HMQC ont été effectués à l'intérieur de Xenopus laevis et les lysats des cellules HeLa et comparés avec ceux observés dans les conditions in vitro ce qui a montré une bonne stabilité de G4 à l'intérieur de la cellule. En outre, l'interaction de d [TG4T]4 avec des ligands spécifiques de G4 présentant trois différents modes d'interaction a également été étudiée. Le ligand 360A a montré un comportement prometteur. Enfin, dans la dernière partie, différentes séquences de promoteur Kras ont été criblés par RMN pour sélectionner des candidats pour la détermination de structure haute résolution. Deux séquences différentes ont été sélectionnées et caractérisées par spectroscopie CD. La stabilisation des structures G4 formées par ces séquences en interaction avec différents ligands a également été étudiée. Une titration RMN 1D 1H entre 22RT et le ligand Braco19 a montré un comportement intéressant de k-ras G4 par la formation d'espèces intermédiaires lors de l'addition de Braco19
G-quadruplexes (G4) are non-canonical nucleic acid structures formed by G-rich sequences mainly localized in telomeres and promoter regions of oncogenes. They are built from the stacking of several G-quartets in the presence of cations. Using NMR spectroscopy, we have characterized the interaction between the TAP ligand and the human telomeric G4 formed by the sequence d(AG3(T2AG3)3). CD and 1D 1H NMR spectroscopy were used to follow the interaction between the two partners. 2D NMR was used to assign unambiguously all 1H resonances in the complex and to explore the binding site. A model depicting the interaction of TAP with 22AG in grooves and loops was generated. Another part of this work consists in the study of tetramolecular G4 formed by TG4T and its interaction with G4 ligands by in-cell NMR. 1H-15N HMQC spectra were performed inside Xenopus laevis and HeLa cell lysates compared to those observed in vitro conditions showing a good stability of G4 inside the cell. Furthermore, the interaction of d[TG4T]4 with three G4 specific ligands presenting different mode of interaction was also investigated. The ligand 360A showed a promising behavior. Finally, in the last part, different sequences of Kras promoter were screened by NMR to select good candidates for high resolution structure determination. Two different sequences were selected and characterized by CD spectroscopy. The stabilization of G4 structures formed by these sequences in interaction with different ligands was also investigated. A 1D 1H NMR titration between Braco19 and 22RT showed an interesting behavior of k-ras G4 by the formation of intermediate species upon the addition of Braco19
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Campbell, Nancy Husni. "Crystallographic and Molecular Modelling Studies of G-Quadruplex-Ligand complexes." Thesis, University College London (University of London), 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.515056.

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Koirala, Deepak P. "Mechanochemistry, Transition Dynamics and Ligand-Induced Stabilization of Human Telomeric G-Quadruplexes at Single-Molecule Level." Kent State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=kent1397919270.

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Qin, Yong. "Targeting the Promoter Regions of PDGF Ligand and Receptor." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/194387.

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Aberrant expression of Platelet-derived growth factor A (PDGF-A) and PDGF receptor-β (PDGFR-β) play critical roles in the angiogenesis and proliferation of several malignancies. In this dissertation I explore the transcriptional regulatory role of the Gquadruplex- forming regions in the promoters of human PDGF-A and PDGFR-β, and identify new targets for developing small molecules to modulate their expression in tumors. For PDGF-A promoter, our studies focus on two essential nuclease hypersensitive elements, NHE(PDGF-A) and 5´-end far upstream 5´-SHS. The structural aspects of the intramolecular G-quadruplexes formed in NHE(PDGF-A) and the ligands to stabilize these secondary DNA structures have been investigated by using singlestranded and duplex DNA of the NHE(PDGF-A). We demonstrate that the G-quadruplexinteractive compound, TMPyP4, can selectively inhibit the basal promoter activity of PDGF-A, suggesting that the NHE(PDGF-A) G-quadruplex acts as a repressor in PDGF-A transcription. We also found that the 5´-SHS G-rich strand oligomer can invade the NHE(PDGF-A) and form a unique three-stranded complex in supercoiled plasmids, which is facilitated by potassium ions and TMPyP4. Therefore, we propose a novel molecular mechanism for transcriptional silencing of the NHE(PDGF-A) by 5´-SHS in the PDGF-A promoter, in that the formation of G-quadruplex in the NHE(PDGF-A) provides a platform for the G-rich strand of 5´-SHS to invade and form a partial duplex DNA with the C-rich strand of the NHE(PDGF-A), resulting in displacement of hnRNP K and thus transcription silencing. Prior to the studies describe here, the promoter of human PDGFR-β had not been identified. Herein, we have cloned and characterized the first functional promoter of human PDGFR-β gene. A crucial highly GC-rich region (NHE(PDGFR-β)) in the human PDGFR-β promoter has been identified by its hypersensitivity to the S1 nuclease. Further studies demonstrate that stable G-quadruplex structures can form in the G-rich strand of NHE(PDGFR-β). The G-quadruplex-interactive molecule, telomestatin, can selectively stabilize G-quadruplexes formed in the human PDGFR-β promoter and inhibit its expression in Daoy cells. On the basis of these results, we propose that ligandmediated stabilization of the G-quadruplex structure in the proximal promoter region of human PDGF-A or PDGFR-β can be used to modulate the expression of these protooncogenes.
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Patel, Sachin Dinesh. "Studies on a designed G-quadruplex binding protein that inhibits human telomerase." Thesis, University of Cambridge, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.620939.

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Books on the topic "G quadruplex binding ligand"

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Affinity and Efficacy. World Scientific Publishing Company, 2011.

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Mason, Peggy. Receiving the Synaptic Message. Oxford University Press, 2017. http://dx.doi.org/10.1093/med/9780190237493.003.0013.

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Ionotropic and metabotropic receptors differ in their speed of action, the variety of effects produced after ligand-binding, and in the number of types present in the nervous system. The participation of two ionotropic glutamate receptors in synaptic plasticity is thought to be the cellular basis of learning. The actions of acetylcholine on nicotinic acetylcholine receptors present at the neuromuscular junction are described. The pharmacological profile of the GABAA receptor, central to most neural functions, is introduced. The properties of metabotropic receptors that are coupled to G proteins, termed G protein-coupled receptors (GPCRs), are detailed. Three canonical second-messenger systems through which GPCRs act are briefly described. An introduction to clinical pharmacology focused on how drugs acting on muscarinic and adrenergic receptors produce peripheral and central psychotropic effects is provided. Finally, the role of connexins and gap junctions in myelination and hearing is introduced.
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Book chapters on the topic "G quadruplex binding ligand"

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Giancola, Concetta, and Bruno Pagano. "Energetics of Ligand Binding to G-Quadruplexes." In Topics in Current Chemistry, 211–42. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/128_2012_347.

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Asamitsu, Sefan. "Simultaneous Binding of Hybrid Molecules Constructed with Dual DNA-Binding Components to a G-Quadruplex and Its Proximal Duplex." In Development of Selective DNA-Interacting Ligands, 85–109. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-7716-1_4.

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Deng, Nanjie. "Using Molecular Dynamics Free Energy Simulation to Compute Binding Affinities of DNA G-Quadruplex Ligands." In Methods in Molecular Biology, 177–99. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9666-7_10.

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Dettler, Jamie M., and Edwin A. Lewis. "Biophysical Studies of the Structure, Stability, and Ligand Binding Properties of G-Quadruplex DNA: Thoughts and Comparisons of the K-ras, c-MYC, and Bcl-2 Oncogene Promoter Sequence Quadruplexes." In ACS Symposium Series, 33–50. Washington, DC: American Chemical Society, 2011. http://dx.doi.org/10.1021/bk-2011-1082.ch003.

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Oyoshi, Takanori. "Characterization of G-Quadruplex DNA- and RNA-Binding Protein." In Long Noncoding RNAs, 57–65. Tokyo: Springer Japan, 2015. http://dx.doi.org/10.1007/978-4-431-55576-6_4.

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Haider, Shozeb, and Stephen Neidle. "Molecular Modeling and Simulation of G-Quadruplexes and Quadruplex-Ligand Complexes." In Methods in Molecular Biology, 17–37. Totowa, NJ: Humana Press, 2009. http://dx.doi.org/10.1007/978-1-59745-363-9_2.

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Lee, Chun-Ying, Christina McNerney, and Sua Myong. "G-Quadruplex and Protein Binding by Single-Molecule FRET Microscopy." In Methods in Molecular Biology, 309–22. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9666-7_18.

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Simon, Philipp, Philipp Schult, and Katrin Paeschke. "Binding and Modulation of G-quadruplex DNA and RNA Structures by Proteins." In Handbook of Chemical Biology of Nucleic Acids, 1–24. Singapore: Springer Nature Singapore, 2022. http://dx.doi.org/10.1007/978-981-16-1313-5_102-1.

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Dean, William L., Robert D. Gray, Lynn DeLeeuw, Robert C. Monsen, and Jonathan B. Chaires. "Putting a New Spin of G-Quadruplex Structure and Binding by Analytical Ultracentrifugation." In Methods in Molecular Biology, 87–103. New York, NY: Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9666-7_5.

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Lee, Hui Sun, and Wonpil Im. "G-LoSA for Prediction of Protein-Ligand Binding Sites and Structures." In Methods in Molecular Biology, 97–108. New York, NY: Springer New York, 2017. http://dx.doi.org/10.1007/978-1-4939-7015-5_8.

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Conference papers on the topic "G quadruplex binding ligand"

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Oliviero, Giorgia, Jussara Amato, Stefano D'Errico, Gennaro Piccialli, Patrick Mailliet, Frédéric Rosu, Edwin De Pauw, and Valérie Gabelica. "Ligand binding to tetra-end-linked (TGGGGT)4 G-quadruplexes: an electrospray mass spectrometry study." In XIVth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2008. http://dx.doi.org/10.1135/css200810333.

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Morel, Elodie, Florence Mahuteau-Betzer, Florian Hamon, Corinne Guetta, and Marie-Paule Teulade-Fichou. "Exploration of metal terpyridine complexes for G-quadruplex DNA binding." In XVIth Symposium on Chemistry of Nucleic Acid Components. Prague: Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 2014. http://dx.doi.org/10.1135/css201414328.

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Lin, Clement, Guanhui Wu, Kaibo Wang, Buket Onel, Saburo Sakai, and Danzhou Yang. "Abstract 1856: Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.sabcs18-1856.

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Lin, Clement, Guanhui Wu, Kaibo Wang, Buket Onel, Saburo Sakai, and Danzhou Yang. "Abstract 1856: Targeting human telomeres by binding of epiberberine to telomeric G-quadruplex." In Proceedings: AACR Annual Meeting 2019; March 29-April 3, 2019; Atlanta, GA. American Association for Cancer Research, 2019. http://dx.doi.org/10.1158/1538-7445.am2019-1856.

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Folini, Marco, Nicola I. Orlotti, Graziella Cimino-Reale, Erika Borghini, Maria Grazia Daidone, Manlio Palumbo, Claudia Sissi, and Nadia Zaffaroni. "Abstract A26: Autophagy acts as a safeguard mechanism against G-quadruplex ligand-mediated telomere damage." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics--Nov 12-16, 2011; San Francisco, CA. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1535-7163.targ-11-a26.

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Cobanoglu, Murat Can, Ugur Sezerman, and Nermin Pinar Karabulut. "Determinig the ligand-specific regions of peptide-binding G-Protein Coupled Receptors." In 2010 5th International Symposium on Health Informatics and Bioinformatics. IEEE, 2010. http://dx.doi.org/10.1109/hibit.2010.5478880.

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Babakuliyev, Alisir, Niladri Maiti, Annie Aglin Antony, Mohammad Javed Ansari, Santosh S. Chobe, and Chandra Kumar Dixit. "Detection of Cancer Cells Using G-Rich DNA Based Target Binding-Switching Calorimetric Biosensor." In International Conference on Recent Advancements in Biomedical Engineering. Switzerland: Trans Tech Publications Ltd, 2022. http://dx.doi.org/10.4028/p-3o604e.

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This paper reports the G-rich ssDNA for the colorimetric detection of cancer cells. The ssDNA-1 sequence has explored for the potential application of “Turn-On” colorimetric sensor for selective and sensitive detection of cancer cells. While complementary G-rich DNA strand form G-quadruplex with hemin molecule, which is more effective to catalyze the peroxidase mimicking activity towards TMB chromogenic substrate. The ssDNA-1 exhibits good selectivity for cancer cells. The colorimetric intensity of TMB was enhanced upon interaction of leukemic lymphoblasts cancer cells. The effect of pH has turned the selective sensing performances of the biosensor for detecting cancer cells with a lower detection limit of 0.54 nM, 0.18 nM, and 0.2 nM respectively.
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Porru, Manuela, Simona Artuso, Luca Pompili, Carla Caruso, Armandodoriano Bianco, Marcella Mottolese, Carla A. Amoreo, Annamaria Biroccio, and Carlo Leonetti. "Abstract 266: The G-quadruplex ligand EMICORON potentiates the antitumor efficacy of chemotherapy on colon cancer experimental models." In Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-266.

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Miyazaki, Takeshi, Yang Pan, Bin Hu, Habibe Demir, Kaushal Joshi, Sachiko Okabe, Takao Yamori, et al. "Abstract 3302: The effects of the g-quadruplex ligand telomestatin to human brain tumor stem cell survival and growth." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-3302.

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Beauvarlet, J., P. Ben Sadoun, G. Labrunie, RN Das, E. Richard, B. Rousseau, E. Darbo, S. Croce, JL Mergny, and M. Djavaheri-Mergny. "PO-446 Anti-tumour efficiency of 20A, a novel G-quadruplex ligand, inin vitroandin vivocancer models: ATM and autophagy interplay." In Abstracts of the 25th Biennial Congress of the European Association for Cancer Research, Amsterdam, The Netherlands, 30 June – 3 July 2018. BMJ Publishing Group Ltd, 2018. http://dx.doi.org/10.1136/esmoopen-2018-eacr25.469.

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Reports on the topic "G quadruplex binding ligand"

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Ebbinghaus, Scot W. Evaluation of the G-quadruplex Binding Drug Telomestatin as an Inhibitor of c-myb in Chronic Myelogenous Leukemia. Fort Belvoir, VA: Defense Technical Information Center, February 2007. http://dx.doi.org/10.21236/ada587004.

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Ebbinghaus, Scot W. Evaluation of the G-quadruplex Binding Drug Telomestatin as an Inhibitor of c-myb in Chronic Myelogenous Leukemia. Fort Belvoir, VA: Defense Technical Information Center, February 2007. http://dx.doi.org/10.21236/ada593319.

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Rafaeli, Ada, and Russell Jurenka. Molecular Characterization of PBAN G-protein Coupled Receptors in Moth Pest Species: Design of Antagonists. United States Department of Agriculture, December 2012. http://dx.doi.org/10.32747/2012.7593390.bard.

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The proposed research was directed at determining the activation/binding domains and gene regulation of the PBAN-R’s thereby providing information for the design and screening of potential PBAN-R-blockers and to indicate possible ways of preventing the process from proceeding to its completion. Our specific aims included: (1) The identification of the PBAN-R binding domain by a combination of: (a) in silico modeling studies for identifying specific amino-acid side chains that are likely to be involved in binding PBAN with the receptor and; (b) bioassays to verify the modeling studies using mutant receptors, cell lines and pheromone glands (at tissue and organism levels) against selected, designed compounds to confirm if compounds are agonists or antagonists. (2) The elucidation ofthemolecular regulationmechanisms of PBAN-R by:(a) age-dependence of gene expression; (b) the effect of hormones and; (c) PBAN-R characterization in male hair-pencil complexes. Background to the topic Insects have several closely related G protein-coupled receptors (GPCRs) belonging to the pyrokinin/PBAN family, one with the ligand pheromone biosynthesis activating neuropeptide or pyrokinin-2 and another with diapause hormone or pyrokinin-1 as a ligand. We were unable to identify the diapause hormone receptor from Helicoverpa zea despite considerable effort. A third, related receptor is activated by a product of the capa gene, periviscerokinins. The pyrokinin/PBAN family of GPCRs and their ligands has been identified in various insects, such as Drosophila, several moth species, mosquitoes, Triboliumcastaneum, Apis mellifera, Nasoniavitripennis, and Acyrthosiphon pisum. Physiological functions of pyrokinin peptides include muscle contraction, whereas PBAN regulates pheromone production in moths plus other functions indicating the pleiotropic nature of these ligands. Based on the alignment of annotated genomic sequences, the primary and secondary structures of the pyrokinin/PBAN family of receptors have similarity with the corresponding structures of the capa or periviscerokinin receptors of insects and the neuromedin U receptors found in vertebrates. Major conclusions, solutions, achievements Evolutionary trace analysisof receptor extracellular domains exhibited several class-specific amino acid residues, which could indicate putative domains for activation of these receptors by ligand recognition and binding. Through site-directed point mutations, the 3rd extracellular domain of PBAN-R was shown to be critical for ligand selection. We identified three receptors that belong to the PBAN family of GPCRs and a partial sequence for the periviscerokinin receptor from the European corn borer, Ostrinianubilalis. Functional expression studies confirmed that only the C-variant of the PBAN-R is active. We identified a non-peptide agonist that will activate the PBAN-receptor from H. zea. We determined that there is transcriptional control of the PBAN-R in two moth species during the development of the pupa to adult, and we demonstrated that this transcriptional regulation is independent of juvenile hormone biosynthesis. This transcriptional control also occurs in male hair-pencil gland complexes of both moth species indicating a regulatory role for PBAN in males. Ultimate confirmation for PBAN's function in the male tissue was revealed through knockdown of the PBAN-R using RNAi-mediated gene-silencing. Implications, both scientific and agricultural The identification of a non-peptide agonist can be exploited in the future for the design of additional compounds that will activate the receptor and to elucidate the binding properties of this receptor. The increase in expression levels of the PBAN-R transcript was delineated to occur at a critical period of 5 hours post-eclosion and its regulation can now be studied. The mysterious role of PBAN in the males was elucidated by using a combination of physiological, biochemical and molecular genetics techniques.
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