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https://www.readbyqxmd.com/read/27925323/synthesis-binding-properties-and-differences-on-cell-uptake-of-g-quadruplex-ligands-based-on-carbohydrate-naphthalene-diimide-conjugates
#1
Matilde Arevalo, Filippo Doria, Efres Belmonte-Reche, Aurore De Rache, Jenny Campos-Salinas, Ricardo Lucas, Eva Falomir, Miguel Carda, Jose María Pérez-Victoria, Jean-Louis Mergny, Mauro Freccero, Juan Carlos Morales
G-quadruplex (G4) are currently being explored as therapeutic targets in cancer and other pathologies. We have synthesized six carbohydrate naphthalene diimide conjugates (carb-NDIs) as G4 ligands to investigate their potential selectivity on G4 binding and on cell penetration. Carb-NDIs have shown certain selectivity for G4 structures against DNA duplexes but the different sugar moieties did not induce a preference for a specific G4 topology. Interestingly, when monosaccharides were attached through a short ethylene linker to the NDI scaffold their cellular uptake was 2-3 fold more efficient than when the sugar was directly attached through its anomeric position...
December 7, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27924036/folding-and-misfolding-pathways-of-g-quadruplex-dna
#2
Adrien Marchand, Valérie Gabelica
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K(+) binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K(+) at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923993/specific-targeting-of-telomeric-multimeric-g-quadruplexes-by-a-new-triaryl-substituted-imidazole
#3
Ming-Hao Hu, Shuo-Bin Chen, Bo Wang, Tian-Miao Ou, Lian-Quan Gu, Jia-Heng Tan, Zhi-Shu Huang
Multiple G-quadruplex units in the 3'-terminal overhang of human telomeric DNA can associate and form multimeric structures. The specific targeting of such distinctive higher-order G-quadruplexes might be a promising strategy for developing selective anticancer agents with fewer side effects. However, thus far, only a few molecules were found to selectively bind to telomeric multimeric G-quadruplexes, and their effects on cancer cells were unknown. In this study, a new triaryl-substituted imidazole derivative called IZNP-1: was synthesized and found to specifically bind to and strongly stabilize telomeric multimeric G-quadruplexes through intercalating into the pocket between the two quadruplex units...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27918050/self-assembled-pt2l2-boxes-strongly-bind-g-quadruplex-dna-and-influence-gene-expression-in-cancer-cells
#4
O Domarco, D Lötsch, J Schreiber, C Dinhof, S Van Schoonhoven, M D García, C Peinador, B K Keppler, W Berger, A Terenzi
Supramolecular Pt(ii) quadrangular boxes bind native and G-quadruplex DNA motifs in a size-dependent fashion. Three Pt molecular squares of distinct size show biological activity against cancer cells and heavily influence the expression of genes known to form G-quadruplexes in their promoter regions. The smallest Pt-box displays less activity but more selectivity for a quadruplex formed in the c-Kit gene.
December 5, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/27917615/design-synthesis-and-evaluation-of-2-9-bis-substituted-aminomethyl-phenyl-1-10-phenanthroline-derivatives-as-g-quadruplex-ligands
#5
Nassima Meriem Gueddouda, Miyanou Rosales Hurtado, Stéphane Moreau, Luisa Ronga, Rabindra Nath Das, Solène Savrimoutou, Sandra Rubio, Adrien Marchand, Oscar Mendoza, Mathieu Marchivie, Lilian Elmi, Albain Chansavang, Vanessa Desplat, Valérie Gabelica, Anne Bourdoncle, Jean-Louis Mergny, Jean Guillon
Genomic sequences able to form guanine quadruplexes (G4) are found in oncogene promoters, in telomeres and in 5' and 3' untranslated regions as well as introns of messenger RNAs. These regions are potential targets for drugs designed to treat cancer. In the present work, we present the design and syntheses of ten new phenantroline derivatives and characterization of their interactions with G4-forming oligonucleotides. We evaluated ligand-induced stabilization and specificity and selectivity of ligands for various G4 conformations using FRET-melting experiments...
December 4, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27915287/light-induced-oxidation-of-the-telomeric-g4-dna-in-complex-with-zn-ii-tetracarboxymethyl-porphyrin
#6
Artemy D Beniaminov, Roman A Novikov, Olga K Mamaeva, Vladimir A Mitkevich, Igor P Smirnov, Mikhail A Livshits, Anna K Shchyolkina, Dmitry N Kaluzhny
Structure-specific ligands are convenient tools for the recognition, targeting or probing of non-canonical DNA structures. Porphyrin derivatives exhibit a preference for interaction with G-quadruplex (G4) structures over canonical duplex DNA and are able to cause photoinducible damage to nucleic acids. Here, we show that Zn(II) 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium)porphyrin ( ZNP1: ) interacts with different conformations of the telomeric sequence d(TAGGG(TTAGGG)3) at submicromolar concentrations without any detectible disturbance of the particular fold...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913687/do-we-know-whether-potential-g-quadruplexes-actually-form-in-long-functional-rna-molecules
#7
REVIEW
Carika Weldon, Ian C Eperon, Cyril Dominguez
The roles of deoxyribonucleic acid (DNA) G-quadruplex structures in gene expression and telomere maintenance have been well characterized. Recent results suggest that such structures could also play pivotal roles in ribonucleic acid (RNA) biology, such as splicing or translation regulation. However, it has been difficult to show that RNA G-quadruplexes (G4s) exist in specific long RNA sequences, such as precursor messenger RNA, in a functional or cellular context. Most current methods for identifying G4s involve the use of short, purified RNA sequences in vitro, in the absence of competition with secondary structures or protein binding...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#8
Sara Lago, Elena Tosoni, Matteo Nadai, Manlio Palumbo, Sara N Richter
BACKGROUND: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS: Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding...
November 30, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27913190/synthesis-and-label-free-characterization-of-a-bimolecular-pna-homo-quadruplex
#9
Brunella Pinto, Giulia Rusciano, Stefano D'Errico, Nicola Borbone, Antonio Sasso, Vincenzo Piccialli, Luciano Mayol, Giorgia Oliviero, Gennaro Piccialli
BACKGROUND: G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS: The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS)...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27905517/g4ipdb-a-database-for-g-quadruplex-structure-forming-nucleic-acid-interacting-proteins
#10
Subodh Kumar Mishra, Arpita Tawani, Amit Mishra, Amit Kumar
Nucleic acid G-quadruplex structure (G4) Interacting Proteins DataBase (G4IPDB) is an important database that contains detailed information about proteins interacting with nucleic acids that forms G-quadruplex structures. G4IPDB is the first database that provides comprehensive information about this interaction at a single platform. This database contains more than 200 entries with details of interaction such as interacting protein name and their synonyms, their UniProt-ID, source organism, target name and its sequences, ∆Tm, binding/dissociation constants, protein gene name, protein FASTA sequence, interacting residue in protein, related PDB entries, interaction ID, graphical view, PMID, author's name and techniques that were used to detect their interactions...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902935/g-quadruplex-fluorescence-sensing-by-core-extended-naphthalene-diimides
#11
Michela Zuffo, Filippo Doria, Silvia Botti, Greta Bergamaschi, Mauro Freccero
BACKGROUND: Fluorescent sensing of G-quadruplex nucleic acids (G4s) is an effective strategy to elucidate their role in vitro and in vivo. Small molecule ligands have often been exploited, producing an emission light up upon binding. Naphthalene diimides (NDIs), although potent G4 binders exhibiting red-NIR fluorophores, have only been marginally exploited, as they are usually quenched upon binding. Contrary, aggregating core-extended naphthalene diimides (cex-NDIs) proved to be effective probes...
November 27, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27902437/development-validation-and-implementation-of-a-quadruplex-real-time-pcr-assay-for-identification-of-potentially-toxigenic-corynebacteria
#12
Aruni De Zoysa, Androulla Efstratiou, Ginder Mann, Timothy G Harrison, Norman K Fry
Toxigenic corynebacteria are uncommon in the UK, however laboratory confirmation by the national reference laboratory (NRL) can inform public health action according to national guidelines. Standard phenotypic tests for identification and toxin expression of isolates can take from ≥24 h to ≥48 h, from receipt. To decrease the time to result, a real-time PCR (qPCR) assay was developed for confirmation of both identification of Corynebacterium diphtheriae and Corynebacterium ulcerans/ Corynebacterium pseudotuberculosis and detection of the diphtheria toxin gene...
November 1, 2016: Journal of Medical Microbiology
https://www.readbyqxmd.com/read/27899628/a-single-molecule-study-of-a-fluorescently-labeled-telomestatin-derivative-and-g-quadruplex-interactions
#13
Parastoo Maleki, Yue Ma, Keisuke Iida, Kazuo Nagasawa, Hamza Balci
The potential use of G-quadruplex (GQ) stabilizing small molecules as anti-cancer drugs has created a flurry of activity on various aspects of these molecules. Telomestatin and oxazole telomestatin derivatives (OTD) are some of the most prominent of such molecules, yet the underlying dynamics of their interactions with GQ and the extent of heterogeneities in these interactions are not known. We performed single molecule measurements to study binding kinetics, rotational freedom, and dwell time distributions of a Cy5-labeled OTD (L1Cy5-7OTD) as it interacted with several different GQ structures...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899568/assembly-of-supramolecular-dna-complexes-containing-both-g-quadruplexes-and-i-motifs-by-enhancing-the-g-repeat-bearing-capacity-of-i-motifs
#14
Yanwei Cao, Shang Gao, Yuting Yan, Michael F Bruist, Bing Wang, Xinhua Guo
The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3' or 5' ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899264/cyclic-ferrocenylnaphthalene-diimide-derivative-as-a-new-class-of-g-quadruplex-dna-binding-ligand
#15
Md Monirul Islam, Shinobu Sato, Shingo Shinozaki, Shigeori Takenaka
To identify an effective ligand that binds to a G-quadruplex structure but not a double-stranded DNA (dsDNA), a set of biophysical and biochemical experiments were carried out using newly synthesized cyclic ferrocenylnaphthalene diimide (cFNDI, 1) or the non-cyclic derivative (2) with various structures of G-quadruplex DNAs and dsDNA. Compound 1 bound strongly to G-quadruplexes DNAs (10(6)M(-1) order) with diminished binding to dsDNA (10(4)M(-1) order) in 100mM AcOH-AcOK buffer (pH 5.5) containing 100mM KCl...
November 15, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27886600/a-lifetime-sensitive-fluorescence-anisotropy-probe-for-dna-based-bioassays-the-case-of-sybr-green
#16
Benoit Chovelon, Emmanuelle Fiore, Patrice Faure, Eric Peyrin, Corinne Ravelet
In standard steady-state fluorescence anisotropy (FA) DNA-based assays, the ligand binding to a given receptor is typically signalled by the rotational correlation time changes of the tracer. Herein, we report a radically different strategy that relies on the peculiar excited state lifetime features of the SYBR Green (SG) dye. This DNA-binding probe exhibits a drastically short lifetime in solution, leading to a high FA signal. Its complexation to oligonucleotides determines a singular and very large depolarization depending on the concerted effects of extreme lifetime enhancement and resonance energy homotransfer...
November 21, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27880931/an-xist-related-small-rna-regulates-kras-g-quadruplex-formation-beyond-x-inactivation
#17
Yuli C Chang, Chien-Chih Chiu, Chung-Yee Yuo, Wen-Ling Chan, Ya-Sian Chang, Wen-Hsin Chang, Shou-Mei Wu, Han-Lin Chou, Ta-Chih Liu, Chi-Yu Lu, Wen-Kuang Yang, Jan-Gowth Chang
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex...
November 17, 2016: Oncotarget
https://www.readbyqxmd.com/read/27880870/formation-and-processing-of-dna-damage-substrates-for-the-hneil-enzymes
#18
Aaron M Fleming, Cynthia J Burrows
Reactive oxygen species (ROS) are harnessed by the cell for signaling at the same time as being detrimental to cellular components such as DNA. The genome and transcriptome contain instructions that can alter cellular processes when oxidized. The guanine (G) heterocycle in the nucleotide pool, DNA, or RNA is the base most prone to oxidation. The oxidatively-derived products of G consistently observed in high yields from hydroxyl radical, carbonate radical, or singlet oxygen oxidations under conditions modeling the cellular reducing environment are discussed...
November 20, 2016: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/27877846/a-label-free-g-quadruplex-based-mercury-detection-assay-employing-the-exonuclease-iii-mediated-cleavage-of-t-hg-2-t-mismatched-dna
#19
Wanhe Wang, Tian-Shu Kang, Philip Wai Hong Chan, Jin-Jian Lu, Xiu-Ping Chen, Chung-Hang Leung, Dik-Lung Ma
We report herein the use of an exonuclease III and G-quadruplex probe to construct a G-quadruplex-based luminescence detection platform for Hg(2+). Unlike common DNA-based Hg(2+) detection methods, when using the dsDNA probe to monitor the hairpin formation, the intercalation of the dsDNA probe may be influenced by the distortion of dsDNA. This 'mix-and-detect' methodology utilized the G-quadruplex probe as the signal transducer and is simple, rapid, convenient to use and can detect down to 20 nM of Hg(2+).
December 2015: Science and Technology of Advanced Materials
https://www.readbyqxmd.com/read/27871228/genome-wide-analysis-of-g-quadruplexes-in-herpesvirus-genomes
#20
Banhi Biswas, Manish Kandpal, Utkarsh Kumar Jauhari, Perumal Vivekanandan
BACKGROUND: G-quadruplexes are increasingly recognized as regulatory elements in human, animal, bacterial and plant genomes. The presence and function of G-quadruplexes are not well studied among herpesviruses; in particular, there are no systematic genome-wide analysis of these important secondary structures in herpesvirus genomes. RESULTS: We performed genome-wide analysis of putative quadruplex sequences (PQS) in human herpesviruses. We found unusually high PQS densities among human herpesviruses...
November 21, 2016: BMC Genomics
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