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G quadruplex

Pramod M Sabale, Arun A Tanpure, Seergazhi G Srivatsan
Double-stranded segments of a genome that can potentially form G-quadruplex (GQ) and/or i-motif (iM) structures are considered to be important regulatory elements. Hence, the development of a common probe that can detect GQ and iM structures and also distinguish them from a duplex structure will be highly useful in understanding the propensity of such segments to adopt duplex or non-canonical four-stranded structures. Here, we describe the utility of a conformation-sensitive fluorescent nucleoside analog, which was originally developed as a GQ sensor, in detecting the iM structures of C-rich DNA oligonucleotides (ONs)...
May 21, 2018: Organic & Biomolecular Chemistry
Viktoria Rakers, Paolo Cadinu, Joshua B Edel, Ramon Vilar
Guanine-rich DNA sequences can fold into quadruple-stranded structures known as G-quadruplexes. These structures have been proposed to play important biological roles and have been identified as potential drug targets. As a result, there is increasing interest in developing small molecules that can bind to G-quadruplexes. So far, these efforts have been mostly limited to conventional batch synthesis. Furthermore, no quick on-line method to assess new G-quadruplex binders has been developed. Herein, we report on two new microfluidic platforms to: (a) readily prepare G-quadruplex binders (based on metal complexes) in flow, quantitatively and without the need for purification before testing; (b) a microfluidic platform (based on FRET melting assays of DNA) that enables the real-time and on-line assessment of G-quadruplex binders in continuous flow...
April 14, 2018: Chemical Science
Zhanmin Liu, Chenhui Yao, Cuiyun Yang, Yanming Wang, Sibao Wan, Junyi Huang
Listeria monocytogenes is an important food-borne pathogen, and it can cause severe diseases. Rapid detection of L. monocytogenes is crucial to control this pathogen. A simple and robust strategy based on the cascade of PCR and G-quadruplex DNAzyme catalyzed reaction was used to detect L. monocytogenes. In the presence of hemin and the aptamer formed during PCR, the catalytic horseradish peroxidase-mimicking G-quadruplex DNAzymes allow the colorimetric responses of target DNA from L. monocytogenes. This assay can detect genomic DNA of L...
May 16, 2018: Analytical Biochemistry
Krishnashish Bose, Christopher J Lech, Brahim Heddi, Anh Tuân Phan
We investigate the self-assembly of short pieces of the Tetrahymena telomeric DNA sequence d[G4 T2 G4 ] in physiologically relevant aqueous solution using atomic force microscopy (AFM). Wire-like structures (G-wires) of 3.0 nm height with well-defined surface periodic features were observed. Analysis of high-resolution AFM images allowed their classification based on the periodicity of these features. A major species is identified with periodic features of 4.3 nm displaying left-handed ridges or zigzag features on the molecular surface...
May 17, 2018: Nature Communications
Wareed Ahmed, Joachim Lingner
Telomerase counteracts telomere shortening and cellular senescence in germ, stem, and cancer cells by adding repetitive DNA sequences to the ends of chromosomes. Telomeres are susceptible to damage by reactive oxygen species (ROS), but the consequences of oxidation of telomeres on telomere length and the mechanisms that protect from ROS-mediated telomere damage are not well understood. In particular, 8-oxoguanine nucleotides at 3' ends of telomeric substrates inhibit telomerase in vitro, whereas, at internal positions, they suppress G-quadruplex formation and were therefore proposed to promote telomerase activity...
May 17, 2018: Genes & Development
Qian Zhu, Lanhua Liu, Yunpeng Xing, Xiaohong Zhou
To meet the severe water pollution status, multi-target biosensor becomes one of research focus. We herein report a novel duplex functional fluorescent biosensor for the label-free and separate detection of Pb2+ and Hg2+ with high sensitivity and selectivity. A K+ -induced fluorescent G-quadruplex probe was assembled by a guanine-rich sequence (AGRO100) and N-methyl mesoporphyrin IX(NMM). It changed into a more stably non-fluorescent G-quadruplex structure and a hairpin-like structure upon binding Pb2+ and Hg2+ ions, respectively...
May 1, 2018: Journal of Hazardous Materials
Y-Q Zhang, J-H Pei, S-S Shi, J Zheng, J-M Wang, X-S Guo, G-Y Cui, X-Y Wang, H-P Zhang, W-Q Hu
OBJECTIVE: To investigate the expression of G-quadruplex antibody BG4 in human gastric cancer AGS cells and assess its functions in attenuating proliferation and promoting apoptosis in gastric cancer. MATERIALS AND METHODS: BG4 high-expression gastric cancer AGS cell line was established by pEGFP-N1-BG4 transient transfection. AGS cells transfected with pEGFP-N1 plasmids were included into the pEGFP-N1 group and those not transfected with plasmids were included into the negative control group...
May 2018: European Review for Medical and Pharmacological Sciences
Yang Chen, Jine Wang, Yajie Zhang, Lijun Xu, Tian Gao, Bing Wang, Renjun Pei
Aptamers are short single-stranded DNA or RNA, which can be selected in vitro by systematic evolution of ligands by exponential enrichment (SELEX). In order to develop novel light-up probes to substitute G-quadruplex (G4), we selected a DNA aptamer for crystal violet (CV), a triphenylmethane light-up dye, by a modified affinity chromatography-based SELEX. The ssDNA pool was first coupled on streptavidin-coated agarose beads through a biotin labeled complementary oligonucleotide, and then the aptamer sequences would be released from agarose beads by CV affinity...
May 17, 2018: Photochemical & Photobiological Sciences
Enrique Victor García-España, Isabel Pont, Jorge González-García, Mario Inclán, Matthew Reynolds, Estefanía Delgado-Pinar, M Teresa Albelda, Ramon Vilar
A new series of triphenylamine-based ligands with one (TPA1PY), two (TPA2PY) or three pending aza-macrocycle(s) (TPA3PY) have been synthesised and studied by means of pH-metric titrations, UV/Vis spectroscopy and fluorescence experiments. The affinity of these ligands for G-quadruplex (G4) DNA and its selectivity over duplex DNA were investigated by FRET melting assays, fluorimetric titrations and circular dichroism (CD) spectroscopy. Interestingly, the interaction of the bi- and specially the tri-branched ligand with G4 leads to a very intense red-shifted fluorescence emission band which may be associated with intermolecular aggregation between the molecule and the DNA...
May 16, 2018: Chemistry: a European Journal
Debasish Dutta, Manish Debnath, Diana Müller, Rakesh Paul, Tania Das, Irene Bessi, Harald Schwalbe, Jyotirmayee Dash
The structural differences among different G-quadruplexes provide an opportunity for site-specific targeting of a particular G-quadruplex structure. However, majority of G-quadruplex ligands described thus far show little selectivity among different G-quadruplexes. In this work, we delineate the design and synthesis of a crescent-shaped thiazole peptide that preferentially stabilizes c-MYC quadruplex over other promoter G-quadruplexes and inhibits c-MYC oncogene expression. Biophysical analysis such as Förster resonance energy transfer (FRET) melting and fluorescence spectroscopy show that the thiazole peptide TH3 can selectively interact with the c-MYC G-quadruplex over other investigated G-quadruplexes and duplex DNA...
May 14, 2018: Nucleic Acids Research
Pablo Armas, Nora Beatriz Calcaterra
During animal development, gene expression is orchestrated by specific and highly evolutionarily conserved mechanisms that take place accurately, both at spatial and temporal levels. The last decades have provided compelling evidence showing that chromatin state plays essential roles in orchestrating most of the stages of development. The DNA molecule can adopt alternative structures different from the helical duplex architecture. G-rich DNA sequences can fold as intrastrand quadruple helix structures called G-quadruplexes or G4-DNA...
May 11, 2018: Mechanisms of Development
Kefeng Wu, Changbei Ma, Han Zhao, Hailun He, Hanchun Chen
Ochratoxin A (OTA) is one of the most common mycotoxins contaminating feed and foodstuffs. Therefore, a great deal of concern is associated with AFB1 toxicity. In this work, a fast and sensitive fluorescence aptamer biosensor has been proposed for the OTA assay. In the absence of OTA, the OTA aptamer can form a G-quadruplex structure with thioflavin T (ThT) dye, which results in increased fluorescence. After joining OTA, OTA aptamer combines with OTA and the G-quadruplex can be formed. Only faint fluorescence was finally observed when ThT weakly reacts with the quadruplex...
May 12, 2018: Toxins
Beatrice Karg, Klaus Weisz
A G-quadruplex forming sequence from the MYC promoter region was modified with syn-favoring 8-bromo-2'-deoxyguanosine residues. Depending on the number and position of modifications in the intramolecular parallel G-quadruplex, substitutions with the bromoguanosine analog at the 5'-tetrad induce conformational rearrangements with concerted all-anti to all-syn transitions for all residues of the modified G-quartet. No unfavorable steric interactions of the C8-substituents in the medium grooves are apparent in the high-resolution structure as determined for a tetrasubstituted MYC quadruplex that exclusively forms the all-syn isomer...
May 14, 2018: Chemistry: a European Journal
Pingdan Yan, Yixiong Hao, Zhaoche Shu, Chunling Gu, Xiaomei Zhou, Xiaoyu Liu, Hua Xiang
The authors describe a novel assay for the detection of methylated DNA site. Rolling circle amplification and CdSe/ZnS quantum dots with high fluorescence efficiency are applied in this method. The CdSe/ZnS quantum dots act as electron donors, and hemin and oxygen (derived from hydrogen peroxide act as acceptors in photoinduced electron transfer. The assay, best performed at excitation/emission peaks of 450/620 nm, is sensitive and specific. Fluorometric response is linear in the 1 pM to 100 nM DNA concentration range, and the lowest detectable concentration of methylated DNA is 142 fM (S/N = 3)...
May 13, 2018: Mikrochimica Acta
Yong Liu, Jiahui Fan, Haitang Yang, Ensheng Xu, Wei Wei, Yuanjian Zhang, Songqin Liu
The cellular enzyme poly ADP (ADP: adenosine diphosphate)-ribose polymerase-1 (PARP-1) plays key roles in DNA repair. Its activity is closely related to various cancer developments. Detection of PARP-1 activity is significant, however, it is relatively difficult since it lacks superiority property that can be used to detect conveniently. PARP-1 lead to the synthesis of hyperbranched poly (ADP-ribose) polymers (PAR) using nicotinamide adenine dinucleotide (NAD+ ) as substrate during DNA damage repairing. In this paper, we found that hyper-branched PAR increased the steric hindrance and reduced the flux of probe ions effectively in anodic aluminum oxide (AAO) nanochannels...
May 4, 2018: Biosensors & Bioelectronics
Jinbo Zhu, Zhiqiang Yan, Weijun Zhou, Chuanbo Liu, Jin Wang, Erkang Wang
Thioflavin T (ThT) was once regarded to be a specific fluorescent probe for the human telomeric G-quadruplex, but more other kinds of DNA were found that can also bind to ThT in recent years. Herein, we focus on G-rich parallel-stranded DNA and utilize fluorescence, absorbance, circular dichroism and surface plasmon resonance spectroscopy to investigate its interaction with ThT. Pyrene label and molecular modelling are applied to unveil the binding mechanism. We find a new class of non-G-quadruplex G-rich parallel-stranded (ps) DNA with the sequence of TG(GA)n can bind to ThT and increase the fluorescence with an enhancement ability superior to G-quadruplex...
May 11, 2018: ACS Sensors
Antonella Virgilio, Teresa Amato, Luigi Petraccone, Francesca Esposito, Nicole Grandi, Enzo Tramontano, Raquel Romero, Shozeb Haider, Isabel Gomez-Monterrey, Ettore Novellino, Luciano Mayol, Veronica Esposito, Aldo Galeone
In this paper, we report our investigations on analogues of the anti-human immunodeficiency virus type 1 (HIV-1) integrase (IN) aptamer T30175 in which the individual thymidines forming the loops were replaced by 5-hydroxymethyl-2'-deoxyuridine residues (H). Circular dichroism, nuclear magnetic resonance and gel electrophoresis investigations clearly indicated that all the modified aptamers preserve the ability to form the original 5'-5' end-stacked head-to-head dimeric G-quadruplex structure, in which each G-quadruplex adopts a parallel arrangement and is characterized by three G-tetrads, three propeller loops and one bulge-loop...
May 10, 2018: Scientific Reports
Agata Głuszyńska, Bernard Juskowiak, Martyna Kuta-Siejkowska, Marcin Hoffmann, Shozeb Haider
The binding affinities of three carbazole derivatives to the intramolecular G-quadruplex (GQ) DNA formed by the sequence 5′-AGGGAGGGCGCTGGGAGGAGGG-3′, derived from the c-KIT 1 oncogene region, were investigated. All carbazole cationic ligands that differed in the substituents on the nitrogen atom were able to stabilize G-quadruplex, as demonstrated using UV-Vis, fluorescence and CD spectroscopic techniques as well as molecular modeling. The spectrophotometric titration results showed spectral features characteristic of these ligands-bathochromic shifts and initial hypochromicity followed by hyperchromicity at higher GQ concentrations...
May 10, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Abigail J Van Riesen, Kaila L Fadock, Prashant S Deore, Ahmed Desoky, Richard A Manderville, Shahin Sowlati-Hashjin, Stacey D Wetmore
Chemically modified aptamers have the opportunity to increase aptamer target binding affinity and provide structure-activity relationships to enhance our understanding of molecular target recognition by the aptamer fold. In the current study, 8-aryl-2'-deoxyguanosine nucleobases have been inserted into the G-tetrad and central TGT loop of the thrombin binding aptamer (TBA) to determine their impact on antiparallel G-quadruplex (GQ) folding and thrombin binding affinity. The aryl groups attached to the dG nucleobase vary greatly in aryl ring size and impact on GQ stability (∼20 °C change in GQ thermal melting (Tm) values) and thrombin binding affinity (17-fold variation in dissociation constant (Kd))...
May 10, 2018: Organic & Biomolecular Chemistry
Yumei Yang, Wenjing Yang, Hongmei Su, Weihai Fang, Xuebo Chen
Herein, mechanistic aspects of the photogeneration and quenching of guanine radical cation through one-electron oxidation of the G-quadruplex of G2T2G2TGTG2T2G2 (TBA) sequence were investigated by a combined quantum mechanical/molecular mechanical (QM/MM) approach at the CASPT2//CASSCF/AMBER level of theory. Herein, one electron promotion of the oxygen lone pair of the photo-excited photosensitizer peroxydisulfate to its O-O σ* orbital was first demonstrated to become tunable through the varied reduction ability of the G base in the presence or absence of interbase hydrogen bonding, thereby dynamically controlling the deprotonation site in G-quadruplex TBA...
May 8, 2018: Physical Chemistry Chemical Physics: PCCP
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