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G quadruplex

Rong Liao, Shiyu Li, Huan Wang, Chunyan Chen, Xiaoming Chen, Changqun Cai
The simultaneous detection of two important microRNAs (miRNAs) can potentially evaluate pathological states. The simultaneous detection of miRNA-26a and miRNA-122 is proposed in this study using a cleverly designed single-labeled, dual-functional fluorescent probe with a 2-aminopurine as a fluorophore, which is a G-quadruplex single-stranded DNA. The probe can partly complement cDNA-1 and cDNA-2. cDNA-1 and cDNA-2 are complementary strands of miRNA-26a and miRNA-122, respectively. When the target miRNAs are added simultaneously, these cDNA (cDNA-1 and cDNA-2) can be competed off from the cDNA∖probe duplex to form a cDNA∖RNA heteroduplex...
August 29, 2017: Analytica Chimica Acta
Harald Schwalbe, Lauris Lannes, Phoebe Young, Christian Richter, Nina Morgner
The human genome contains GC-rich sequences able to form tetraplex secondary structures known as G-quadruplex and i-motif. Such sequences are notably present in the promoter region of oncogenes and are proposed to function as regulatory elements of the gene expression. The P1 promoter of BCL2 contains a 39-mer C-rich sequence (Py39wt) which can fold into a hairpin or an i-motif in a pH-dependent manner in vitro. The protein hnRNP LL was identified to recognise the i-motif over the hairpin conformation and act as an activating transcription factor...
August 14, 2017: Chembiochem: a European Journal of Chemical Biology
Han Sun, Wanbo Li, Zhen-Zhen Dong, Chong Hu, Chung-Hang Leung, Dik-Lung Ma, Kangning Ren
A paper-based microfluidic device based on unconventional principle was developed and used to detect lead ions through a two-step process including heated incubation and subsequent mixing. The device was made by generating a superhydrophobic pattern, which defines channel and reservoir barriers, on a water-impermeable paper substrate, followed by loading and drying the reagents in the defined reservoirs. Different from the conventional paper-based devices that are made of water-permeable paper, the as-prepared device holds water drops in discrete reservoirs, and the water drops will not move unless the device is titled along the direction of the predefined channels...
August 1, 2017: Biosensors & Bioelectronics
Shuai Chen, Pin Liu, Kewen Su, Xuan Li, Zhen Qin, Wei Xu, Jun Chen, Chaorui Li, Jingfu Qiu
In this work, novel octahedral Cu2O-Au nanocomposites were synthesized and first applied in an electrochemical aptasensor to detect thrombin (TB) with the aid of a DNAzyme for signal amplification. The octahedral Cu2O-Au nanocomposites have not only simultaneously served as signal amplifying molecules but have also been utilized as an ideal loading platform to immobilize a large number of electroactive substances and recognition probes. Gold nanoparticles (AuNPs) were grown directly on the surface of the octahedral Cu2O nanocrystals, and the Cu2O-Au nanocomposites obtained had the advantages of large surface areas and excellent biocompatibilities...
August 5, 2017: Biosensors & Bioelectronics
Yan-Cheng Wu, Shi-He Luo, Wen-Jie Mei, Liang Cao, Han-Qing Wu, Zhao-Yang Wang
An efficient route without metal catalyst has been developed for synthesis of 4-biphenylamino-5-halo-2(5H)-furanones. The antitumor activities against various tumor cells of all the compounds have been evaluated by MTT assay. Among them, the compound 3j exhibits significant inhibitory activity against MCF-7 human breast cancer cells with an IC50 value of 11.8 μM and low toxicity toward HaCaT human normal cells. The mechanism studies confirm that 3j can induce cell cycle arrest at G2/M phase in MCF-7 cells...
August 4, 2017: European Journal of Medicinal Chemistry
Giorgia Oliviero, Stefano D'Errico, Brunella Pinto, Fabrizia Nici, Principia Dardano, Ilaria Rea, Luca De Stefano, Luciano Mayol, Gennaro Piccialli, Nicola Borbone
Obtaining DNA nanostructures with potential applications in drug discovery, diagnostics, and electronics in a simple and affordable way represents one of the hottest topics in nanotechnological and medical sciences. Herein, we report a novel strategy to obtain structurally homogeneous DNA G-wire nanostructures of known length, starting from the short unmodified G-rich oligonucleotide d(5'-CGGT-3'-3'-GGC-5') (1) incorporating a 3'-3' inversion of polarity site. The reported approach allowed us to obtain long G-wire assemblies through 5'-5' π-π stacking interactions in between the tetramolecular G-quadruplex building blocks that form when 1 is annealed in the presence of potassium ions...
August 2017: ChemistryOpen
Katsuhito Kino, Masayo Hirao-Suzuki, Masayuki Morikawa, Akane Sakaga, Hiroshi Miyazawa
Guanine is the most readily oxidized of the four DNA bases, and guanine oxidation products cause G:C-T:A and G:C-C:G transversions through DNA replication. 8-Oxo-7,8-dihydroguanine (8-oxoG) causes G:C-T:A transversions but not G:C-C:G transversions, and is more readily oxidized than guanine. This review covers four major findings. (i) 2,2,4-Triamino-5(2H)-oxazolone (Oz) is produced from guanine and 8-oxoG under various oxidative conditions. Guanine is incorporated opposite Oz by DNA polymerases, except REV1...
2017: Genes and Environment: the Official Journal of the Japanese Environmental Mutagen Society
Cheng Qian, Hengqing Fu, Kevin A Kovalchik, Huihui Li, David Da Yong Chen
A free solution method was developed for evaluating specific binding affinity and stoichiometry of small molecules with oligo DNA subsequent to cation induced G quadruplex formation. A nonlinear curve fitting equation capable of extracting specific binding constants in the presence of non-specific binding without the need of reference compounds was proposed and tested. Electrospray ionization mass spectrometry (ESI-MS) was first used to rapidly screen the small molecule candidates, then the stoichiometry and affinity constants of the native state binding pair in solution were obtained with capillary electrophoresis frontal analysis (CE-FA)...
August 6, 2017: Analytical Chemistry
Chiara Platella, Serena Guida, Laura Bonmassar, Angelo Aquino, Enzo Bonmassar, Giampiero Ravagnan, Daniela Montesarchio, Giovanni N Roviello, Domenica Musumeci, Maria Pia Fuggetta
BACKGROUND: trans-resveratrol (tRES) is a polyphenolic stilbene found in plant products which has attracted great attention because of its antioxidant, anti-inflammatory and anticancer properties. METHODS: The possible correlation between tRES-induced suppression of melanoma cell growth and its influence on telomerase expression has been investigated by biological assays. Moreover, in order to gain new knowledge about possible mechanisms of action of tRES as antineoplastic agent, its interaction with biologically relevant secondary structure-forming DNA sequences, its aggregation properties and copper-binding activity have been studied by CD, UV and fluorescence spectroscopies...
August 2, 2017: Biochimica et Biophysica Acta
Zhuang Hao, Yibo Zhu, Xuejun Wang, Pavana Rotti, Christopher DiMarco, Scott Tyler, Xuezeng Zhao, John F Engelhardt, James C Hone, Qiao Lin
This paper presents an approach to the real-time, label-free, specific and sensitive detection of insulin using a graphene aptameric nanosensor. The nanosensor is configured as a field effect transistor (FET), whose graphene conducting channel is functionalized with a guanine-rich IGA3 aptamer. The negatively charged aptamer folds into a compact and stable anti-parallel or parallel G-quadruplex conformation upon binding with insulin, resulting in a change in the carrier density of graphene and thus its electrical conductance...
August 3, 2017: ACS Applied Materials & Interfaces
Riccardo Rigo, Claudia Sissi
The proximal promoter of c-KIT contains a peculiar domain that comprise three closely located short G-rich sequences able to fold into non-canonical DNA secondary structures called G-quadruplexes (G4). Here, we focused on a sequence corresponding to two consecutive G4 forming (kit2 and kit*) and, by electrophoretic, SPR and spectroscopic techniques, we demon-strated that they retain the ability to fold into G4 when inserted in the extended sequence. Noteworthy, we highlighted the occurrence of a crosstalk between the two forming units...
August 1, 2017: Biochemistry
Jaewon Min, Woodring E Wright, Jerry W Shay
Alternative lengthening of telomeres (ALT) is a telomerase-independent telomere maintenance mechanism that occurs in a subset of cancers. By analyzing telomerase positive cells and their hTERC knockout derived ALT human cell lines, we show that ALT cells harbor more fragile telomeres representing telomere replication problems. ALT-associated replication defects trigger mitotic DNA synthesis (MiDAS) at telomeres in a RAD52-dependent, but RAD51-independent, manner. Telomeric MiDAS is a conservative DNA synthesis process, potentially mediated by break-induced replication, similar to type II ALT survivors in S...
July 31, 2017: Molecular and Cellular Biology
Emanuela Torelli, Marisa Manzano, Sachin K Srivastava, Robert S Marks
In the quest of greater sensitivity and specificity of diagnostic systems, one continually searches for alternative DNA hybridization methods, enabling greater versatility and where possible field-enabled detection of target analytes. We present, herein, a hybrid molecular self-assembled scaffolded DNA origami entity, intimately immobilized via capture probes linked to aminopropyltriethoxysilane, onto a glass optical fiber end-face transducer, thus producing a novel biosensor. Immobilized DNA nanorobots with a switchable flap can then be actuated by a specific target DNA present in a sample, by exposing a hemin/G-quadruplex DNAzyme, which then catalyzes the generation of chemiluminescence, once the specific fiber probes are immersed in a luminol-based solution...
July 21, 2017: Biosensors & Bioelectronics
Qi Qiao, Li Wang, Fei-Long Meng, Joyce K Hwang, Frederick W Alt, Hao Wu
Activation-induced cytidine deaminase (AID) initiates both class switch recombination (CSR) and somatic hypermutation (SHM) in antibody diversification. Mechanisms of AID targeting and catalysis remain elusive despite its critical immunological roles and off-target effects in tumorigenesis. Here, we produced active human AID and revealed its preferred recognition and deamination of structured substrates. G-quadruplex (G4)-containing substrates mimicking the mammalian immunoglobulin switch regions are particularly good AID substrates in vitro...
August 3, 2017: Molecular Cell
Zuzana Dvořáková, Michaela Vorlíčková, Daniel Renčiuk
BACKGROUND: The DNA lesions, resulting from oxidative damage, were shown to destabilize human telomere four-repeat quadruplex and to alter its structure. Long telomere DNA, as a repetitive sequence, offers, however, other mechanisms of dealing with the lesion: extrusion of the damaged repeat into loop or shifting the quadruplex position by one repeat. METHODS: Using circular dichroism and UV absorption spectroscopy and polyacrylamide electrophoresis, we studied consequences of lesions at different positions of the model five-repeat human telomere DNA sequences on the structure and stability of their quadruplexes in sodium and in potassium...
July 26, 2017: Biochimica et Biophysica Acta
Chun Kit Kwok, Catherine J Merrick
Guanine (G)-rich sequences in nucleic acids can assemble into G-quadruplex structures that involve G-quartets linked by loop nucleotides. The structural and topological diversity of G-quadruplexes have attracted great attention for decades. Recent methodological advances have advanced the identification and characterization of G-quadruplexes in vivo as well as in vitro, and at a much higher resolution and throughput, which has greatly expanded our current understanding of G-quadruplex structure and function...
July 26, 2017: Trends in Biotechnology
Chao-Da Xiao, Takumi Ishizuka, Yan Xu
In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations...
July 27, 2017: Scientific Reports
Jaeran Lee, Sok Won Kim
In G-rich DNA, it is well known that the form changes from single-strand DNA to G-quadruplex due to cations. In this study, we analyze the diffusion coefficient and fluorescence intensity obtained by fluorescence correlation spectroscopy for short G-rich DNA of the (G3T1)4 sequence labeled as 5-Carboxytetramethylrhodamine (TAMRA) with variation of the K(+) ion concentration. At a K(+) ion concentration of more than 200 mM, the single-strand DNA was changed to the G-quadruplex. The size of the G-quadruplex decreased to 86% than the size of the single strand DNA at K(+) ion concentration of 0 M...
July 26, 2017: Journal of Fluorescence
João Ferreira, Tiago Santos, Patrícia Pereira, Marta C Corvo, João A Queiroz, Fani Sousa, Carla Cruz
G-quadruplex (G4) is involved in many biological processes, such as telomere function, gene expression and DNA replication. The selective isolation of G4 using affinity ligands that bind tightly and selectively is a valuable strategy for discovering new G4 binders for the separation of G4 from duplexes or the discrimination of G4 structures. In this work, one affinity chromatographic support was prepared using a naphthalene amine as a G4 binder. The ligand was immobilized on epoxy-activated Sepharose CL-6B using a long spacer arm and was characterized by HR-MAS spectroscopy...
August 7, 2017: Analyst
Xiao-Yu Li, Yi-Chen Du, Yu-Peng Zhang, De-Ming Kong
An exonucleolytic digestion-assisted exponential rolling circle amplification (RCA) strategy was developed for sensitive and sequence-specific detection of target DNA embedded in long-stranded genomic DNA. Herein, Phi29 DNA polymerase plays two important roles as exonuclease and polymerase. Long-stranded genomic DNAs can be broken into small DNA fragments after ultrasonication. The fragments that contain target DNA, hybridize with a linear padlock probe to trigger the formation of a circular RCA template. The tails protruding from the 3'-end of the target DNA sequences are then digested by the 3' → 5' exonuclease activity of Phi29 DNA polymerase even if they fold into a double-stranded structure...
July 24, 2017: Scientific Reports
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