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G quadruplex

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https://www.readbyqxmd.com/read/28642152/g-quadruplex-dynamics
#1
REVIEW
Robert W Harkness, Anthony K Mittermaier
G-quadruplexes (GQs) are four-stranded nucleic acid secondary structures formed by guanosine (G)-rich DNA and RNA sequences. It is becoming increasingly clear that cellular processes including gene expression and mRNA translation are regulated by GQs. GQ structures have been extensively characterized, however little attention to date has been paid to their conformational dynamics, despite the fact that many biological GQ sequences populate multiple structures of similar free energies, leading to an ensemble of exchanging conformations...
June 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28641941/role-of-recombination-and-replication-fork-restart-in-repeat-instability
#2
REVIEW
Erica J Polleys, Nealia C M House, Catherine H Freudenreich
Eukaryotic genomes contain many repetitive DNA sequences that exhibit size instability. Some repeat elements have the added complication of being able to form secondary structures, such as hairpin loops, slipped DNA, triplex DNA or G-quadruplexes. Especially when repeat sequences are long, these DNA structures can form a significant impediment to DNA replication and repair, leading to DNA nicks, gaps, and breaks. In turn, repair or replication fork restart attempts within the repeat DNA can lead to addition or removal of repeat elements, which can sometimes lead to disease...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28636312/combining-protein-and-mirna-quantification-for-bladder-cancer-analysis
#3
Ruixue Duan, Zhenyu Zhang, Fuxin Zheng, Longwang Wang, Ju Guo, Tianchi Zhang, Xiaomeng Dai, Shengwei Zhang, Dong Yang, Renrui Kuang, Gongxian Wang, Chaohong He, Abdul Hakeem, Chang Shu, Ping Yin, Xiaoding Lou, Fuqing Zeng, Huageng Liang, Fan Xia
We combine the telomerase extension reaction and microRNA (miRNA)-induced rolling circle amplification, followed by graphene oxide (GO) and nicking enzyme assisted signal amplification, to analyze telomerase and miRNA 21 in urine samples with following merits. Firstly, it is a binary assay and can simultaneously output double signals which corresponds to the quantities of telomerase and miRNA, respectively. Secondly, telomerase activity is firstly enhanced by using DNA molecular beacon probe to inhibit the formation of G-quadruplex...
June 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28633570/enantioselective-light-switch-effect-of-%C3%AE-and-%C3%AE-ru-phenanthroline-2-dipyrido-3-2-a-2-3-c-phenazine-2-bound-to-g-quadruplex-dna
#4
Jin Ha Park, Hyun Suk Lee, Myung Duk Jang, Sung Wook Han, Seog K Kim, Young-Ae Lee
The interaction of Δ- and Λ-[Ru(phen)2DPPZ](2+) (DPPZ = dipyrido[3,2-a:2', 3'-c]phenazine, phen = phenanthroline) with a G-quadruplex formed from 5'-G2T2G2TGTG2T2G2-3'(15-mer) was investigated. The well-known enhancement of luminescence intensity (the 'light-switch' effect) was observed for the [Ru(phen)2DPPZ](2+) complexes upon formation of an adduct with the G-quadruplex. The emission intensity of the G-quadruplex-bound Λ-isomer was 3-fold larger than that of the Δ-isomer when bound to the G-quadruplex, which is opposite of the result observed in the case of double stranded DNA (dsDNA); the light switch effect is larger for the dsDNA-bound Δ-isomer...
June 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28629775/8-oxo-7-8-dihydroguanine-friend-and-foe-epigenetic-like-regulator-versus-initiator-of-mutagenesis
#5
REVIEW
Aaron M Fleming, Cynthia J Burrows
A high flux of reactive oxygen species during oxidative stress results in oxidative modification of cellular components including DNA. Oxidative DNA "damage" to the heterocyclic bases is considered deleterious because polymerases may incorrectly read the modifications causing mutations. A prominent member in this class is the oxidized guanine base 8-oxo-7,8-dihydroguanine (OG) that is moderately mutagenic effecting G→T transversion mutations. Recent reports have identified that formation of OG in G-rich regulatory elements in the promoters of the VEGF, TNFα, and SIRT1 genes can increase transcription via activation of the base excision repair (BER) pathway...
June 9, 2017: DNA Repair
https://www.readbyqxmd.com/read/28627887/controlling-the-catalytic-functions-of-dnazymes-within-constitutional-dynamic-networks-of-dna-nanostructures
#6
Shan Wang, Liang Yue, Zohar Shpilt, Alessandro Cecconello, Jason S Kahn, Jean-Marie Lehn, Itamar Willner
Mimicking complex cellular dynamic chemical networks being up-regulated or down-regulated by external triggers is one of the challenges in system chemistry. Constitutional dynamic networks, CDNs, composed of exchangeable components that respond to environmental triggers by self-adaption, provide general means to mimic biosystems. We use the structural and functional information encoded in nucleic acid nanostructures to construct effector (input)-triggered constitutional dynamic networks that reveal adaptable catalytic properties...
June 19, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28626564/integration-of-g-quadruplex-and-dna-templated-ag-ncs-for-nonarithmetic-information-processing
#7
Ru-Ru Gao, Tian-Ming Yao, Xiao-Yan Lv, Yan-Yan Zhu, Yi-Wei Zhang, Shuo Shi
To create sophisticated molecular logic circuits from scratch, you may not believe how common the building blocks can be and how diverse and powerful such circuits can be when scaled up. Using the two simple building blocks of G-quadruplex and silver nanoclusters (Ag NCs), we experimentally construct a series of multifunctional, label-free, and multi-output logic circuits to perform nonarithmetic functions: a 1-to-2 decoder, a 4-to-2 encoder, an 8-to-3 encoder, dual transfer gates, a 2 : 1 multiplexer, and a 1 : 2 demultiplexer...
June 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28622804/g-quadruplex-based-exo-iii-assisted-signal-amplification-aptasensor-for-the-colorimetric-detection-of-adenosine
#8
Lei Xu, Xin Shen, Bingzhi Li, Chunhong Zhu, Xuemin Zhou
Adenosine is an endogenous nucleotide pivotally involved in nucleic acid and energy metabolism. Its excessive existence may indicate tumorigenesis, typically lung cancer. Encouraged by its significance as the clinical biomarker, sensitive assay methods towards adenosine have been popularized, with high cost and tedious procedures as the inevitable defects. Herein, we report a label-free aptamer-based exonuclease III (Exo III) amplification colorimetric aptasensor for the highly sensitive and cost-effective detection of adenosine...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28622642/highly-sensitive-electrochemical-thrombin-aptasensor-based-on-peptide-enhanced-electrocatalysis-of-hemin-g-quadruplex-and-nanocomposite-as-nanocarrier
#9
Yongmei Wu, Lina Zou, Sheng Lei, Qian Yu, Baoxian Ye
In this work, we first conjugated a short peptide to thrombin binding aptamer (TBA) and bond hemin to the hybrid, effectively rendering hemin/G4-peptide more active over the original hemin/G4, so that a highly sensitive electrochemical thrombin (TB) aptasensor was developed based on it and PtNTs@rGO nanocomposite. It was the first report on the application of hemin/G4-peptide in electrochemical aptasensor. PtNTs@rGO with large surface area served as excellent nanocarrier for high loading of hemin/G4-peptide hybrids, resulting in the formation of hemin/G4-peptide-PtNTs@rGO bioconjugate as the secondary aptamer and further signal enhancement...
June 11, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28621518/a-photoelectrochemical-bioanalysis-platform-for-cells-monitoring-based-on-dual-signal-amplification-using-in-situ-generation-of-electron-acceptor-coupled-with-heterojunction
#10
Ruyan Li, Yue Zhang, Wenwen Tu, Zhihui Dai
Using in suit generation of electron acceptor coupled with heterojunction as dual signal amplification, a simple photoelectrochemical (PEC) bioanalysis platform was designed. The synergic effect between the PEC activities of carbon nitride (C3N4) nanosheets and PbS quantum dots (QDs) achieved almost 9 fold photocurrent intensity increment, compared with the C3N4 alone. After the G-quadruplex/hemin/Pt NPs with catalase-like activity towards H2O2 was introduced, oxygen was in situ generated and acted as electron donor, improving charge separation efficiency and further enhancing photocurrent response...
June 16, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28620664/development-of-an-rna-aptamer-that-acquires-binding-capacity-against-hiv-1-tat-protein-via-g-quadruplex-formation-in-response-to-potassium-ions
#11
Yudai Yamaoki, Takashi Nagata, Tsukasa Mashima, Masato Katahira
For the development of K(+)-responsive RNA aptamers, we proposed a new general strategy that makes use of a G-quadruplex formation in response to K(+). This is the first report of developing an RNA aptamer that demonstrates ON/OFF switching of its target-binding activity by sensing the addition/removal of K(+).
June 16, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28620243/targeting-glioma-stem-cells-in-vivo-by-a-g-quadruplex-stabilizing-synthetic-macrocyclic-hexaoxazole
#12
Takahiro Nakamura, Sachiko Okabe, Haruka Yoshida, Keisuke Iida, Yue Ma, Shogo Sasaki, Takao Yamori, Kazuo Shin-Ya, Ichiro Nakano, Kazuo Nagasawa, Hiroyuki Seimiya
G-quadruplex (G4) is a higher-order nucleic acid structure that is formed by guanine-rich sequences. G4 stabilization by small-molecule compounds called G4 ligands often causes cytotoxicity, although the potential medicinal impact of this effect has not been fully established. Here we demonstrate that a synthetic G4 ligand, Y2H2-6M(4)-oxazole telomestatin derivative (6OTD), limits the growth of intractable glioblastoma (grade IV glioma) and glioma stem cells (GSCs). Experiments involving a human cancer cell line panel and mouse xenografts revealed that 6OTD exhibits antitumor activity against glioblastoma...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620169/structural-insight-for-the-recognition-of-g-quadruplex-structure-at-human-c-myc-promoter-sequence-by-flavonoid-quercetin
#13
Arpita Tawani, Subodh Kumar Mishra, Amit Kumar
Small molecule ligands that could stabilize G-quadruplex structure formed at the promoter region of human c-myc oncogene will regulate its expression in cancer cells. Flavonoids, a group of naturally available small molecule, have been known for their various promising effects on human health. In present study, we have performed detailed biophysical studies for the interaction of human c-myc G-quadruplex DNA with nine representative flavonoids: Luteolin, Quercetin, Rutin, Genistein, Kaempferol, Puerarin, Hesperidin, Myricetin and Daidzein...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28618365/a-highly-sensitive-and-widely-adaptable-plasmonic-aptasensor-using-berberine-for-small-molecule-detection
#14
Jin-Ho Park, Ju-Young Byun, Hyungjun Jang, Donggu Hong, Min-Gon Kim
Localized surface plasmon resonance (LSPR) biosensors allow label-free detection of small molecules in molecular binding events; however, they are limited by a relatively low sensitivity and narrow dynamic range. Here, we report highly sensitive small-molecule detection by LSPR peak shift exploiting the G-quadruplex (GQx) structure-binding characteristic of known GQx binders to enhance the LSPR signal of a plasmonic aptasensor. Six known GQx binders (thiazole orange, malachite green, crystal violet, zinc protoporphyrin IX, thioflavin T, and berberine) were tested for their ability to enhance the LSPR signal...
June 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28617612/effect-of-urea-on-g-quadruplex-stability
#15
Lusine Aslanyan, Jordan Ko, Byul G Kim, Ishkhan Vardanyan, Yeva B Dalyan, Tigran V Chalikian
G-quadruplexes represent a class of noncanonical nucleic acid structures implicated in transcriptional regulation, cellular function, and disease. An understanding of the forces involved in stabilization/destabilization of the G-quadruplex conformation relative to the duplex or single-stranded conformation is a key to elucidating the biological role of G-quadruplex-based genomic switches and the quest for therapeutic means for controlled induction or suppression of a G-quadruplex at selected genomic loci. Solute-solvent interactions provide a ubiquitous and, in many cases, the determining thermodynamic force in maintaining and modulating the stability of nucleic acids...
June 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28612854/fragile-x-mental-retardation-protein-recognizes-a-g-quadruplex-structure-within-the-survival-motor-neuron-domain-containing-1-mrna-5-utr
#16
Damian S McAninch, Ashley M Heinaman, Cara N Lang, Kathryn R Moss, Gary J Bassell, Mihaela Rita Mihailescu, Timothy L Evans
G quadruplex structures have been predicted by bioinformatics to form in the 5'- and 3'-untranslated regions (UTRs) of several thousand mature mRNAs and are believed to play a role in translation regulation. Elucidation of these roles has primarily been focused on the 3'-UTR, with limited focus on characterizing the G quadruplex structures and functions in the 5'-UTR. Investigation of the affinity and specificity of RNA binding proteins for 5'-UTR G quadruplexes and the resulting regulatory effects have also been limited...
June 14, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28611443/identification-of-a-gene-cluster-for-telomestatin-biosynthesis-and-heterologous-expression-using-a-specific-promoter-in-a-clean-host
#17
Keita Amagai, Haruo Ikeda, Junko Hashimoto, Ikuko Kozone, Miho Izumikawa, Fumitaka Kudo, Tadashi Eguchi, Takemichi Nakamura, Hiroyuki Osada, Shunji Takahashi, Kazuo Shin-Ya
Telomestatin, a strong telomerase inhibitor with G-quadruplex stabilizing activity, is a potential therapeutic agent for treating cancers. Difficulties in isolating telomestatin from microbial cultures and in chemical synthesis are bottlenecks impeding the wider use. Therefore, improvement in telomestatin production and structural diversification are required for further utilization and application. Here, we discovered the gene cluster responsible for telomestatin biosynthesis, and achieved production of telomestatin by heterologous expression of this cluster in the engineered Streptomyces avermitilis SUKA strain...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28609545/new-ruthenium-based-probes-for-selective-g-quadruplex-targeting
#18
Guillaume Piraux, Laure Bar, Michaël Abraham, Thomas Lavergne, Hélène Jamet, Jérôme Dejeu, Lionel Marcélis, Éric Defrancq, Benjamin Elias
Telomeric regions containing G-quadruplexes (G4s) structures play a pivotal role in the development of cancers. The development of specific binders for G4s is thus of great interest in order to get deeper understanding of the role of these structures, and to ultimately develop new anti-cancer drugs candidates. For several years, RuII complexes have been studied as efficient probe for DNA. Their main interest is the tunability of their structures and properties, and the possibility to use light excitation as a tool to probe the environment of these complexes or selectively trigger a reaction with a biological target...
June 13, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28605593/simultaneous-drug-targeting-of-the-promoter-myc-g-quadruplex-and-bcl2-i-motif-in-diffuse-large-b-cell-lymphoma-delays-tumor-growth
#19
Samantha Kendrick, Andrea Muranyi, Vijay Gokhale, Laurence H Hurley, Lisa M Rimsza
Secondary DNA structures are uniquely poised as therapeutic targets due to their molecular switch function in turning gene expression on or off and scaffold-like properties for protein and small molecule interaction. Strategies to alter gene transcription through these structures thus far involve targeting single DNA conformations. Here we investigate the feasibility of simultaneously targeting different secondary DNA structures to modulate two key oncogenes, cellular-myelocytomatosis (MYC) and B-cell lymphoma gene-2 (BCL2), in diffuse large B-cell lymphoma (DLBCL)...
June 12, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28605461/determining-the-folding-and-binding-free-energy-of-dna-based-nanodevices-and-nanoswitches-using-urea-titration-curves
#20
Andrea Idili, Francesco Ricci, Alexis Vallée-Bélisle
DNA nanotechnology takes advantage of the predictability of DNA interactions to build complex DNA-based functional nanoscale structures. However, when DNA functional and responsive units that are based on non-canonical DNA interactions are employed it becomes quite challenging to predict, understand and control their thermodynamics. In response to this limitation, here we demonstrate the use of isothermal urea titration experiments to estimate the free energy involved in a set of DNA-based systems ranging from unimolecular DNA-based nanoswitches to more complex DNA folds (e...
June 9, 2017: Nucleic Acids Research
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