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https://www.readbyqxmd.com/read/28088762/the-super-n-motifs-model-a-novel-alignment-free-approach-for-representing-and-comparing-rna-secondary-structures
#1
Jean-Pierre Séhi Glouzon, Jean-Pierre Perreault, Shengrui Wang
MOTIVATION: Comparing ribonucleic acid (RNA) secondary structures of arbitrary size uncovers structural patterns that can provide a better understanding of RNA functions. However, performing fast and accurate secondary structure comparisons is challenging when we take into account the RNA configuration (i.e. linear or circular), the presence of pseudoknot and G-quadruplex (G4) motifs and the increasing number of secondary structures generated by high-throughput probing techniques. To address this challenge, we propose the super-n-motifs model based on a latent analysis of enhanced motifs comprising not only basic motifs but also adjacency relations...
January 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28087374/what-stoichiometries-determined-by-mass-spectrometry-reveal-about-the-ligand-binding-mode-to-g-quadruplex-nucleic-acids
#2
Michael J Lecours, Adrien Marchand, Ahdia Anwar, Corinne Guetta, W Scott Hopkins, Valérie Gabelica
G-quadruplexes (G4s) have become important drug targets to regulate gene expression and telomere maintenance. Many studies on G4 ligand binding focus on determining the ligand binding affinities and selectivities. Ligands, however, can also affect the G4 conformation. Here we explain how to use electrospray ionization mass spectrometry (ESI-MS) to monitor simultaneously ligand binding and cation binding stoichiometries. The changes in potassium binding stoichiometry upon ligand binding hint at ligand-induced conformational changes involving a modification of the number of G-quartets...
January 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28072547/mild-photochemical-biofunctionalization-of-glass-microchannels
#3
Rui Rijo Carvalho, Sidharam P Pujari, Digvijay Gahtory, Elwin X Vrouwe, Bauke Albada, Han Zuilhof
The ability to locally modify the inside of microfluidic channels with bioactive molecules is of ever-rising relevance. In this article, we show the direct photochemical coupling of a N-hydroxysuccinimide-terminated ω-alkene onto hydrogen-terminated silicon oxide, and its subsequent functionalization with a catalytically active DNAzyme. To achieve this local attachment of a DNAzyme, we prepared hydrogen-phenyl-terminated glass (H-Φ-glass) by the reaction of glass with H-SiPhCl2. The presence of a radical-stabilizing substituent on the Si atom (i...
January 10, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28070084/a-label-free-and-turn-on-fluorescence-strategy-for-dna-detection-with-a-wide-detection-range-based-on-exonuclease-iii-aided-target-recycling-amplification
#4
Hualin Yang, Xiaoda Song, Baomiao Ding, Zhenshun Li, Xingping Zhang
In the present work, a simple and sensitive turn-on fluorescence method for DNA detection was developed. It was explored based on the N-methyl mesoporphyrin IX (NMM)/G-quadruplex DNA system as a reporter and exonuclease III (Exo III)-aided target recycling amplification to ensure sensitivity. Our method showed an ultra-wide detection range from 10 fM to 100 nM with a low linear detection limit of 0.76 nM. It also had excellent selectivity in a selectivity experiment.
2017: Analytical Sciences: the International Journal of the Japan Society for Analytical Chemistry
https://www.readbyqxmd.com/read/28069994/rhau-helicase-stabilizes-g4-in-its-nucleotide-free-state-and-destabilizes-g4-upon-atp-hydrolysis
#5
Huijuan You, Simon Lattmann, Daniela Rhodes, Jie Yan
The DEAH-box ATP-dependent RHAU helicases specifically unfold RNA and DNA G-quadruplexes (G4s). However, it remains unclear how the RHAU's G4 unfolding activity is coupled to different stages of the ATPase cycle. Here, using a single-molecule manipulation approach, we show that binding of Drosophila RHAU stabilizes an intramolecularly folded parallel DNA G4 against mechanical unfolding in its nucleotide-free and in its AMP-PNP or ADP bound states, while it destabilizes the G4 when coupled to ATP hydrolysis...
January 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28069813/residues-in-the-recq-c-terminal-domain-of-the-human-werner-syndrome-helicase-are-involved-in-unwinding-g-quadruplex-dna
#6
Amit Ketkar, Markus Voehler, Tresor Mukiza, Robert L Eoff
The structural and biophysical properties typically associated with G-quadruplex (G4) structures renders them a significant block for DNA replication, which must be overcome for cell division to occur. The Werner syndrome protein (WRN) is a RecQ-family helicase that has been implicated in the efficient processing of G4 DNA structures. The aim of the current study was to identify the residues of WRN involved in the binding and ATPase-driven unwinding of G4 DNA. Using a c-Myc G4 DNA model sequence and recombinant WRN, we have determined that the RecQ-C-terminal (RQC) domain of WRN imparts a 2-fold preference for binding to G4 DNA relative to non-G4 DNA substrates...
January 9, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28067256/polypurine-reverse-hoogsteen-pprh-oligonucleotides-can-form-triplexes-with-their-target-sequences-even-under-conditions-where-they-fold-into-g-quadruplexes
#7
Anna Solé, Emmanuelle Delagoutte, Carlos J Ciudad, Véronique Noé, Patrizia Alberti
Polypurine reverse-Hoogsteen (PPRH) oligonucleotides are non-modified DNA molecules composed of two mirror-symmetrical polypurine stretches linked by a five-thymidine loop. They can fold into reverse-Hoogsteen hairpins and bind to their polypyrimidine target sequence by Watson-Crick bonds forming a three-stranded structure. They have been successfully used to knockdown gene expression and to repair single-point mutations in cells. In this work, we provide an in vitro characterization (UV and fluorescence spectroscopy, gel electrophoresis and nuclease assays) of the structure and stability of two repair-PPRH oligonucleotides and of the complexes they form with their single-stranded targets...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28065761/g-quadruplexes-unfolding-by-rhau-helicase
#8
Nassima Meriem Gueddouda, Oscar Mendoza, Dennis Gomez, Anne Bourdoncle, Jean-Louis Mergny
G-quadruplexes (G4) are RNA and DNA secondary structures formed by the stacking of guanine quartets in guanine rich sequences. Quadruplex-prone motifs may be found in key genomic regions such as telomeres, ribosomal DNA, transcriptional activators and regulators or oncogene promoters. A number of proteins involved in various biological processes are able to interact with G4s. Among them, proteins dedicated to nucleic acids unwinding such as WRN, BLM, FANCJ or PIF1, can unfold G4 structures. Mutations of these helicases are linked to genome instability and to increases in cancer risks...
January 5, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28063390/sensitive-fluorescent-detection-of-dna-methyltransferase-using-nicking-endonuclease-mediated-multiple-primers-like-rolling-circle-amplification
#9
Juan Huang, Xiao-Yu Li, Yi-Chen Du, Li-Na Zhang, Ke-Ke Liu, Li-Na Zhu, De-Ming Kong
Sensitive and reliable detection of DNA methyltransferase (MTase) is of great significance for both early tumor diagnosis and therapy. In this study, a simple, label-free and sensitive DNA MTase-sensing method was developed on the basis of a nicking endonuclease-mediated multiple primers-like rolling circle amplification (RCA) strategy. In this method, a dumbbell RCA template was prepared by blunt-end ligation of two molecules of hairpin DNA. In addition to the primer-binding sequence, the dumbbell template contained another three important parts: 5'-CCGG-3' sequences in double-stranded stems, nicking endonuclease recognition sites and C-rich sequences in single-stranded loops...
December 30, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28063389/g-quadruplex-based-fluorometric-biosensor-for-label-free-and-homogenous-detection-of-protein-acetylation-related-enzymes-activities
#10
Huixia Wang, Yong Li, Kunli Zhao, Siyi Chen, Qin Wang, Bin Lin, Zhou Nie, Shouzhuo Yao
Reversible protein acetylation, one of the key types of post-translational modifications, is composed of histone acetylation and deacetylation, which is typically catalyzed by histone acetyltransferases (HATs) and histone deacetylases (HDACs) respectively. Herein, a label-free fluorescent method has been established for the homogeneous bioassay of HAT/HDAC activity and respective inhibitors. The proposed approach is primarily based on the electrostatic interaction between G-quadruplexes (G4s) and acetylation-related peptides, which results in marked change of fluorescent intensity of G4/Thioflavin T (ThT) complexes...
December 30, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28063336/evaluation-of-size-exclusion-chromatography-for-the-analysis-of-phosphorothioate-oligonucleotides
#11
Atsuko Shimoyama, Aki Fujisaka, Satoshi Obika
We evaluated size exclusion chromatography (SEC) for the detection of high-order structure of phosphorothioate oligonucleotides (PS-oligo). Because of strong interaction between PS-oligo and column packing material, peaks were broader and elution time was longer than those of the corresponding natural DNA oligonucleotides. However, single- and double-stranded structures of PS-oligo were clearly separated and discriminated, while single-stranded with high-order structures such as G-quadruplex and hairpin structure were not distinguished from each other...
December 29, 2016: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28054200/the-functions-of-the-multi-tasking-pfh1-pif1-helicase
#12
REVIEW
Nasim Sabouri
Approximately, 1% of the genes in eukaryotic genomes encode for helicases, which make the number of helicases expressed in the cell considerably high. Helicases are motor proteins that participate in many central aspects of the nuclear and mitochondrial genomes, and based on their helicase motif conservation, they are divided into different helicase families. The Pif1 family of helicases is an evolutionarily conserved helicase family that is associated with familial breast cancer in humans. The Schizosaccharomyces pombe Pfh1 helicase belongs to the Pif1 helicase family and is a multi-tasking helicase that is important for replication fork progression through natural fork barriers, for G-quadruplex unwinding, and for Okazaki fragment maturation, and these activities are potentially shared by the human Pif1 helicase...
January 4, 2017: Current Genetics
https://www.readbyqxmd.com/read/28054120/assessment-of-human-telomeric-g-quadruplex-structures-using-surface-enhanced-raman-spectroscopy
#13
Snežana Miljanić, Marina Ratkaj, Marija Matković, Ivo Piantanida, Paola Gratteri, Carla Bazzicalupi
G-Quadruplex (G4) structures of a human telomeric 24-mer (5'-TTAGGGTTAGGGTTAGGGTTAGGG-3') sequence (Tel24) stabilized by sodium and potassium ions have been assessed using surface-enhanced Raman scattering (SERS) spectroscopy. The distinctive SERS spectra of Tel24 in the presence of 100 mM Na(+) and 100 mM K(+) were obtained and the SERS bands characteristic of the antiparallel basket-type and the mixed hybrid (3+1) structures, respectively, were identified and assigned. The influence of the SERS - active substrate on the scattering enhancement was studied using citrate- and chloride-covered silver nanoparticles, in the absence and presence of the aggregating agent (0...
January 4, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28054065/the-evaluation-of-5-amino-and-5-hydroxyuracil-derivatives-as-potential-quadruplex-forming-agents
#14
Gábor Paragi, Zoltán Kupihár, Gábor Endre, Célia Fonseca Guerra, Lajos Kovács
5-Substituted uracils (NH2 or OH groups in position 5) have been examined theoretically and experimentally as potential building blocks in quadruplex structures. Our high level Density Functional Theory (DFT) calculations showed that the tetramer formation and stacking energies for 5-substituted uracils are similar to the energies of purine-based xanthine (X) or guanine (G) structures. As tetrads of 5-substituted uracils cover almost exactly the same area as purine tetrads, mixed tetrads or quadruplex structures based on X or G and 5-substituted uracil motifs are possible...
January 5, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28052120/structural-analysis-of-g-quadruplex-formation-at-the-human-mest-promoter
#15
Aaron J Stevens, Martin A Kennedy
The promoter region of the imprinted gene MEST contains several motifs capable of forming G-quadruplex (G4) structures, which appear to contribute to consistent allelic dropout during polymerase chain reaction (PCR) analysis of this region. Here, we extend our previous analysis of MEST G4 structures by applying fluorescent footprinting techniques to assess non B-DNA structure and topology in dsDNA from the full MEST promoter region, under conditions that mimic PCR. We demonstrate that the buffer used for PCR provides an extremely favourable milieu for G4 formation, and that cytosine methylation helps maintain G4 structures during PCR...
2017: PloS One
https://www.readbyqxmd.com/read/28045140/precipitation-selex-identification-of-dna-aptamers-for-calcium-phosphate-materials-synthesis
#16
K R Baillargeon, K Meserve, S Faulkner, S Watson, H Butts, P Deighan, A E Gerdon
DNA aptamers that enhance calcium phosphate mineral formation were identified using a novel precipitation SELEX method. The evolved DNA library was substantially enriched in G nucleotides and in predicted G-quadruplex structures, suggesting their importance in the mechanism of mineralization. This work could readily be extended to provide additional novel DNA aptamers for materials synthesis.
January 3, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28043077/a-sensitive-label-free-electrochemical-detection-of-telomerase-activity-without-modification-or-immobilization
#17
Xu Liu, Min Wei, Ensheng Xu, Haitang Yang, Wei Wei, Yuanjian Zhang, Songqin Liu
Telomerase has become one of the most typical tumor marker because it is closely related to cancers. In this paper, a simple label-free electrochemical detection of telomerase activity by using methylene blue (MB) as a G-quadruplex binding probe was proposed, avoiding commonly used complex label procedures, nano-probe synthesis, complicated electrode modification, probe immobilization or signal amplification. In the presence of telomerase substrate (TS) primer, the binding of MB on primer was weak. When repeats of (TTAGGG) were extended on the TS primer under the action of telomerase, they formed multiple G-quadruplexes with the help of K(+)...
December 24, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28038373/a-facile-label-free-g-quadruplex-based-fluorescent-aptasensor-method-for-rapid-detection-of-atp
#18
Haisheng Liu, Changbei Ma, Feng Ning, Hanchun Chen, Hailun He, Kemin Wang, Jun Wang
The present work demonstrates a simple, rapid and label-free ATP detection method using a fluorescent aptasensor that is based on G-quadruplex formation. In the absence of ATP, the Thioflavin T (ThT) dye binds to the G-rich ATP aptamer and forms an ATP aptamer/ThT G-quadruplex complex, which results in high fluorescence intensity. Upon addition of ATP, the ATP aptamer/ThT complex will be replaced by the formation of an ATP aptamer/ATP complex. During this process, separation of the ThT dye from the ATP aptamer/ThT complex decreases the fluorescence intensity of the reaction mixture dramatically...
December 21, 2016: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28031943/supramolecular-polymer-formation-by-cyclic-dinucleotides-and-intercalators-affects-dinucleotide-enzymatic-processing
#19
Shizuka Nakayama, Jie Zhou, Yue Zheng, Henryk Szmacinski, Herman O Sintim
BACKGROUND: Cyclic dinucleotides form supramolecular aggregates with intercalators, and this property could be utilized in nanotechnology and medicine. METHODS & RESULTS: Atomic force microscopy and electrophoretic mobility shift assays were used to show that cyclic diguanylic acid (c-di-GMP) forms G-wires in the presence of intercalators. The average fluorescence lifetime of thiazole orange, when bound to c-di-GMP was greater than when bound to DNA G-quadruplexes or dsDNA...
March 2016: Future Science OA
https://www.readbyqxmd.com/read/28029775/combining-a-ru-ii-building-block-and-rapid-screening-approach-to-identify-dna-structure-selective-light-switch-compounds
#20
Erin Wachter, Diego Moyá, Edith C Glazer
A chemically reactive Ru(II) "building block", able to undergo condensation reactions with substituted diamines, was utilized to create a small library of luminescent "light switch" dipyrido-[3,2-a:2',3'-c] phenazine (dppz) complexes. The impact of substituent identity, position, and the number of substituents on the light switch effect was investigated. An unbiased, parallel screening approach was used to evaluate the selectivity of the compounds for a variety of different biomolecules, including protein, nucleosides, single stranded DNA, duplex DNA, triplex DNA, and G-quadruplex DNA...
December 28, 2016: ACS Combinatorial Science
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