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https://www.readbyqxmd.com/read/28806644/effects-of-the-fluorine-substituent-positions-of-the-intercalating-ligands-on-the-binding-behavior-and-third-strand-stabilization-of-two-ru-ii-complexes-toward-poly-u-%C3%A2-poly-a-poly-u-triplex-rna
#1
Mengna Peng, Wen Ni, Lifeng Tan
Two new Ru(II) polypyridyl complexes containing fluorine substituents, [Ru(bpy)2(o-fpip)](2+) (Ru1, bpy=2,2'-bipyridine, o-fpip=2-(2-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) and [Ru(bpy)2(p-fpip)](2+) (Ru2, p-fpip=2-(4-fluorophenyl)imidazo[4,5-f] [1,10]phenanthroline) have been synthesized as binders for poly(U)•poly(A)∗poly(U) triplex RNA. The binding of the two complexes with the triplex RNA has been investigated by spectroscopic methods and viscosity measurements. Analysis of the electronic absorption spectra indicates that the association of intercalating Ru2 with the triplex RNA is greater than that of Ru1, which is also supported by spectroscopic titrations and viscosity measurements...
August 8, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28800432/linear-and-circular-dichroism-characterization-of-thionine-binding-mode-with-dna-polynucleotides
#2
Eimer Mary Tuite, Bengt Nordén
The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases...
August 1, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28795795/mass-defect-based-dimethyl-pyrimidinyl-ornithine-dipyro-tags-for-multiplex-quantitative-proteomics
#3
Dustin C Frost, Amanda R Buchberger, Lingjun Li
We have developed a novel amine-reactive mass defect-based chemical tag, dimethyl pyrimidinyl ornithine (DiPyrO), that is compact in size, is suitable for various biological samples, and enables highly multiplexed quantification of peptides at the MS1 level without increasing mass spectral complexity. The DiPyrO tag structure incorporates heavy isotopes in a variety of configurations to impart as much as 45.3 mDa or as little as 5.8 mDa per tag between labeled peptides. Notably, peptides containing lysine are labeled with two tags, doubling the imparted mass defect to up to 90...
August 10, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28793207/divalent-ion-mediated-dna-dna-interactions-a%C3%A2-comparative-study-of-triplex-and-duplex
#4
Zhong-Liang Zhang, Yuan-Yan Wu, Kun Xi, Jian-Ping Sang, Zhi-Jie Tan
Ion-mediated interaction between DNAs is essential for DNA condensation, and it is generally believed that monovalent and nonspecifically binding divalent cations cannot induce the aggregation of double-stranded (ds) DNAs. Interestingly, recent experiments found that alkaline earth metal ions such as Mg(2+) can induce the aggregation of triple-stranded (ts) DNAs, although there is still a lack of deep understanding of the surprising findings at the microscopic level. In this work, we employed all-atom dynamic simulations to directly calculate the potentials of mean force (PMFs) between tsDNAs, between dsDNAs, and between tsDNA and dsDNA in Mg(2+) solutions...
August 8, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28769061/particle-triplexes-cluster-in-the-tumor-suppressor-wwox-and-may-extend-throughout-the-human-genome
#5
Valerie Bríd O'Leary, Jan Smida, Fabian Andreas Buske, Laura Garcia Carrascosa, Omid Azimzadeh, Doris Maugg, Sarah Hain, Soile Tapio, Wolfgang Heidenreich, James Kerr, Matt Trau, Saak Victor Ovsepian, Michael John Atkinson
The long non-coding RNA PARTICLE (Gene PARTICL- 'Promoter of MAT2A-Antisense RadiaTion Induced Circulating LncRNA) partakes in triple helix (triplex) formation, is transiently elevated following low dose irradiation and regulates transcription of its neighbouring gene - Methionine adenosyltransferase 2A. It now emerges that PARTICLE triplex sites are predicted in many different genes across all human chromosomes. In silico analysis identified additional regions for PARTICLE triplexes at >1600 genomic locations...
August 2, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28764969/peptide-nucleic-acids-advanced-tools-for-biomedical-applications
#6
REVIEW
Anjali Gupta, Anuradha Mishra, Nidhi Puri
Peptide Nucleic Acids (PNAs) are the DNA/RNA analogues in which sugar-phosphate backbone is replaced by N-2-aminoethylglycine repeating units. PNA contains neutral backbone hence due to the absence of electrostatic repulsion, its hybridization shows remarkable stability towards complementary oligonucleotides. PNAs are highly resistant to cleavage by chemicals and enzymes due to the substrate specific nature of enzymes and therefore not degraded inside the cells. PNAs are emerging as new tools in the market due to their applications in antisense and antigene therapies by inhibiting translation and transcription respectively...
July 29, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28755398/microfluidic-lithography-of-bioinspired-helical-micromotors
#7
Yunru Yu, Luoran Shang, Wei Gao, Ze Zhao, Huan Wang, Yuanjin Zhao
Attracted by the biomachines of nature, considerable efforts have been devoted to developing artificial micro/nanomotors, which are helpful in diverse potential biomedical and environmental areas. Here, we present a novel flow lithography integrated microfluidic spinning and spiraling system for the continuous and controllable generation of bioinspired helical micromotors. Benefit from the fast online gelation and polymerization, the resultant helical micromotors could be imparted with Janus, triplex, and core-shell cross-sectional structures that have never been achieved by other methods...
July 29, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28709087/novel-electrochemiluminescence-of-silver-nanoclusters-fabricated-on-triplex-dna-scaffolds-for-label-free-detection-of-biothiols
#8
Lingyan Feng, Li Wu, Feifei Xing, Lianzhe Hu, Jinsong Ren, Xiaogang Qu
Electrochemiluminescence (ECL) of metal nanoclusters and their application have been widely reported due to the good biocompatibility, fascinating electrocatalytic activity and so on. Using DNA as synthesis template opens new opportunities to modulate the physical properties of AgNCs. Triplex DNA has been reported for the site-specific, homogeneous and highly stable silver nanoclusters (AgNCs) fabrication from our recent research. Here we further explore their extraordinary ECL properties and applications in biosensor utilization...
July 6, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28686662/comparison-of-a-new-multiplex-real-time-pcr-with-the-kato-katz-thick-smear-and-copro-antigen-elisa-for-the-detection-and-differentiation-of-taenia-spp-in-human-stools
#9
COMPARATIVE STUDY
Dinh Ng-Nguyen, Mark A Stevenson, Pierre Dorny, Sarah Gabriël, Tinh Van Vo, Van-Anh Thi Nguyen, Trong Van Phan, Sze Fui Hii, Rebecca J Traub
BACKGROUND: Taenia solium, the cause of neurocysticercosis (NCC), has significant socioeconomic impacts on communities in developing countries. This disease, along with taeniasis is estimated to infect 2.5 to 5 million people globally. Control of T. solium NCC necessitates accurate diagnosis and treatment of T. solium taeniasis carriers. In areas where all three species of Taenia tapeworms (T. solium, Taenia saginata and Taenia asiatica) occur sympatrically, conventional microscope- and copro-antigen based diagnostic methods are unable to distinguish between these three Taenia species...
July 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28681829/molecular-characterisation-of-uropathogenic-escherichia-coli-isolates-at-a-tertiary-care-hospital-in-south-india
#10
Arindam Chakraborty, Prabha Adhikari, Shalini Shenoy, Vishwas Saralaya
Uropathogenic Escherichia coli (UPEC) express a multitude of virulence factors (VFs) to break the inertia of the mucosal barrier of the urinary tract. The aim of the present study was undertaken to characterised the UPEC strains and to correlate carriage of specific virulence markers with different phylogroups and also to correlate these findings with clinical outcome of patients. A total of 156 non-repeated, clinically significant UPEC isolates were studied. Virulent genes were determined by two set of multiplex polymerase chain reaction (PCR)...
April 2017: Indian Journal of Medical Microbiology
https://www.readbyqxmd.com/read/28674450/triplex-dna-based-bioanalytical-platform-for-highly-sensitive-homogeneous-electrochemical-detection-of-melamine
#11
Xiaojuan Liu, Mengmeng Song, Feng Li
Melamine detection has attracted much attention since the discovery of the damage of melamine to human health. Herein, we have developed a sensitive homogeneous electroanalytical platform for melamine detection, which is relied on the formation of triplex molecular beacon integrated with exonuclease III (Exo III)-mediated signal amplification. The formation of triplex molecular beacon was triggered by the recognition and incorporation of melamine to the abasic (AP) site contained in the triplex stem. The stem of the triplex molecular beacon was designed to have a protruding double-strand DNA, which can be recognized and hydrolyzed by Exo III for releasing methylene blue (MB)-labeled mononucleotide...
July 3, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28673433/low-intensity-shockwave-therapy-improves-hemodynamic-parameters-in-patients-with-vasculogenic-erectile-dysfunction-a-triplex-ultrasonography-based-sham-controlled-trial
#12
Dimitrios Kalyvianakis, Dimitrios Hatzichristou
BACKGROUND: Although several reports have documented the subjective improvement of erectile function after low-intensity extracorporeal shockwave therapy (LI-ESWT) in patients with vasculogenic erectile dysfunction (ED), objective assessment data of penile hemodynamics are lacking. AIM: To assess penile hemodynamics before and 3 months after LI-ESWT in a group of patients with documented vasculogenic ED. METHODS: This was a double-blinded, randomized, sham-controlled trial...
July 2017: Journal of Sexual Medicine
https://www.readbyqxmd.com/read/28670571/dna-triplex-forming-purine-repeat-containing-genes-in-acinetobacter-baumannii-and-their-association-with-infection-and-adaptation
#13
Himanshu N Singh, Moganty R Rajeswari
No abstract text is available yet for this article.
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28663444/atomic-structure-of-the-human-cytomegalovirus-capsid-with-its-securing-tegument-layer-of-pp150
#14
Xuekui Yu, Jonathan Jih, Jiansen Jiang, Z Hong Zhou
Herpesviruses possess a genome-pressurized capsid. The 235-kilobase genome of human cytomegalovirus (HCMV) is by far the largest of any herpesvirus, yet it has been unclear how its capsid, which is similar in size to those of other herpesviruses, is stabilized. Here we report a HCMV atomic structure consisting of the herpesvirus-conserved capsid proteins MCP, Tri1, Tri2, and SCP and the HCMV-specific tegument protein pp150-totaling ~4000 molecules and 62 different conformers. MCPs manifest as a complex of insertions around a bacteriophage HK97 gp5-like domain, which gives rise to three classes of capsid floor-defining interactions; triplexes, composed of two "embracing" Tri2 conformers and a "third-wheeling" Tri1, fasten the capsid floor...
June 30, 2017: Science
https://www.readbyqxmd.com/read/28652006/3d-nus-a-web-server-for-automated-modeling-and-visualization-of-non-canonical-3-dimensional-nucleic-acid-structures
#15
L Ponoop Prasad Patro, Abhishek Kumar, Narendar Kolimi, Thenmalarchelvi Rathinavelan
The inherent conformational flexibility of nucleic acids facilitates the formation of a range of conformations such as duplex, triplex, quadruplex, etc. that play crucial roles in biological processes. Elucidation of the influence of non-canonical base pair mismatches on DNA/RNA structures at different sequence contexts to understand the mismatch repair, misregulation of alternative splicing mechanisms and the sequence-dependent effect of RNA-DNA hybrid in relevance to antisense strategy demand their three-dimensional structural information...
August 4, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28641941/role-of-recombination-and-replication-fork-restart-in-repeat-instability
#16
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...
August 2017: DNA Repair
https://www.readbyqxmd.com/read/28636339/binding-differences-of-two-homochiral-ru-bpy-2dppz-2-complexes-with-poly-u-%C3%A2-poly-a-poly-u-triplex-rna
#17
Meng-Na Peng, Zhi-Yuan Zhu, Li-Feng Tan
The first investigation of chiral ruthenium(II) complexes Δ- and Λ-[Ru(bpy)2dppz](2+) and triplex RNA poly(U)·poly(A)*poly(U) was carried out, which showed that Δ enantiomer displayed significant ability in stabilizing model triplex RNA.
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28635252/proton-fueled-reversible-dna-hybridization-chain-assembly-for-ph-sensing-and-imaging
#18
Lan Liu, Jin-Wen Liu, Zhi-Mei Huang, Han Wu, Na Li, Li-Juan Tang, Jian-Hui Jiang
Design of DNA self-assembly with reversible responsiveness to external stimuli is of great interest for diverse applications. We for the first time develop a pH-responsive, fully reversible hybridization chain reaction (HCR) assembly that allows sensitive sensing and imaging of pH in living cells. Our design relies on the triplex forming sequences that form DNA triplex with toehold regions under acidic conditions and then induce a cascade of strand displacement and DNA assembly. The HCR assembly has shown dynamic responses in physiological pH ranges with excellent reversibility and demonstrated the potential for in vitro detection and live-cell imaging of pH...
June 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28630686/fecal-carriage-of-extended-spectrum-%C3%AE-lactamase-and-carbapenemase-producing-enterobacteriaceae-in-egyptian-patients-with-community-onset-gastrointestinal-complaints-a-hospital-based-cross-sectional-study
#19
H M Abdallah, N Alnaiemi, E A Reuland, B B Wintermans, A Koek, A M Abdelwahab, A Samy, K W Abdelsalam, C M J E Vandenbroucke-Grauls
OBJECTIVES: The aim of this study was to determine the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among Enterobacteriaceae isolated from ambulatory patients with gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt in the period between January 2013 and May 2013. METHODS: One hundred and thirteen Enterobacteriaceae isolates were recovered from 100 consecutive Egyptian patients with community-onset gastrointestinal complaints...
2017: Antimicrobial Resistance and Infection Control
https://www.readbyqxmd.com/read/28627887/controlling-the-catalytic-functions-of-dnazymes-within-constitutional-dynamic-networks-of-dna-nanostructures
#20
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 systems 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...
July 10, 2017: Journal of the American Chemical Society
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