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https://www.readbyqxmd.com/read/28641941/role-of-recombination-and-replication-fork-restart-in-repeat-instability
#1
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/28636339/binding-differences-of-two-homochiral-ru-bpy-2dppz-2-complexes-with-poly-u-%C3%A2-poly-a-poly-u-triplex-rna
#2
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
#3
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
#4
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
#5
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/28624806/targeting-the-tumor-promoting-microenvironment-in-met-amplified-nsclc-cells-with-a-novel-inhibitor-of-pro-hgf-activation
#6
Benjamin Y Owusu, Shantasia Thomas, Phanindra Venukadasula, Zhenfu Han, James W Janetka, Robert A Galemmo, Lidija Klampfer
Targeted therapeutic agents, such as inhibitors of epithelial growth factor receptor (EGFR), have transformed the management of non-small cell lung cancer (NSCLC) patients. MET-amplified NSCLC cells display resistance to EGFR-targeting agents, but are addicted to MET signaling for survival and proliferation and are sensitive to MET inhibition. However, responsive cancer cells invariably develop resistance to MET-targeted treatment.The tumor microenvironment plays a major role in resistance to anticancer therapy...
May 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28612519/glucosyltransferase-dependent-and-independent-effects-of-tcdb-on-the-proteome-of-hep-2-cells
#7
Jelena Erdmann, Johannes Junemann, Anke Schröder, Ingo Just, Ralf Gerhard, Andreas Pich
Toxin B (TcdB) of the nosocomial pathogen C. difficile has been reported to exhibit a glucosyltransferase dependent and independent effect on treated HEp-2 cells at toxin concentration above 0.3 nM. In order to investigate and further characterize both effects epithelial cells were treated with wild type TcdB and glucosyltransferase-deficient TcdBNXN and their proteomes were analyzed by LC-MS. Triplex SILAC labeling was used for quantification. Identification of 5212 and quantification of 4712 protein groups was achieved...
June 14, 2017: Proteomics
https://www.readbyqxmd.com/read/28606420/pressure-transmission-area-and-maximum-pressure-transmission-of-different-thermoplastic-resin-denture-base-materials-under-impact-load
#8
Hubban Nasution, Krid Kamonkhantikul, Mansuang Arksornnukit, Hidekazu Takahashi
PURPOSES: The purposes of the present study were to examine the pressure transmission area and maximum pressure transmission of thermoplastic resin denture base materials under an impact load, and to evaluate the modulus of elasticity and nanohardness of thermoplastic resin denture base. METHODS: Three injection-molded thermoplastic resin denture base materials [polycarbonate (Basis PC), ethylene propylene (Duraflex), and polyamide (Valplast)] and one conventional heat-polymerized acrylic resin (PMMA, SR Triplex Hot) denture base, all with a mandibular first molar acrylic resin denture tooth set in were evaluated (n=6)...
June 9, 2017: Journal of Prosthodontic Research
https://www.readbyqxmd.com/read/28605461/determining-the-folding-and-binding-free-energy-of-dna-based-nanodevices-and-nanoswitches-using-urea-titration-curves
#9
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
https://www.readbyqxmd.com/read/28604066/simultaneous-identification-of-haemophilus-influenzae-and-haemophilus-haemolyticus-using-real-time-pcr
#10
Erin P Price, Tegan M Harris, Jessie Spargo, Elizabeth Nosworthy, Jemima Beissbarth, Anne B Chang, Heidi C Smith-Vaughan, Derek S Sarovich
AIM: To design a highly specific and sensitive multiplex real-time PCR assay for the differentiation of the pathogen Haemophilus influenzae from its nonpathogenic near-neighbor Haemophilus haemolyticus. MATERIALS & METHODS: A comparison of 380 Haemophilus spp. genomes was used to identify loci specific for each species. Novel PCR assays targeting H. haemolyticus (hypD) and H. influenzae (siaT) were designed. RESULTS & DISCUSSION: PCR screening across 143 isolates demonstrated 100% specificity for hypD and siaT...
June 12, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28602196/sequence-specific-recognition-of-hiv-1-dsdna-in-the-large-amount-of-normal-dsdna-based-upon-nicking-enzyme-signal-amplification-and-triplex-dna
#11
Houya Zhu, Manjun Zhang, Li Zou, Ruimin Li, Liansheng Ling
A sensitive fluorescent strategy for sequence specific recognition of HIV dsDNA was established based upon Nicking Enzyme Signal Amplification (NESA) and triplex formation. dsDNA sequence from the site 7960 to site 7991 of the HIV1 dsDNA gene was designed as target dsDNA, which was composed of two complementary strands Oligonucleotide 1 with the sequence of 3'-CTT CCT TAT CTT CTT CTT CCA CCT CTC TCT CT-5' (Oligo-1) and Oligonucleotide 2 with the sequence of 5'-GAA GGA ATA GAA GAA GAA GGT GGA GAG AGA GA-3' (Oligo-2)...
October 1, 2017: Talanta
https://www.readbyqxmd.com/read/28590848/exploring-the-qsar-s-predictive-truthfulness-of-the-novel-n-tuple-discrete-derivative-indices-on-benchmark-datasets
#12
O Martínez-Santiago, Y Marrero-Ponce, R Vivas-Reyes, O M Rivera-Borroto, E Hurtado, M A Treto-Suarez, Y Ramos, F Vergara-Murillo, M E Orozco-Ugarriza, Y Martínez-López
Graph derivative indices (GDIs) have recently been defined over N-atoms (N = 2, 3 and 4) simultaneously, which are based on the concept of derivatives in discrete mathematics (finite difference), metaphorical to the derivative concept in classical mathematical analysis. These molecular descriptors (MDs) codify topo-chemical and topo-structural information based on the concept of the derivative of a molecular graph with respect to a given event (S) over duplex, triplex and quadruplex relations of atoms (vertices)...
May 2017: SAR and QSAR in Environmental Research
https://www.readbyqxmd.com/read/28573341/identification-of-methicillin-resistant-staphylococcus-aureus-mrsa-using-simultaneous-detection-of-meca-nuc-and-femb-by-loop-mediated-isothermal-amplification-lamp
#13
Changguo Chen, Qiangyuan Zhao, Jianwei Guo, Yanjun Li, Qiuyuan Chen
The aim of this study was to develop a rapid detection assay to identify methicillin-resistant Staphylococcus aureus by simultaneous testing for the mecA, nuc, and femB genes using the loop-mediated isothermal amplification (LAMP) method. LAMP primers were designed using online bio-software ( http://primerexplorer.jp/e/ ), and amplification reactions were performed in an isothermal temperature bath. The products were then examined using 2% agarose gel electrophoresis. MecA, nuc, and femB were confirmed by triplex TaqMan real-time PCR...
June 2, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28571974/effect-of-the-3-halo-substitution-of-the-2-deoxy-aminopyridinyl-pseudocytidine-derivatives-on-the-selectivity-and-stability-of-antiparallel-triplex-dna-with-a-cg-inversion-site
#14
Lei Wang, Yosuke Taniguchi, Hidenori Okamura, Shigeki Sasaki
Triplex formation against a target duplex DNA has the potential to become a tool for the genome research. However, there is an intrinsic restriction on the duplex DNA sequences capable of forming the triplex DNA. Recently, we demonstrated the selective formation of the stable antiparallel triplexes containing the CG inversion sites using the 2'-deoxy-1-methylpseudocytidine derivative (ΨdC), whose amino group was conjugated with the 2-aminopyridine at its 5-position as an additional hydrogen bonding unit (AP-ΨdC)...
May 19, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28559129/one-step-cross-genogroup-multiplex-rt-qpcr-with-an-internal-control-system-for-the-detection-of-infectious-pancreatic-necrosis-virus-ipnv
#15
Marc Hoferer, Anne Braun, Julia Skrypski, Sabine Bock, Sabine Thalheim, Reinhard Sting
Infectious pancreatic necrosis virus (IPNV) causes great losses in fish hatcheries world-wide. The detection of IPNV can be challenging in certain circumstances, particularly due to low viral load and the genetic variability of this RNA virus. For the first time, this project created a quantitative triplex real-time reverse transcription PCR (RT-qPCR), including an endogenous control system, for specific, sensitive and rapid detection of IPNV in routine diagnostics. Multiple sequence alignment of 46 nucleotide sequences of the segment A genome obtained from the NCBI database allowed the design of two RT-qPCR systems covering the IPNV genogroup 1 and genogroups 2-5, respectively...
May 27, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28545966/third-strand-stabilization-of-poly-u-%C3%A2-poly-a-poly-u-triplex-by-the-naturally-occurring-flavone-luteolin-a-multi-spectroscopic-approach
#16
Richa Tiwari, Lucy Haque, Sutanwi Bhuiya, Suman Das
Naturally occurring flavonoid luteolin (LTN) was found to interact with double stranded poly(A).poly(U) and triple stranded poly(U)·poly(A)*poly(U) with association constants of the order of 10(4)M(-1). The association was monitored by various spectroscopic and viscometric techniques. Non-cooperative binding was observed for the association of LTN with two different polymorphic forms of RNA. Intercalation mode of binding was confirmed by fluorescence quenching and viscometric experiments. Thermal melting profiles indicated greater stabilization of the Hoogsteen base paired third strand (∼16°C) compared to Watson-Crick double strand (∼5°C) of RNA by LTN...
May 22, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28530559/meat-species-identification-by-two-direct-triplex-real-time-pcr-assays-using-low-resolution-melting
#17
Phuvadol Thanakiatkrai, Thitika Kitpipit
We developed and validated the first direct multiplex real-time PCR assay with melt curve analysis for the identification of different types of meat. The assay detects six commonly eaten meat species and provides the following benefits: ease of use, shortened analysis time, and decreased analysis cost. Species-specific primers were designed from cytochrome b, cytochrome oxidase I, and 16S rRNA genes to generate PCR products with specific melting peaks that differentiate pork, beef, horsemeat, duck meat, ostrich meat, and chicken...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28528442/herpesvirus-capsid-assembly-and-dna-packaging
#18
Jason D Heming, James F Conway, Fred L Homa
Herpes simplex virus type I (HSV-1) is the causative agent of several pathologies ranging in severity from the common cold sore to life-threatening encephalitic infection. During productive lytic infection, over 80 viral proteins are expressed in a highly regulated manner, resulting in the replication of viral genomes and assembly of progeny virions. The virion of all herpesviruses consists of an external membrane envelope, a proteinaceous layer called the tegument, and an icosahedral capsid containing the double-stranded linear DNA genome...
2017: Advances in Anatomy, Embryology, and Cell Biology
https://www.readbyqxmd.com/read/28522581/conformational-dynamics-of-the-frameshift-stimulatory-structure-in-hiv-1
#19
Dustin B Ritchie, Tonia R Cappellano, Collin Tittle, Negar Rezajooei, Logan Rouleau, William Ka Sikkema, Michael T Woodside
Programmed ribosomal frameshifting (PRF) in HIV-1 is thought to be stimulated by a hairpin in the mRNA, although a pseudoknot-like triplex has also been proposed. Because the conformational dynamics of the stimulatory structure under tension applied by the ribosomal helicase during translation may play an important role in PRF, we used optical tweezers to apply tension to the HIV stimulatory structure and monitor its unfolding and refolding dynamics. The folding and unfolding kinetics and energy landscape of the hairpin were measured by ramping the force on the hairpin up and down, providing a detailed biophysical characterisation...
May 18, 2017: RNA
https://www.readbyqxmd.com/read/28515050/the-mapping-of-predicted-triplex-dna-rna-in-the-drosophila-genome-reveals-a-prominent-location-in-development-and-morphogenesis-related-genes
#20
Claude Pasquier, Sandra Agnel, Alain Robichon
Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored...
May 17, 2017: G3: Genes—Genomes—Genetics
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