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https://www.readbyqxmd.com/read/28425774/profile-of-the-triplex-assay-for-detection-of-chlamydia-gonorrhea-and-trichomonas-using-the-bd-max%C3%A2-system
#1
Barbara Van Der Pol
Chlamydia, gonorrhea and trichomonas are the most common curable STI. Improved access to testing could reduce infection rates and prevent sequelae. Nucleic acid amplification tests are the recommend class of diagnostic assay for these infections which are often asymptomatic. Areas Covered: A description of the BD MAX™ System (MAX) and the BD MAX CT/GC/TV assay is provided along with data from a large US clinical trial. The capacity of the system for other tests and for lab developed assays is also described...
April 20, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28391510/evaluation-of-two-triplex-one-step-qrt-pcr-assays-for-the-quantification-of-human-enteric-viruses-in-environmental-samples
#2
Kata Farkas, Dafydd E Peters, James E McDonald, Alexis de Rougemont, Shelagh K Malham, Davey L Jones
Human enteric viruses are responsible for waterborne and shellfish-associated disease outbreaks worldwide. Quantitative reverse transcription PCR (qRT-PCR) is often used to assess the health risks associated with shellfish and environmental water, but viral titres in sediments are less commonly investigated. In this study, we developed and validated two multiplex qRT-PCR assays for aquatic sediment and shellfish samples targeting viruses that are a common cause of gastroenteritis (norovirus GI, GII and hepatitis A virus), two emerging viruses (sapovirus and hepatitis E virus), along with mengovirus (MgV), which is often used as a sample process control for the assessment of RNA extraction efficiency...
April 8, 2017: Food and Environmental Virology
https://www.readbyqxmd.com/read/28390431/mycoplasma-detection-by-triplex-real-time-pcr-in-bronchoalveolar-lavage-fluid-from-bovine-respiratory-disease-complex-cases
#3
Jan B W J Cornelissen, Freddy M de Bree, Fimme J van der Wal, Engbert A Kooi, Miriam G J Koene, Alex Bossers, Bregtje Smid, Adriaan F Antonis, Henk J Wisselink
BACKGROUND: In this study we evaluated the RespoCheck Mycoplasma triplex real-time PCR for the detection in bronchoalveolar lavage fluid (BALF) of Mycoplasma (M.) dispar, M. bovis and M. bovirhinis, all three associated with bovine respiratory disease (BRD). Primers and probes of the RespoCheck Mycoplasma triplex real-time PCR are based on the V3/V4 region of the 16S rRNA gene of the three Mycoplasma species. RESULTS: The analytical sensitivity of the RespoCheck triplex real-time PCR was, as determined by spiking experiments of the Mycoplasma strains in Phosphate Buffered Saline, 300 colony forming units (cfu)/mL for M...
April 8, 2017: BMC Veterinary Research
https://www.readbyqxmd.com/read/28383784/folding-topology-of-a-short-coiled-coil-peptide-structure-templated-by-an-oligonucleotide-triplex
#4
Chenguang Lou, Niels Johan Christensen, Manuel C Martos-Maldonado, Søren Roi Midtgaard, Maria Ejlersen, Peter W Thulstrup, Kasper K Sørensen, Knud J Jensen, Jesper Wengel
The rational design of a well-defined protein-like tertiary structure formed by small peptide building blocks is still a formidable challenge. Using peptide-oligonucleotide conjugates (POC) as building blocks, we here present the self-assembly of miniature coiled coil α-helical peptides guided by oligonucleotide duplex and triplex formation. POC synthesis was achieved by copper-free alkyne-azide cycloaddition between three oligonucleotides and a 23-mer peptide, which by itself exhibited multiple oligomeric states in solution...
April 6, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28380870/high-performance-refractive-index-sensor-based-on-low-q-factor-ring-resonators-and-fft-processing-of-wavelength-scanning-data
#5
Lefteris Gounaridis, Panos Groumas, Erik Schreuder, George Tsekenis, Athanasios Marousis, Rene Heideman, Hercules Avramopoulos, Christos Kouloumentas
We extend our previous simulation study and we present experimental results regarding our Fast Fourier Transform method for the calculation of the resonance shifts in biosensors based on micro-ring resonators (MRRs). For the simulation study, we use a system model with a tunable laser at 850 nm, an MRR with 1.5∙10<sup>4</sup> quality factor, and a detection system with 50 dB maximum signal-to-noise ratio, and investigate the impact on the system performance of factors like the number of the resonance peaks inside the scanning window, the wavelength dependence of the laser power, and the asymmetry of the transfer functions of the MRRs...
April 3, 2017: Optics Express
https://www.readbyqxmd.com/read/28372729/development-of-a-thermostabilised-triplex-lamp-assay-with-dry-reagent-four-target-lateral-flow-dipstick-for-detection-of-entamoeba-histolytica-and-non-pathogenic-entamoeba-spp
#6
Phiaw Chong Foo, Yean Yean Chan, Maizan Mohamed, Weng Kin Wong, A B Nurul Najian, Boon Huat Lim
This study highlighted the development of a four target nitrocellulose-based nucleic acid lateral flow immunoassay biosensor in a dry-reagent strip format for interpretation of double-labelled double-stranded amplicons from thermostabilised triplex loop-mediated isothermal amplification assay. The DNA biosensor contained two test lines which captured biotin and texas red labelled amplicons; a LAMP internal amplification control line that captured digoxigenin labelled amplicon; and a chromatography control line that validated the functionality of the conjugated gold nanoparticles and membrane...
May 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28371376/a-smart-responsive-dual-aptamers-targeted-bubble-generating-nanosystem-for-cancer-triplex-therapy-and-ultrasound-imaging
#7
Feifei Zhao, Jie Zhou, Xiangjie Su, Yuhui Wang, Xiaosa Yan, Shaona Jia, Bin Du
The absence of targeted, single treatment methods produces low therapeutic value for treating cancers. To increase the accumulation of drugs in tumors and improve the treatment effectiveness, near-infrared 808 nm photothermal responsive dual aptamers-targeted docetaxel (DTX)-containing nanoparticles is proposed. In this system, DTX and NH4 HCO3 are loaded in thermosensitive liposomes. The surface of liposomes is coated with gold nanoshells and connected with sulfydryl (SH) modified AS1411 and S2.2 aptamers...
March 30, 2017: Small
https://www.readbyqxmd.com/read/28370485/19f-nmr-spectroscopic-analysis-of-the-binding-modes-in-triple-helical-pna-microrna-complexes
#8
Pasi Markus Virta, Ville Tähtinen, Lotta Granqvist, Merita Murtola, Roger Strömberg
Triplex-forming peptide nucleic acids (TFPNAs) were targeted to double helical regions of 19F-labelled RNA hairpin models (a UA-rich duplex with a hexaethylene glycol (heg) loop and a miR-215 model). In addition to the conventional UV- and CD-based detection, the binding was monitored by 19F NMR spectroscopy. Detailed information considering the stoichiometry and transition between the triple helical PNA/RNA- and (PNA)2/RNA-binding modes could be obtained. γ-(R)-hydroxymethyl-modified (thymine-1-yl- and 2-aminopyridin-3-yl-acetyl derivatives) TFPNAs were additionally synthesized, targeted to the same RNA models and the effect of the γ-(R)-hydroxymethyl group on the binding was studied...
March 28, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28362093/selective-and-robust-stabilization-of-triplex-dna-structures-using-cationic-comb-type-copolymers
#9
Asako Yamayoshi, Daisuke Miyoshi, Yu-Ki Zouzumi, Yohei Matsuyama, Jumpei Ariyoshi, Naohiko Shimada, Akira Murakami, Takehiko Wada, Atsushi Maruyama
DNA sequences capable of forming triplexes induce DNA double-strand breaks that have attracted attention in genome editing technologies (e.g., CRISPR/Cas9 system, TALEN, and ZFN). Therefore, novel functional tools that stabilize triplex DNA structures must be further investigated to spark renewed interest. In this study, we investigated the unique character of cationic comb-type copolymers for the selective stabilization of triplex DNA. The melting temperature (Tm) of triplex DNA increased from 24.5 ºC to 73...
March 31, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28347279/simultaneous-detection-of-respiratory-syncytial-virus-and-human-metapneumovirus-by-one-step-multiplex-real-time-rt-pcr-in-patients-with-respiratory-symptoms
#10
Huey-Ling You, Shun-Jen Chang, Hong-Ren Yu, Chia-Chin Li, Chang-Han Chen, Wei-Ting Liao
BACKGROUND: Both respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) are important viral pathogens causing respiratory tract infection (RTI) in the pediatric population. However, the clinical manifestations of RSV and hMPV infections are similar. Therefore, a reliable and rapid diagnostic tool is needed for diagnostic performance. METHODS: In order to optimize diagnosis efficiency of RTI, the aim of this study is to establish a rapid and advanced method for simultaneous detecting RSV and hMPV in nasopharyngeal aspirates specimens from patients...
March 27, 2017: BMC Pediatrics
https://www.readbyqxmd.com/read/28334873/alternative-dna-structure-formation-in-the-mutagenic-human-c-myc-promoter
#11
Imee Marie A Del Mundo, Maha Zewail-Foote, Sean M Kerwin, Karen M Vasquez
Mutation 'hotspot' regions in the genome are susceptible to genetic instability, implicating them in diseases. These hotspots are not random and often co-localize with DNA sequences potentially capable of adopting alternative DNA structures (non-B DNA, e.g. H-DNA and G4-DNA), which have been identified as endogenous sources of genomic instability. There are regions that contain overlapping sequences that may form more than one non-B DNA structure. The extent to which one structure impacts the formation/stability of another, within the sequence, is not fully understood...
February 21, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28332825/oligonucleotides-containing-aminated-2-amino-lna-nucleotides-synthesis-and-strong-binding-to-complementary-dna-and-rna
#12
Chenguang Lou, Simone V Samuelsen, Niels Johan Christensen, Birte Vester, Jesper Wengel
Mono- and diaminated 2'-amino-LNA monomers were synthesized and introduced into oligonucleotides. Each modification imparts significant stabilization of nucleic acid duplexes and triplexes, excellent sequence selectivity, and significant nuclease resistance. Molecular modeling suggested that structural stabilization occurs via intrastrand electrostatic attraction between the protonated amino groups of the aminated 2'-amino-LNA monomers and the host oligonucleotide backbone.
April 5, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28331957/digital-triplex-dna-assay-based-on-plasmonic-nanocrystals
#13
Guohua Li, Liang Zhu, Yonghong He, Hui Tan, Shuqing Sun
A new analytical method has been developed to detect three kinds of DNA simultaneously based on magnetic beads and color-encoded plasmonic nanocrystals. Magnetic beads modified with capture DNA are employed to collect the specific target DNA, and color-encoded plasmonic nanocrystals are applied to signal the target through DNA hybridization. As a proof of concept, three types of representative metal nanocrystals of gold nanoparticle (AuNP), gold nanorod (AuNR), and gold/silver nanoparticle (Au/AgNP) were employed to signal three dissimilar virus-related protective antigen genes, Ebola virus (EV), Variola virus (VV), and Bacillus anthracis (BA), respectively...
March 22, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28276503/ultrasensitive-colorimetric-detection-of-circulating-tumor-dna-using-hybridization-chain-reaction-and-the-pivot-of-triplex-dna
#14
Ruimin Li, Li Zou, Yanwei Luo, Manjun Zhang, Liansheng Ling
This work presents an amplified colorimetric biosensor for circulating tumor DNA (ctDNA), which associates the hybridization chain reaction (HCR) amplification with G-Quadruplex DNAzymes activity through triplex DNA formation. In the presence of ctDNA, HCR occurs. The resulting HCR products are specially recognized by one sequence to include one GGG repeat and the other containing three GGG repeats, through the synergetic effect of triplex DNA and asymmetrically split G-Quadruplex forming. Such design takes advantage of the amplification property of HCR and the high peroxidase-like catalytic activity of asymmetrically split G-Quadruplex DNAzymes by means of triplex DNA formation, which produces color signals in the presence of ctDNA...
March 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28270074/molecular-and-thermodynamic-studies-on-dna-triplex-formed-in-the-promoter-region-of-hmgb1-gene-as-a-selective-target-for-anticancer-drugs
#15
Neelam Lohani, Rajeswari Raja Moganty
HMGB1 (High Mobility Group Box-1) is a very versatile highly abundant architectural protein that plays multiple roles in human health and diseases. Under physiological condition it serves an amazing assortment of roles in different compartments of cell. The reported high expression of HMGB1 in almost all types of human cancers and inflammatory diseases make it a critical molecular therapeutic target. In the present study we have mobilized a proximal twenty one bp nucleotide (21RY) which is in the promoter region (-55 to-75) of hmgb1 gene and targeted it with triplex forming oligonucleotide (TFO) in combination with two widely used chemotherapeutic drugs actinomycin (ACT) and adriamycin (ADM)...
February 13, 2017: Anti-cancer Agents in Medicinal Chemistry
https://www.readbyqxmd.com/read/28266759/bioinspired-helical-microfibers-from-microfluidics
#16
Yunru Yu, Fanfan Fu, Luoran Shang, Yao Cheng, Zhongze Gu, Yuanjin Zhao
Helical objects are among the most important and landmark structures in nature, and represent an emerging group of materials with unique spiral geometry; because of their enriched physical and chemical properties, they can have multiple functionalities. However, the fabrication of such complex helical materials at the micro- or nanoscale level remains a challenge. Here, a coaxial capillary microfluidic system, with the functions of consecutive spinning and spiraling, is presented for scalable generation of helical microfibers...
March 7, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28248966/a-magnesium-induced-triplex-pre-organizes-the-sam-ii-riboswitch
#17
Susmita Roy, Heiko Lammert, Ryan L Hayes, Bin Chen, Regan LeBlanc, T Kwaku Dayie, José N Onuchic, Karissa Y Sanbonmatsu
Our 13C- and 1H-chemical exchange saturation transfer (CEST) experiments previously revealed a dynamic exchange between partially closed and open conformations of the SAM-II riboswitch in the absence of ligand. Here, all-atom structure-based molecular simulations, with the electrostatic effects of Manning counter-ion condensation and explicit magnesium ions are employed to calculate the folding free energy landscape of the SAM-II riboswitch. We use this analysis to predict that magnesium ions remodel the landscape, shifting the equilibrium away from the extended, partially unfolded state towards a compact, pre-organized conformation that resembles the ligand-bound state...
March 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28248486/stimuli-responsive-dna-based-hydrogels-from-basic-principles-to-applications
#18
Jason S Kahn, Yuwei Hu, Itamar Willner
The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology...
March 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28248374/ultra-fast-analog-to-digital-converter-based-on-a-nonlinear-triplexer-and-an-optical-coder-with-a-photonic-crystal-structure
#19
Farhad Mehdizadeh, Mohammad Soroosh, Hamed Alipour-Banaei, Ebrahim Farshidi
In this paper, we propose what we believe is a novel all-optical analog-to-digital converter (ADC) based on photonic crystals. The proposed structure is composed of a nonlinear triplexer and an optical coder. The nonlinear triplexer is for creating discrete levels in the continuous optical input signal, and the optical coder is for generating a 2-bit standard binary code out of the discrete levels coming from the nonlinear triplexer. Controlling the resonant mode of the resonant rings through optical intensity is the main objective and working mechanism of the proposed structure...
March 1, 2017: Applied Optics
https://www.readbyqxmd.com/read/28240889/correction-to-triplex-forming-peptide-nucleic-acid-probe-having-thiazole-orange-as-a-base-surrogate-for-fluorescence-sensing-of-double-stranded-rna
#20
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
No abstract text is available yet for this article.
February 27, 2017: Journal of the American Chemical Society
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