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https://www.readbyqxmd.com/read/28531327/interstrand-cross-links-arising-from-strand-breaks-at-true-abasic-sites-in-duplex-dna
#1
Zhiyu Yang, Nathan E Price, Kevin M Johnson, Yinsheng Wang, Kent S Gates
Interstrand cross-links are exceptionally bioactive DNA lesions. Endogenous generation of interstrand cross-links in genomic DNA may contribute to aging, neurodegeneration, and cancer. Abasic (Ap) sites are common lesions in genomic DNA that readily undergo spontaneous and amine-catalyzed strand cleavage reactions that generate a 2,3-didehydro-2,3-dideoxyribose sugar remnant (3'ddR5p) at the 3'-terminus of the strand break. Interestingly, this strand scission process leaves an electrophilic α,β-unsaturated aldehyde residue embedded within the resulting nicked duplex...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531158/impact-analysis-of-flow-shaping-in-ethernet-avb-tsn-and-afdx-from-network-calculus-and-simulation-perspective
#2
Feng He, Lin Zhao, Ershuai Li
Ethernet-AVB/TSN (Audio Video Bridging/Time-Sensitive Networking) and AFDX (Avionics Full DupleX switched Ethernet) are switched Ethernet technologies, which are both candidates for real-time communication in the context of transportation systems. AFDX implements a fixed priority scheduling strategy with two priority levels. Ethernet-AVB/TSN supports a similar fixed priority scheduling with an additional Credit-Based Shaper (CBS) mechanism. Besides, TSN can support time-triggered scheduling strategy. One direct effect of CBS mechanism is to increase the delay of its flows while decreasing the delay of other priority ones...
May 22, 2017: Sensors
https://www.readbyqxmd.com/read/28531137/synthesis-and-excellent-duplex-stability-of-oligonucleotides-containing-2-amino-lna-functionalized-with-galactose-units
#3
Rajesh Kumar, Annika Ries, Jesper Wengel
A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2'-N-alkyne 2'-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.
May 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28531121/a-qpcr-based-tool-to-diagnose-the-presence-of-harmful-cyanobacteria-and-cyanotoxins-in-drinking-water-sources
#4
Yi-Ting Chiu, Yi-Hsuan Chen, Ting-Shaun Wang, Hung-Kai Yen, Tsair-Fuh Lin
Harmful cyanobacteria have been an important concern for drinking water quality for quite some time, as they may produce cyanotoxins and odorants. Microcystis and Cylindrospermopsis are two common harmful cyanobacterial genera detected in freshwater lakes and reservoirs, with microcystins (MCs) and cylindrospermopsin (CYN) as their important metabolites, respectively. In this study, two sets of duplex qPCR systems were developed, one for quantifying potentially-toxigenic Microcystis and Microcystis, and the other one for cylindrospermopsin-producing cyanobacteria and Cylindrospermopsis...
May 20, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28529057/structural-basis-for-the-versatile-and-methylation-dependent-binding-of-ctcf-to-dna
#5
Hideharu Hashimoto, Dongxue Wang, John R Horton, Xing Zhang, Victor G Corces, Xiaodong Cheng
The multidomain CCCTC-binding factor (CTCF), containing a tandem array of 11 zinc fingers (ZFs), modulates the three-dimensional organization of chromatin. We crystallized the human CTCF DNA-binding domain in complex with a known CTCF-binding site. While ZF2 does not make sequence-specific contacts, each finger of ZF3-7 contacts three bases of the 15-bp consensus sequence. Each conserved nucleotide makes base-specific hydrogen bonds with a particular residue. Most of the variable base pairs within the core sequence also engage in interactions with the protein...
May 15, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28527820/adventitial-cystic-disease-of-radial-artery-apropos-of-a-case-and-review-of-literature
#6
Álvaro Torres-Blanco, Luis Ariel Pepén-Moquete, Vicente Molina-Nácher, Francisco Gómez-Palonés
Adventitial cystic disease is an uncommon condition that is characterized by the collection of mucinous material that accumulates in the adventitial layer of the artery. Predominantly, this entity affects the popliteal artery, whereas it is extremely rare in the radial artery. We report a 72-year-old female patient that underwent surgical treatment of an adventitial cyst of the right radial artery. The involved arterial segment was resected, and reconstruction by means of the interposition of a saphenous vein graft was performed...
May 11, 2017: Cardiovascular Pathology: the Official Journal of the Society for Cardiovascular Pathology
https://www.readbyqxmd.com/read/28527203/value-of-different-ultrasound-elastography-techniques-in-patients-with-venous-malformations-prior-to-and-after-sclerotherapy
#7
V I Teusch, A P Piehler, W Uller, R Müller-Wille, L Prantl, C Stroszczynski, W A Wohlgemuth, E M Jung
AIM: Comparison of different ultrasound elastography techniques for detection of changes after sclerotherapy within venous malformations. MATERIAL AND METHODS: In patients with venous malformations sonography was executed at exactly the same position prior to and after ethanol-gel sclerotherapy. Both examinations included B-Mode, vascular sonography with Color-Coded Duplex Sonography, and additional sonography with different elastography techniques (strain, qualitative and quantitative Acoustic Radiation Force Impulse (ARFI) elastography) with a linear transducer (6-9 MHz)...
May 19, 2017: Clinical Hemorheology and Microcirculation
https://www.readbyqxmd.com/read/28522907/droplet-digital-pcr-for-quantification-of-itga6-in-a-stool-mrna-assay-for-the-detection-of-colorectal-cancers
#8
Elizabeth Herring, Shigeru Kanaoka, Éric Tremblay, Jean-François Beaulieu
AIM: To investigate the use of droplet digital polymerase chain reaction (ddPCR) for detecting host mRNA markers in stools as a non-invasive test for colorectal cancer screening. METHODS: ddPCR and quantitative PCR were compared side by side for their performance in the detection of ITGA6 and ITGA6A transcripts in stool samples obtained from patients with various types of colorectal lesions (advanced adenomas and stage II-IV colorectal cancers) and control (patients displaying no pathological findings) using duplex TaqMan reactions for both methods...
April 28, 2017: World Journal of Gastroenterology: WJG
https://www.readbyqxmd.com/read/28516136/primers-and-probe-design-and-precision-assessment-of-the-real-time-rt-pcr-assay-in-coxsackievirus-a10-and-enterovirus-detection
#9
Jingfang Chen, Rusheng Zhang, Xinhua Ou, Dong Yao, Zheng Huang, Linzhi Li, Biancheng Sun
This data article contains data related to the research article entitled "Rapid detection of enterovirus and Coxsackievirus A10 by a TaqMan based duplex one-step real time RT-PCR assay" (Chen at al., 2017) [1]. Primers and probe sequence design are among the most critical factors in real-time polymerase chain reaction (PCR) assay optimization. Linearity, sensitivity, specificity and precision are the crucial criteria which are used to evaluate the performance of a new method. This data article report the primers and probe design and precision assessment of the new assay...
June 2017: Data in Brief
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
#10
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
https://www.readbyqxmd.com/read/28514894/successful-repair-of-acute-type-b-and-retrograde-type-a-aortic-dissection-with-kidney-ischemia
#11
Jeko M Madjarov, Michael G Katz, Hector Crespo-Soto, Svetozar Madzharov, Timothy Roush, Francis Robicsek
Acute dissection of thoracic aorta carries a risk of renal ischemia followed by the development of a kidney failure. The optimal surgical and nonsurgical management of these patients, timing of intervention, and the factors predicting renal recovery are not well delineated and remain controversial. We present a case of acute type B thoracic aortic dissection with left kidney ischemia. Evaluation of renal function was performed by the means of internationally accepted Risk, Injury, Failure, Loss of kidney function, End stage kidney disease and Acute Kidney Injury Network classifications for acute kidney injury, renal duplex sonography, and intravascular ultrasound that demonstrated left renal artery dissection with a flap completely compressing the true lumen...
January 1, 2017: Vascular and Endovascular Surgery
https://www.readbyqxmd.com/read/28514850/dna-dendrimer-streptavidin-nanocomplex-an-efficient-signal-amplifier-for-construction-of-biosensing-platforms
#12
Yan Zhao, Shichao Hu, Huaming Wang, Kaiwen Yu, Yan Guan, Xiaoyun Liu, Na Li, Feng Liu
We develop a DNA dendrimer-streptavidin (SA) nanocomplex as a novel signal amplifier to create biosensing platforms for disease-related species. The DNA dendrimer-SA nanocomplex is fabricated by crosslinking the nonlinear hybridization chain reaction based DNA dendrimer with the SA-coupled linker DNA, and possesses multiple sticky ends, a high molecular weight, and a hyperbranched nanostructure with large numbers of DNA duplexes. Taking advantages of the DNA dendrimer-SA nanocomplex and a label-free quartz crystal microbalance (QCM) technology, we first construct a mass-sensitive QCM biosensing platform for nucleic acids, which displays high selectivity and sensitivity with the detection limit of 0...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28513698/unzipping-and-shearing-dna-with-electrophoresed-nanoparticles-in-hydrogels
#13
Keitel Cervantes-Salguero, Ibuki Kawamata, Shin-Ichiro M Nomura, Satoshi Murata
We show electric control of unzipping and shearing dehybridization of a DNA duplex anchored to a hydrogel. Tensile force is applied by electrophoresing (25 V cm(-1)) gold nanoparticles pulling the DNA duplex. The pulled DNA strand is gradually released from the hydrogel. The unzipping release rate is faster than shearing; for example, 3-fold for a 15 base pair duplex, which helps to design electrically driven DNA devices.
May 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28513176/selective-inhibition-of-e-coli-rna-and-dna-topoisomerase-i-by-hoechst-33258-derived-mono-and-bisbenzimidazoles
#14
Nihar Ranjan, Sandra Story, Geraldine Fulcrand, Fenfei Leng, Muzammil Ahmad, Ada King, Souvik Sur, Weidong Wang, Yuk-Ching Tse-Dinh, Dev Priya Arya
A series of Hoechst 33258 based mono and bisbenzimidazoles have been synthesized and their E. coli DNA topoisomerase I inhibition, binding to B-DNA duplex and antibacterial activity has been evaluated. Bisbenzimidazoles with alkynyl side chains display excellent E. coli DNA topoisomerase I inhibition properties with IC50 values < 5.0 μM. Several bisbenzimidazoles (3, 6, 7, 8) also inhibit RNA topoisomerase activity of E. coli DNA topoisomerase I. Bisbenzimidazoles inhibit antibacterial growth much better than mono-benzimidazoles for gram positive strains...
May 17, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28512311/dramatic-improvement-of-strain-hardening-and-ductility-to-95-in-highly-deformable-high-strength-duplex-lightweight-steels
#15
Seok Su Sohn, Hyejin Song, Jai-Hyun Kwak, Sunghak Lee
Ferrite + austenite duplex lightweight steels have been actively developed by adding low-density Al for overcoming a limitation of stiffness deterioration by a traditional approach to obtain a weight reduction. Multiple-stage deformation mechanism in lightweight steels, i.e., simultaneous formation of deformation-induced martensite and deformation twin and additional plasticity by twinning, has been nominated as an attractive strategy, but shows a steady flow behavior with early plastic instability. Here, we present a newly designed Fe-0...
May 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28510342/constructing-a-robust-fluorescent-dna-stabilized-silver-nanocluster-probe-module-by-attaching-a-duplex-moiety
#16
Ruoyun Lin, Guangyu Tao, Yang Chen, Mingxing Chen, Feng Liu, Na Li
Fluorescent DNA-templated silver nanoclusters (DNA-Ag NCs) have been an excellent luminescence probe and operation unit in assorted applications. However, the fluorescence property of DNA-Ag NCs is very sensitive to elongation or modification of the DNA template, limiting the breadth of applications. In this work, we propose a strategy to construct a robust fluorescent DNA-Ag NCs probe module by attaching a duplex moiety to the nanocluster-bearing sequence. Fluorescence intensity of the DNA-Ag NCs can be enhanced by 90 fold upon hybridization of the elongated moiety...
May 16, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28510224/dna-supercoiling-is-a-fundamental-regulatory-principle-in-the-control-of-bacterial-gene-expression
#17
REVIEW
Charles J Dorman, Matthew J Dorman
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination...
September 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28510216/dna-supercoiling-is-a-fundamental-regulatory-principle-in-the-control-of-bacterial-gene-expression
#18
REVIEW
Charles J Dorman, Matthew J Dorman
Although it has become routine to consider DNA in terms of its role as a carrier of genetic information, it is also an important contributor to the control of gene expression. This regulatory principle arises from its structural properties. DNA is maintained in an underwound state in most bacterial cells and this has important implications both for DNA storage in the nucleoid and for the expression of genetic information. Underwinding of the DNA through reduction in its linking number potentially imparts energy to the duplex that is available to drive DNA transactions, such as transcription, replication and recombination...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28507706/ph-and-ligand-induced-release-of-loads-from-dna-acrylamide-hydrogel-microcapsules
#19
Wei-Ching Liao, Sivan Lilienthal, Jason S Kahn, Marianna Riutin, Yang Sung Sohn, Rachel Nechushtai, Itamar Willner
Herein, a method to construct stimuli-responsive DNA-acrylamide-based hydrogel microcapsules has been presented. This method involves the use of polyacrylamide chains modified with predesigned nucleic acid hairpin units and optionally single-strand tethers that provide the required hybridization and recognition functions to yield substrate-loaded stimuli-responsive hydrogel-based microcapsules. The synthesis of the microcapsules involves the loading of CaCO3 microparticles with the respective load substrates and the functionalization of the CaCO3 template particles with nucleic acid promoter units...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28507681/complementary-oligonucleotides-regulate-induced-fit-ligand-binding-in-duplexed-aptamers
#20
Jeffrey D Munzar, Andy Ng, Mario Corrado, David Juncker
Duplexed aptamers (DAs) are engineered by hybridizing an aptamer-complementary element (ACE, e.g. a DNA oligonucleotide) to an aptamer; to date, ACEs have been presumed to sequester the aptamer into a non-binding duplex state, in line with a conformational selection-based model of ligand binding. Here, we uncover that DAs can actively bind a ligand from the duplex state through an ACE-regulated induced fit mechanism. Using a widely-studied ATP DNA aptamer and a solution-based equilibrium assay, DAs were found to exhibit affinities up to 1 000 000-fold higher than predicted by conformational selection alone, with different ACEs regulating the level of induced fit binding, as well as the cooperative allostery of the DA (Hill slope of 1...
March 1, 2017: Chemical Science
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