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https://www.readbyqxmd.com/read/28934473/the-conserved-au-dinucleotide-at-the-5-end-of-nascent-u1-snrna-is-optimized-for-the-interaction-with-nuclear-cap-binding-complex
#1
Chung-Shu Yeh, Shang-Lin Chang, Jui-Hui Chen, Hsuan-Kai Wang, Yue-Chang Chou, Chun-Hsiung Wang, Shih-Hsin Huang, Amy Larson, Jeffrey A Pleiss, Wei-Hau Chang, Tien-Hsien Chang
Splicing is initiated by a productive interaction between the pre-mRNA and the U1 snRNP, in which a short RNA duplex is established between the 5' splice site of a pre-mRNA and the 5' end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5'-end of the U1 snRNA is highly conserved, despite the absence of an apparent role in the formation of the duplex. To explore this conundrum, we varied this AU dinucleotide into all possible permutations and analyzed the resulting molecular consequences...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934467/the-important-conformational-plasticity-of-dsra-srna-for-adapting-multiple-target-regulation
#2
Pengzhi Wu, Xiaodan Liu, Lingna Yang, Yitong Sun, Qingguo Gong, Jihui Wu, Yunyu Shi
In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem-loops of DsrA. We first solved the NMR structure of the first stem-loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28934140/applications-of-pna-based-artificial-restriction-dna-cutters
#3
REVIEW
Narumi Shigi, Jun Sumaoka, Makoto Komiyama
More than ten years ago, artificial restriction DNA cutters were developed by combining two pseudo-complementary peptide nucleic acid (pcPNA) strands with either Ce(IV)/EDTA or S1 nuclease. They have remarkably high site-specificity and can cut only one predetermined site in the human genome. In this article, recent progress of these man-made tools have been reviewed. By cutting the human genome site-selectively, desired fragments can be clipped from either the termini of chromosomes (telomeres) or from the middle of genome...
September 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28932480/crystal-structure-of-n-4-hy-droxy-benz-yl-acetone-thio-semicarbazone
#4
Saray Argibay-Otero, Ezequiel M Vázquez-López
The structure of the title compound, C11H15N3OS, shows the flexibility due to the methyl-ene group at the thio-amide N atom in the side chain, resulting in the mol-ecule being non-planar. The dihedral angle between the plane of the benzene ring and that defined by the atoms of the thio-semicarbazide arm is 79.847 (4)°. In the crystal, the donor-acceptor hydrogen-bond character of the -OH group dominates the inter-molecular associations, acting as a donor in an O-H⋯S hydrogen bond, as well as being a double acceptor in a centrosymmetric cyclic bridging N-H⋯O,O' inter-action [graph set R2(2)(4)]...
September 1, 2017: Acta Crystallographica. Section E, Crystallographic Communications
https://www.readbyqxmd.com/read/28931822/a-dual-specific-targeting-approach-based-on-the-simultaneous-recognition-of-duplex-and-quadruplex-motifs
#5
Thi Quynh Ngoc Nguyen, Kah Wai Lim, Anh Tuân Phan
Small-molecule ligands targeting nucleic acids have been explored as potential therapeutic agents. Duplex groove-binding ligands have been shown to recognize DNA in a sequence-specific manner. On the other hand, quadruplex-binding ligands exhibit high selectivity between quadruplex and duplex, but show limited discrimination between different quadruplex structures. Here we propose a dual-specific approach through the simultaneous application of duplex- and quadruplex-binders. We demonstrated that a quadruplex-specific ligand and a duplex-specific ligand can simultaneously interact at two separate binding sites of a quadruplex-duplex hybrid harbouring both quadruplex and duplex structural elements...
September 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28931317/a-new-depsidone-derivative-from-the-leaves-of-garcinia-polyantha
#6
Alain Meli Lannang, Denis Kehdinga Sema, Simplice J N Tatsimo, V F Tsague Tankeu, Hycienth F Tegha, Jean Duplex Wansi, Yoshihito Shiono, Norbert Sewald
One new depsidone, polyanthadepsidone A (1), together with four known compounds were isolated from the dichloromethane extract of the leaves of Garcinia polyantha. The structures of all compounds were determined by comprehensive analyses of their 1D and 2D NMR and EI mass spectral data. All the isolates exhibited suppressive effect on phagocytosis response upon activation with serum opsonised zymosan in the IC50 range of 4.5-23.80 μM, tested in vitro for oxidative burst studies of whole blood.
September 20, 2017: Natural Product Research
https://www.readbyqxmd.com/read/28930804/venous-thromboembolism-in-gynecological-malignancy
#7
Abigail Cohen, Chung Sim Lim, Alun Huw Davies
OBJECTIVE: Venous thromboembolism (VTE) is a recognized complication of gynecological malignancy and represents a leading cause of morbidity and mortality in these patients. The review aimed to discuss the incidence, risk factors, and clinical presentation of VTE before examining the literature on the diagnosis, prevention, and management in the context of uterine, cervical, ovarian, and vulval cancers. METHODS/MATERIALS: A literature search was performed using Ovid Medline and Embase with the following words: "gynecological malignancy," "pelvic tumor," "venous thromboembolism," "deep vein thrombosis" and "pulmonary embolism...
September 19, 2017: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/28930746/early-assessment-of-the-risk-factors-for-diabetic-retinopathy-can-reduce-the-risk-of-peripheral-arterial-and-cardiovascular-diseases-in-type-2-diabetes
#8
Juan Tang, Tao Li, Pinhong Li, Yuefei Ma, Momo Liu, Qiaoyun Shan, Fengqi Guo, Ting Zhou, Qianping Wei
BACKGROUNDS: There is still a lack of consensus about how to assess the risk of peripheral arterial disease (PAD) and cardiovascular disease (CVD) in patients with diabetic retinopathy (DR). AIMS: We investigated the risk factors for DR and their association with PAD and CVD in patients with type 2 diabetes (T2D). METHODS: A total of 1,421 patients diagnosed with T2D participated in this study. DR stages were classified as non-DR, nonproliferative DR (NPDR), or proliferative DR (PDR)...
September 21, 2017: Ophthalmic Research
https://www.readbyqxmd.com/read/28929373/security-belt-for-wireless-implantable-medical-devices
#9
Selman Kulaç
In this study, a new protective design compatible with existing non-secure systems was proposed, since it is focused on the secure communication of wireless IMD systems in all transmissions. This new protector is an external wearable device and appears to be a belt fitted around for the patients IMD implanted. However, in order to provide effective full duplex transmissions and physical layer security, some sophisticated transceiver antennas have been placed on the belt. In this approach, beam-focused multi-antennas in optimal positions on the belt are randomly switched when transmissions to the IMD are performed and multi-jammer switching with MRC combining or majority-rule based receiving techniques are applied when transmissions from the IMD are carried out...
September 19, 2017: Journal of Medical Systems
https://www.readbyqxmd.com/read/28927817/development-and-evaluation-of-a-two-step-multiplex-taqman-real-time-pcr-assay-for-detection-quantification-of-different-genospecies-of-borrelia-burgdorferi-sensu-lato
#10
Mónica Nunes, Ricardo Parreira, Teresa Carreira, João Inácio, Maria Luísa Vieira
Nowadays, at least four clinically important B. burgdorferi sensu lato (s.l.) genospecies (B. afzelii, B. garinii, B. burgdorferi sensu stricto (s.s.) and B. lusitaniae) circulate in Portugal. Each genospecies has a different tropism that resuls in a diverse array of clinical manifestations. The standard diagnostic procedure used is normally simple, nevertheless, during the "window-period" phase, in which specific antibodies cannot yet be detected, diagnosis becomes difficult, and calls for reliable, sensitive and specific laboratory methods, such as molecular tests...
September 11, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28927554/catheter-foam-sclerotherapy-of-the-great-saphenous-vein-with-perisaphenous-tumescence-infiltration-and-saphenous-irrigation
#11
Attilio Cavezzi, Giovanni Mosti, Fausto Campana, Lorenzo Tessari, Luca Bastiani, Simone U Urso
OBJECTIVES: This was a prospective observational study to assess the short- to mid-term efficacy and safety of catheter foam sclerotherapy (CFS) of the great saphenous vein (GSV), including peri-saphenous tumescence infiltration (PST) and intra-saphenous saline irrigation (ISI), in combination with phlebectomy of the varicose tributaries. METHODS: Eighty-eight limbs in 82 patients (19 male, 63 female, mean age 55.7 years) affected by varices related to GSV incompetence were submitted to CFS of the refluxing GSV segment after PST and ISI, combined with phlebectomy of the varicose tributaries...
September 15, 2017: European Journal of Vascular and Endovascular Surgery
https://www.readbyqxmd.com/read/28927535/potentiation-of-hydrogen-peroxide-toxicity-from-catalase-inhibition-to-stable-dna-iron-complexes
#12
Tulip Mahaseth, Andrei Kuzminov
Hydrogen peroxide (H2O2) is unique among general toxins, because it is stable in abiotic environments at ambient temperature and neutral pH, yet rapidly kills any type of cells by producing highly-reactive hydroxyl radicals. This life-specific reactivity follows the distribution of soluble iron, Fe(II) (which combines with H2O2 to form the famous Fenton's reagent),Fe(II) is concentrated inside cells, but is virtually absent outside them. Because of the immediate danger of H2O2, all cells have powerful H2O2 scavengers, the equally famous catalases, which enable cells to survive thousand-fold higher concentrations of H2O2 and, in combination with adequate movement of H2O2 across membranes, make the killing H2O2 concentrations virtually impractical to generate in vivo...
July 2017: Mutation Research
https://www.readbyqxmd.com/read/28926069/rna-directed-off-on-switch-of-rnase-h-activity-using-boronic-ester-formation
#13
Maëva Reverte, Ivan Barvik, Jean-Jacques Vasseur, Michael Smietana
RNase H is a non-specific endonuclease which degrades selectively the RNA strand in DNA/RNA duplexes. We demonstrate in the present study that 5'-boronic acid modified oligonucleotides hybridized to a RNA target sequence converts RNase H to an inactivated enzyme complex. The dynamic formation of a boronate ester upon addition of a diol moiety disrupts the enzyme-inhibitor complex and reactivates RNase H. Moreover, we show that reactivation of RNase H function can also be engineered through short RNA trimers inputs that fashion RNase H from a non-specific DNA-guided enzyme into an informational and programmable RNA-guided one...
September 19, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28925971/superplastic-deformation-mechanisms-of-superfine-nanocrystalline-duplex-pm-tial-based-alloy
#14
Xuebo Gong, Zhenxin Duan, Wen Pei, Hua Chen
In this paper, the equiaxed superfine/nanocrystalline duplex PM-TiAl-based alloy with (γ + α₂) microstructure, Ti-45Al-5Nb (at %), has been synthesized by high-energy ball milling and vacuum hot pressing sintering. Superplastic deformation behavior has been investigated at 1000 °C and 1050 °C with strain rates from 5 × 10(-5) s(-1) to 1 × 10(-3) s(-1). The effects of deformation on the microstructure and mechanical behaviors of high Nb containing TiAl alloy have been characterized and analyzed. The results showed that, the ultimate tensile strength of the alloy was 58...
September 19, 2017: Materials
https://www.readbyqxmd.com/read/28925529/cerebrovascular-response-to-the-cold-pressor-test-the-critical-role-of-carbon-dioxide
#15
Michael M Tymko, Thijs P Kerstens, Kevin W Wildfong, Philip N Ainslie
In addition to increasing sympathetic nervous activity, blood pressure, and cerebral blood flow (CBF), the cold pressor test (CPT) stimulates pain receptors, which may increase ventilation above metabolic demand; this response likely reduces the partial pressure of end-tidal carbon dioxide (PET CO2 ), and will attenuate elevations in CBF. We hypothesized: (1) CPT would elicit hyperventilation, effectively lowering PET CO2 ; (2) the CBF response will be elevated during an isocapnic (controlled PET CO2 ), compared to a poikilocapnic CPT (uncontrolled PET CO2 ); (3) In response to CPT, the common carotid artery (CCA) will vasodilatate, while the internal carotid artery (ICA) will remain unchanged to help regulate CBF...
September 19, 2017: Experimental Physiology
https://www.readbyqxmd.com/read/28924040/a-b-z-junction-induced-by-an-a-a-mismatch-in-gac-repeats-in-the-gene-for-cartilage-oligomeric-matrix-protein-promotes-binding-with-the-hz%C3%AE-adar1-protein
#16
Narendar Kolimi, Yogeeshwar Ajjugal, Thenmalarchelvi Rathinavelan
GAC repeat expansion from five to seven in the exonic region of the gene for cartilage oligomeric matrix protein (COMP) leads to pseudoachondroplasia, a skeletal abnormality. However, the molecular mechanism by which GAC expansions in the COMP gene lead to skeletal dysplasias is poorly understood. Here, we used MD simulations which indicate that an A...A mismatch in a d(GAC)6.d(GAC)6 duplex induces negative supercoiling, leading to a local B-to-Z DNA transition. This transition facilitates the binding of d(GAC)7...
September 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28922369/crimean-congo-hemorrhagic-fever-virus-nucleocapsid-protein-has-dual-rna-binding-modes
#17
Subbiah Jeeva, Sean Pador, Brittany Voss, Safder Saieed Ganaie, Mohammad Ayoub Mir
Crimean Congo hemorrhagic fever, a zoonotic viral disease, has high mortality rate in humans. There is currently no vaccine for Crimean Congo hemorrhagic fever virus (CCHFV) and chemical interventions are limited. The three negative sense genomic RNA segments of CCHFV are specifically encapsidated by the nucleocapsid protein into three ribonucleocapsids, which serve as templates for the viral RNA dependent RNA polymerase. Here we demonstrate that CCHFV nucleocapsid protein has two distinct binding modes for double and single strand RNA...
2017: PloS One
https://www.readbyqxmd.com/read/28921499/synthesis-of-the-phosphoramidite-units-for-benzene-glycol-nucleic-acid
#18
Yusuke Maeda, Nazuki Niwa, Yoshihito Ueno
Benzene-glycol nucleic acid-DNA chimeras form thermally and thermodynamically stable duplexes with complementary RNAs, and have base-discriminating abilities. This unit describes the synthesis of four nucleoside analogs, an adenine, cytosine, thymine, and guanine analogs with base-benzene-glycol structure. The synthesis starts with conversion of (S)-mandelic acid in arylboronic acid derivative, common intermediate. Nucleobase coupling of the intermediate and phosphitylation afford to phosphoroamidite units...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28920942/exponential-growth-and-selection-in-self-replicating-materials-from-dna-origami-rafts
#19
Xiaojin He, Ruojie Sha, Rebecca Zhuo, Yongli Mi, Paul M Chaikin, Nadrian C Seeman
Self-replication and evolution under selective pressure are inherent phenomena in life, and but few artificial systems exhibit these phenomena. We have designed a system of DNA origami rafts that exponentially replicates a seed pattern, doubling the copies in each diurnal-like cycle of temperature and ultraviolet illumination, producing more than 7 million copies in 24 cycles. We demonstrate environmental selection in growing populations by incorporating pH-sensitive binding in two subpopulations. In one species, pH-sensitive triplex DNA bonds enable parent-daughter templating, while in the second species, triplex binding inhibits the formation of duplex DNA templating...
September 18, 2017: Nature Materials
https://www.readbyqxmd.com/read/28920119/synthesis-and-thermal-stabilities-of-oligonucleotides-containing-2-o-4-c-methylene-bridged-nucleic-acid-with-a-phenoxazine-base
#20
Yuki Kishimoto, Akane Fujii, Osamu Nakagawa, Tetsuya Nagata, Takanori Yokota, Yoshiyuki Hari, Satoshi Obika
We designed and synthesized a novel artificial 2'-O,4'-C-methylene bridged nucleic acid (2',4'-BNA/LNA) with a phenoxazine nucleobase and named this compound BNAP. Oligodeoxynucleotide (ODN) containing BNAP showed higher binding affinities toward complementary DNA and RNA as compared to ODNs bearing 2',4'-BNA/LNA with 5-methylcytosine or 2'-deoxyribonucleoside with phenoxazine. Thermodynamic analysis revealed that BNAP exhibits properties associated with the phenoxazine moiety in DNA/DNA duplexes and characteristics associated with the 2',4'-BNA/LNA moiety in DNA/RNA duplexes...
September 18, 2017: Organic & Biomolecular Chemistry
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