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https://www.readbyqxmd.com/read/28441772/structural-and-biochemical-properties-of-novel-self-cleaving-ribozymes
#1
REVIEW
Ki-Young Lee, Bong-Jin Lee
Fourteen well-defined ribozyme classes have been identified to date, among which nine are site-specific self-cleaving ribozymes. Very recently, small self-cleaving ribozymes have attracted renewed interest in their structure, biochemistry, and biological function since the discovery, during the last three years, of four novel ribozymes, termed twister, twister sister, pistol, and hatchet. In this review, we mainly address the structure, biochemistry, and catalytic mechanism of the novel ribozymes. They are characterized by distinct active site architectures and divergent, but similar, biochemical properties...
April 24, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28436514/cpg-loaded-mos2-nanosheets-as-multifunctional-agents-for-photothermal-enhanced-cancer-immunotherapy
#2
Qiusen Han, Xinhuan Wang, Xinghang Jia, Shuangfei Cai, Wei Liang, Yan Qin, Rong Yang, Chen Wang
Single or few-layered MoS2 nanosheets, as a novel class of 2D nanomaterials, have received tremendous attention due to their fantastic physical and chemical properties. Here, we fabricated MoS2-PEG-CpG with a small and uniform size as a multifunctional platform for photothermal enhanced immunotherapy. MoS2 nanosheets were fabricated by chemical exfoliation and further probe sonication. To realize MoS2-based adjuvant delivery, MoS2 nanosheets were functionalized with cytosine-phosphate-guanine (CpG) and polyethylene glycol (PEG) to form MoS2-PEG-CpG nanoconjugates...
April 24, 2017: Nanoscale
https://www.readbyqxmd.com/read/28436463/relation-between-molecular-electronic-structure-and-nuclear-spin-induced-circular-dichroism
#3
Petr Štěpánek, Sonia Coriani, Dage Sundholm, Vasily A Ovchinnikov, Juha Vaara
The recently theoretically described nuclear spin-induced circular dichroism (NSCD) is a promising method for the optical detection of nuclear magnetization. NSCD involves both optical excitations of the molecule and hyperfine interactions and, thus, it offers a means to realize a spectroscopy with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine)...
April 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28432611/comparison-of-human-erythrocyte-purine-nucleotide-metabolism-and-blood-purine-and-pyrimidine-degradation-product-concentrations-before-and-after-acute-exercise-in-trained-and-sedentary-subjects
#4
Wioleta Dudzinska, M Suska, A Lubkowska, K Jakubowska, M Olszewska, K Safranow, D Chlubek
This study aimed at evaluating the concentration of erythrocyte purine nucleotides (ATP, ADP, AMP, IMP) in trained and sedentary subjects before and after maximal physical exercise together with measuring the activity of purine metabolism enzymes as well as the concentration of purine (hypoxanthine, xanthine, uric acid) and pyrimidine (uridine) degradation products in blood. The study included 15 male elite rowers [mean age 24.3 ± 2.56 years; maximal oxygen uptake (VO2max) 52.8 ± 4.54 mL/kg/min; endurance and strength training 8...
April 21, 2017: Journal of Physiological Sciences: JPS
https://www.readbyqxmd.com/read/28430443/theoretical-investigation-of-the-binding-of-nucleobases-to-cucurbiturils-by-dispersion-corrected-dft-approaches
#5
Natarajan Sathiyamoorthy Venkataramanan, Ambigapathy Suvitha
The encapsulation of nucleobases, inside CB7 has gained prominence due to its use as anticancer and antiviral drugs. With this respect, the nonconvalent interactions exists in the nucleobases encapsulated inside the CB7 cavity have been analyzed employing the dispersion corrected density functional theory. The CBn cavity has the ability to encapsulate two guest nucleobases molecules, when they are aligned in parallel configuration. The computed association energy using the two and three body correction method computed at B3LYP-D3 level is close to the experimental estimate...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28430197/g-quadruplex-organic-frameworks
#6
Yi-Lin Wu, Noah E Horwitz, Kan-Sheng Chen, Diego A Gomez-Gualdron, Norman S Luu, Lin Ma, Timothy C Wang, Mark C Hersam, Joseph T Hupp, Omar K Farha, Randall Q Snurr, Michael R Wasielewski
Two-dimensional covalent organic frameworks often π stack into crystalline solids that allow precise spatial positioning of molecular building blocks. Inspired by the hydrogen-bonded G-quadruplexes found frequently in guanine-rich DNA, here we show that this structural motif can be exploited to guide the self-assembly of naphthalene diimide and perylene diimide electron acceptors end-capped with two guanine electron donors into crystalline G-quadruplex-based organic frameworks, wherein the electron donors and acceptors form ordered, segregated π-stacked arrays...
May 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28429897/single-nucleotide-polymorphisms-v4-and-t1-of-the-adam33-gene-in-venezuelan-patients-with-asthma-or-chronic-obstructive-pulmonary-disease
#7
Daniela Martínez, Diego Lema, Dolores Del Carmen Moreno, Alexis Hipólito García, Jenny Valentina Garmendia, Juan Bautista De Sanctis
ADAM33 is a metalloproteinase important in the extracellular matrix for tissue remodeling, and, consequently, in asthma and chronic obstructive pulmonary disease (COPD). Several polymorphisms of the ADAM33 gene have been associated with enzyme activity. One of the most studied polymorphisms is V4, cytosine for guanine in the 3 'UTR region, and T1, adenine for guanine in the exon 19 of the gen. The aim of this study was to ascertain the possible association among single polymorphisms of ADAM33, V4 and T1, in Venezuelan patients with asthma or COPD...
June 2016: Investigación Clínica
https://www.readbyqxmd.com/read/28427088/a-phase-2-study-of-temozolomide-in-pretreated-metastatic-colorectal-cancer-with-mgmt-promoter-methylation
#8
M A Calegari, A Inno, S Monterisi, A Orlandi, D Santini, M Basso, A Cassano, M Martini, T Cenci, I de Pascalis, F Camarda, B Barbaro, L M Larocca, S Gori, G Tonini, C Barone
BACKGROUND: Presently, few options are available for refractory colorectal cancer (CRC). O6-methyl-guanine-DNA-methyltransferase (MGMT) promoter methylation is a frequent and early event in CRC tumourigenesis. This epigenetic silencing is a predictor of response to the alkylating drug temozolomide in glioblastoma. Preclinical evidences and some case reports showed temozolomide activity in CRC with MGMT silencing, but the available data from clinical trials are inconsistent. METHODS: This was a multicentre, phase 2 trial, planned according to a two-stage Simon's optimal design to investigate activity and safety of temozolomide in refractory CRC harbouring MGMT promoter methylation...
April 20, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28426879/acute-exposure-to-dehp-metabolite-mehp-cause-genotoxicity-mutagenesis-and-carcinogenicity-in-mammalian-chinese-hamster-ovary-cells
#9
Yu-Jung Chang, Chia-Yi Tseng, Pei-Ying Lin, Yu-Chen Chuang, Ming-Wei Chao
Di-(2-ethylhexyl) phthalate (DEHP), the common plasticizer used in the production of polyvinyl chloride, can be converted to the more potent metabolite mono-ethylhexyl phthalate (MEHP). Epidemiological studies have shown an association with elevated induction of rat hepatic cancer and reproductive toxicity in response to MEHP exposure. However, the mechanism of genotoxicity and carcinogenicity induced by MEHP treatment remains unclear. As a means to elucidate the mechanisms of action, lethality and mutagenicity in the adenine phosphoribosyltransferase (aprt+/-) gene induced in several CHO cell types by MEHP were assessed...
March 1, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28426288/post-translational-modifications-of-rab-gtpases
#10
Swapnil Rohidas Shinde, Subbareddy Maddika
Rab GTPases, the highly conserved members of Ras GTPase superfamily are central players in the vesicular trafficking. They are critically involved in intracellular trafficking pathway, beginning from formation of vesicles on donor membranes, defining trafficking specificity to facilitating vesicle docking on target membranes. Given the dynamic roles of Rabs during different stages of vesicular trafficking, mechanisms for their spatial and temporal regulation are crucial for normal cellular function. Regulation of Rab GTPase activity, localization and function has always been focused in and around the association of GDP dissociation inhibitor (GDI), Guanine nucleotide Exchange Factor (GEFs) and GTPase accelerating protein (GAP) to Rabs...
February 28, 2017: Small GTPases
https://www.readbyqxmd.com/read/28426082/deciphering-of-interactions-between-platinated-dna-and-hmgb1-by-hydrogen-deuterium-exchange-mass-spectrometry
#11
Yuanyuan Wang, Zhifeng Du, Wei Zheng, Kui Wu, Decheng Xu, Qun Luo, Yao Zhao, Juanjuan Han, Yangzhong Liu, Fuyi Wang
A high mobility group box 1 (HMGB1) protein has been reported to recognize both 1,2-intrastrand crosslinked DNA by cisplatin (1,2-cis-Pt-DNA) and monofunctional platinated DNA using trans-[PtCl2(NH3)(thiazole)] (1-trans-PtTz-DNA). However, the molecular basis of recognition between the trans-PtTz-DNA and HMGB1 remains unclear. In the present work, we described a hydrogen/deuterium exchange mass spectrometry (HDX-MS) method in combination with docking simulation to decipher the interactions of platinated DNA with domain A of HMGB1...
April 20, 2017: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/28425987/biological-activity-of-tumor-treating-fields-in-preclinical-glioma-models
#12
Manuela Silginer, Michael Weller, Roger Stupp, Patrick Roth
Glioblastoma is the most common and aggressive form of intrinsic brain tumor with a very poor prognosis. Thus, novel therapeutic approaches are urgently needed. Tumor-treating fields (TTFields) may represent such a novel treatment option. The aim of this study was to investigate the effects of TTFields on glioma cells, as well as the functional characterization of the underlying mechanisms. Here, we assessed the anti-glioma activity of TTFields in several preclinical models. Applying TTFields resulted in the induction of cell death in a frequency- and intensity-dependent manner in long-term glioma cell lines, as well as glioma-initiating cells...
April 20, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28425525/exploiting-hydrogen-bonding-interactions-to-probe-smaller-linear-and-cyclic-diamines-binding-to-g-quadruplexes-a-dft-and-molecular-dynamics-study
#13
Mrinal Kanti Si, Anik Sen, Bishwajit Ganguly
G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves...
April 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28420712/sec71-functions-as-a-gef-for-the-small-gtpase-arf1-to-govern-dendrite-pruning-of-drosophila-sensory-neurons
#14
Yan Wang, Heng Zhang, Meng Shi, Yih-Cherng Liou, Lei Lu, Fengwei Yu
Pruning, whereby neurons eliminate their exuberant neurites, is central for the maturation of the nervous system. In Drosophila, sensory neurons, ddaCs, selectively prune their larval dendrites without affecting their axons during metamorphosis. However, it is unknown whether the secretory pathway plays a role in dendrite pruning. Here, we show that the small GTPase Arf1, an important regulator of secretory pathway, is specifically required for dendrite pruning of ddaC/D/E sensory neurons but dispensable for apoptosis of ddaF neurons...
April 18, 2017: Development
https://www.readbyqxmd.com/read/28420501/bioinformatics-analysis-of-gene-expression-profiles-in-b-cells-of-postmenopausal-osteoporosis-patients
#15
Min Ma, Shulin Luo, Wei Zhou, Liangyu Lu, Junfeng Cai, Feng Yuan, Feng Yin
OBJECTIVE: The aim of this study was to gain a better understanding of the molecular mechanisms and identify more critical genes associated with the pathogenesis of postmenopausal osteoporosis (PMOP). MATERIALS AND METHODS: Microarray data of GSE13850 were download from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified either in B cells from postmenopausal female nonsmokers with high bone mineral density (BMD) compared with those with low BMD (defined as DEG1 group) or in B cells from postmenopausal female smokers with high BMD compared with postmenopausal female nonsmokers with high BMD (defined as DEG2 group)...
April 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28419165/soaking-suggests-alternative-facts-only-co-crystallization-discloses-major-ligand-induced-interface-rearrangements-of-a-homodimeric-trna-binding-protein-indicating-a-novel-mode-of-inhibition
#16
Frederik Rainer Ehrmann, Johann Stojko, Alexander Metz, François Debaene, Luzi Jakob Barandun, Andreas Heine, François Diederich, Sarah Cianférani, Klaus Reuter, Gerhard Klebe
For the efficient pathogenesis of Shigella, the causative agent of bacillary dysentery, full functionality of tRNA-guanine transglycosylase (TGT) is mandatory. TGT performs post-transcriptional modifications of tRNAs in the anticodon loop taking impact on virulence development. This suggests TGT as a putative target for selective anti-shigellosis drug therapy. Since bacterial TGT is only functional as homodimer, its activity can be inhibited either by blocking its active site or by preventing dimerization. Recently, we discovered that in some crystal structures obtained by soaking the full conformational adaptation most likely induced in solution upon ligand binding is not displayed...
2017: PloS One
https://www.readbyqxmd.com/read/28418097/genome-and-epigenome-of-a-novel-marine-thaumarchaeota-strain-suggest-viral-infection-phosphorothioation-dna-modification-and-multiple-restriction-systems
#17
Nathan A Ahlgren, Yangyang Chen, David M Needham, Alma E Parada, Rohan Sachdeva, Vicki Trinh, Ting Chen, Jed A Fuhrman
Marine Thaumarchaeota are abundant ammonia-oxidizers but have few representative laboratory-cultured strains. We report the cultivation of Candidatus Nitrosomarinus catalina SPOT01, a novel strain that is less warm-temperature tolerant than other cultivated Thaumarchaeota. Using metagenomic recruitment, strain SPOT01 comprises a major portion of Thaumarchaeota (4-54%) in temperate Pacific waters. Its complete 1.36 Mbp genome possesses several distinguishing features: putative phosphorothioation (PT) DNA modification genes; a region containing probable viral genes; and putative urea utilization genes...
April 18, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28416612/a-biochemical-and-biophysical-model-of-g-quadruplex-dna-recognition-by-positive-coactivator-of-transcription-4
#18
Wezley C Griffin, Jun Gao, Alicia K Byrd, Shubeena Chib, Kevin D Raney
DNA sequences that are guanine-rich have received considerable attention due to their potential to fold into a secondary, four-stranded DNA structure termed G-quadruplex (G4) which has been implicated in genomic instability and some human diseases. We have previously identified positive coactivator of transcription (PC4), a single-stranded DNA (ssDNA) binding protein, as a novel G4 interactor. Here, to expand on these previous observations, we biochemically and biophysically characterized the interaction between PC4 and G4DNA...
April 17, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28413933/primer-in-genetics-and-genomics-article-3-explaining-human-diversity-the-role-of-dna
#19
Catherine Y Read
Genetic variation lays the foundation for diversity and enables humans to adapt to changing environments. The order of the nucleotides adenine, guanine, cytosine, and thymine on the deoxyribonucleic acid (DNA) molecules of the nuclear chromosomes and mitochondrial DNA (mtDNA) plays an important role in normal cell division, tissue development, and reproduction but is susceptible to alteration from a large number of random, inherited, or environmental events. Variations can range from a change in a single nucleotide to duplication of entire chromosomes...
May 2017: Biological Research for Nursing
https://www.readbyqxmd.com/read/28412358/impact-of-g-quadruplex-loop-conformation-in-the-pitx1-mrna-on-protein-and-small-molecule-interaction
#20
Emmanuel O Ariyo, Evan P Booy, Edis Dzananovic, Ewan K McRae, Markus Meier, Kevin McEleney, Jorg Stetefeld, Sean A McKenna
Intramolecular G-quadruplexes (G4s) are G-rich nucleic acid structures that fold back on themselves via interrupting loops to create stacked planar G-tetrads, in which four guanine bases associate via Hoogsteen hydrogen bonding. The G4 structure is further stabilized by monovalent cations centered between the stacked tetrads. The G-tetrad face on the top and bottom planes of G4s are often the site of interaction with proteins and small molecules. To investigate the potential impact of interrupting loops on both G4 structure and interaction with proteins/small molecules, we characterized a specific G4 from the 3'-UTR of PITX1 mRNA that contains loops of 6 nucleotides using biophysical approaches...
April 12, 2017: Biochemical and Biophysical Research Communications
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