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https://www.readbyqxmd.com/read/28330193/a-rapid-method-for-isolation-of-genomic-dna-from-food-borne-fungal-pathogens
#1
S Umesha, H M Manukumar, Sri Raghava
Food contaminated with fungal pathogens can cause extremely harmful effects to human even when present in low concentrations. Researchers now pay more attention towards rapid DNA extraction for the quick screening, which is highly demanded in diverse research field. Molecular description of many fungal species is identified by different molecular characteristics. Hence, the efficient isolation of genomic DNA and amplification using PCR is a prerequisite for molecular characterization. Here, we used an improved Sodium dodecyl sulfate-Cetyltrimethyl ammonium bromide-Chloroform-isoamyl alcohol method by combining Sodium dodecyl sulfate with cetyl methylammonium bromide without addition of proteinase K, RNase K, and β-mercaptoethanol...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28317959/packing-energetics-determine-the-folding-routes-of-the-rnase-h-proteins
#2
Shilpa Yadahalli, Shachi Gosavi
Comparative studies of proteins from a family have been used to understand the factors that determine the folding routes of proteins. It has been conjectured that the folding mechanism of ribonuclease-H (RNase-H) proteins is determined by the topology of their fold. To test this hypothesis, we computationally studied the folding of four proteins from the RNase-H family, which have the overall RNase-H fold, but whose topologies differ in the region termed CORE in E. coli RNase-H. We simulated the folding of these proteins using molecular dynamics (MD) simulations of a coarse-grained structure-based model (SBM) which captures the effects of topology and found that the four proteins had similar folding routes...
March 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28306242/excision-repair-initiated-enzyme-assisted-bicyclic-cascade-signal-amplification-for-ultrasensitive-detection-of-uracil-dna-glycosylase
#3
Li-Juan Wang, Ming Ren, Qianyi Zhang, Bo Tang, Chun-Yang Zhang
Uracil-DNA glycosylase (UDG) is an important base excision repair (BER) enzyme responsible for the repair of uracil-induced DNA lesion and the maintenance of genomic integrity, while the aberrant expression of UDG is associated with a variety of cancers. Thus the accurate detection of UDG activity is essential to biomedical research and clinical diagnosis. Here, we develop a fluorescent method for ultrasensitive detection of UDG activity using excision repair-initiated enzyme-assisted bicyclic cascade signal amplification...
March 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28302473/quantitative-relationship-between-chemical-properties-and-bioactivities-of-anti-microrna-oligonucleotides-targeted-to-tumor-associated-microrna-21
#4
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
Synthetic anti-microRNA oligonucleotides (AMOs) are promising drug candidates to inactivate disease-related microRNAs because of their sequence-specific binding to their targets and the variety of chemical modifications available. Over the last decade, the qualitative relationships between the chemical properties of AMOs and bioactivity (inactivation of their target miRNAs) have been studied to enhance their bioactivity. On the other hand, in real-world drug development, drugs must be designed case-by-case, taking many factors into account...
March 13, 2017: Biochimie
https://www.readbyqxmd.com/read/28299484/characterization-of-a-new-badnavirus-from-wisteria-sinensis
#5
Yongqiang Li, Congliang Deng, Yan Qiao, Xiaoli Zhao, Qi Zhou
The complete genome sequence of a previously undescribed badnavirus isolated from a wisteria plant exhibiting mosaic and crinkle symptoms in Beijing, China, was determined. The circular double-stranded DNA genome of this virus was 7362 bp in size with four open reading frames (ORFs 1 to 4) on the plus strand. Sequence analysis showed that this virus shared the highest (69%) nucleotide (nt) sequence identity with pagoda yellow mosaic associated virus (PYMAV). In the RT-RNase H region of the ORF-3 encoded polyprotein, this virus shared 74% nt sequence identity with PYMAV...
March 15, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28281253/microrna-biosensing-with-two-dimensional-surface-plasmon-resonance-imaging
#6
Ho Pui Ho, Fong Chuen Loo, Shu Yuen Wu, Dayong Gu, Ken-Tye Yong, Siu Kai Kong
Two-dimensional surface plasmon resonance (2D-SPR) imaging, which provides a real-time, sensitive, and high-throughput analysis of surface events in a two dimensional manner, is a valuable tool for studying biomolecular interactions and biochemical reactions without using any tag labels. The sensing principle of 2D-SPR includes angular, wavelength, and phase interrogation. In this chapter, the 2D-SPR imaging technique is applied for sensing a target microRNA by its corresponding oligonucleotide probes, with sequence complementarity, immobilized on the gold SPR sensing surface...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28278199/monitoring-integrity-and-localization-of-modified-single-stranded-rna-oligonucleotides-using-ultrasensitive-fluorescence-methods
#7
Philipp Heissig, Waldemar Schrimpf, Philipp Hadwiger, Ernst Wagner, Don C Lamb
Short single-stranded oligonucleotides represent a class of promising therapeutics with diverse application areas. Antisense oligonucleotides, for example, can interfere with various processes involved in mRNA processing through complementary base pairing. Also RNA interference can be regulated by antagomirs, single-stranded siRNA and single-stranded microRNA mimics. The increased susceptibility to nucleolytic degradation of unpaired RNAs can be counteracted by chemical modification of the sugar phosphate backbone...
2017: PloS One
https://www.readbyqxmd.com/read/28271277/sequence-specific-backbone-resonance-assignments-and-microsecond-timescale-molecular-dynamics-simulation-of-human-eosinophil-derived-neurotoxin
#8
Donald Gagné, Chitra Narayanan, Khushboo Bafna, Laurie-Anne Charest, Pratul K Agarwal, Nicolas Doucet
Eight active canonical members of the pancreatic-like ribonuclease A (RNase A) superfamily have been identified in human. All structural homologs share similar RNA-degrading functions, while also cumulating other various biological activities in different tissues. The functional homologs eosinophil-derived neurotoxin (EDN, or RNase 2) and eosinophil cationic protein (ECP, or RNase 3) are known to be expressed and secreted by eosinophils in response to infection, and have thus been postulated to play an important role in host defense and inflammatory response...
March 7, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28268090/both-r-loop-removal-and-ribonucleotide-excision-repair-activities-of-rnase-h2-contribute-substantially-to-chromosome-stability
#9
Deborah A Cornelio, Hailey N C Sedam, Jessica A Ferrarezi, Nadia M V Sampaio, Juan Lucas Argueso
Cells carrying deletions of genes encoding H-class ribonucleases display elevated rates of chromosome instability. The role of these enzymes is to remove RNA-DNA associations including persistent mRNA-DNA hybrids (R-loops) formed during transcription, and ribonucleotides incorporated into DNA during replication. RNases H1 and H2 can degrade the RNA component of R-loops, but only RNase H2 can initiate accurate ribonucleotide excision repair (RER). In order to examine the specific contributions of these activities to chromosome stability, we measured rates of loss-of-heterozygosity (LOH) in diploid Saccharomyces cerevisiae yeast strains carrying the rnh201-RED separation-of-function allele, encoding a version of RNase H2 that is RER-defective, but partly retains its other activity...
February 20, 2017: DNA Repair
https://www.readbyqxmd.com/read/28258464/sequential-fragment-ion-filtering-and-endoglycosidase-assisted-identification-of-intact-glycopeptides
#10
Zixiang Yu, Xinyuan Zhao, Fang Tian, Yang Zhao, Yong Zhang, Yi Huang, Xiaohong Qian, Wantao Ying
Detailed characterization of glycoprotein structures requires determining both the sites of glycosylation as well as the glycan structures associated with each site. In this work, we developed an analytical strategy for characterization of intact N-glycopeptides in complex proteome samples. In the first step, tryptic glycopeptides were enriched using ZIC-HILIC. Secondly, a portion of the glycopeptides was treated with endoglycosidase H (Endo H) to remove high-mannose (Man) and hybrid N-linked glycans. Thirdly, a fraction of the Endo H-treated glycopeptides was further subjected to PNGase F treatment in (18)O water to remove the remaining complex glycans...
March 3, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28254698/natural-product-inspired-esters-and-amides-of-ferulic-and-caffeic-acid-as-dual-inhibitors-of-hiv-1-reverse-transcriptase
#11
Vijay P Sonar, Angela Corona, Simona Distinto, Elias Maccioni, Rita Meleddu, Benedetta Fois, Costantino Floris, Nilesh V Malpure, Stefano Alcaro, Enzo Tramontano, Filippo Cottiglia
Using an HIV-1 Reverse Transcriptase (RT)-associated RNase H inhibition assay as lead, bioguided fractionation of the dichloromethane extract of the Ocimum sanctum leaves led to the isolation of five triterpenes (1-5) along with three 3-methoxy-4-hydroxy phenyl derivatives (6-8). The structure of this isolates were determined by 1D and 2D NMR experiments as well as ESI-MS. Tetradecyl ferulate (8) showed an interesting RNase H IC50 value of 12.4 μM and due to the synthetic accessibility of this secondary metabolite, a structure-activity relationship study was carried out...
April 21, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28253237/translation-complex-profile-sequencing-to-study-the-in-vivo-dynamics-of-mrna-ribosome-interactions-during-translation-initiation-elongation-and-termination
#12
Nikolay E Shirokikh, Stuart K Archer, Traude H Beilharz, David Powell, Thomas Preiss
Messenger RNA (mRNA) translation is a tightly controlled process that is integral to gene expression. It features intricate and dynamic interactions of the small and large subunits of the ribosome with mRNAs, aided by multiple auxiliary factors during distinct initiation, elongation and termination phases. The recently developed ribosome profiling method can generate transcriptome-wide surveys of translation and its regulation. Ribosome profiling records the footprints of fully assembled ribosomes along mRNAs and thus primarily interrogates the elongation phase of translation...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28252184/using-morpholinos-to-control-gene-expression
#13
Jon D Moulton
Morpholino oligonucleotides are stable, uncharged, water-soluble molecules used to block complementary sequences of RNA, preventing processing, read-through, or protein binding at those sites. Morpholinos are typically used to block translation of mRNA and to block splicing of pre-mRNA, though they can block other interactions between biological macromolecules and RNA. Morpholinos are effective, specific, and lack non-antisense effects. They work in any cell that transcribes and translates RNA, but must be delivered into the nuclear/cytosolic compartment to be effective...
March 2, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28242172/synthesis-of-antisense-oligonucleotides-containing-acyclic-alkynyl-nucleoside-analogs-and-their-biophysical-and-biological-properties
#14
Aya Ogata, Yusuke Maeda, Yoshihito Ueno
The synthesis of oligonucleotide (ON) analogs, which can be used as antisense molecules, has recently gained much attention. Here, we report the synthesis and properties of an ON analog containing acyclic thymidine and cytidine analogs with a 4-pentyl-1,2-diol instead of the d-ribofuranose moiety. The incorporation of these analogs into the ON improved its nuclease resistance to 3'-exonucleases. Furthermore, it was found that the incorporation of the acyclic thymidine analog into a DNA/RNA duplex accelerates the RNA cleavage of a DNA/RNA duplex by Escherichia coli RNase H...
February 17, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28239425/block-ionomer-complexes-consisting-of-sirna-and-araft-synthesized-hydrophilic-block-cationic-copolymers-ii-the-influence-of-cationic-block-charge-density-on-gene-suppression
#15
Keith H Parsons, Andrew C Holley, Gabrielle A Munn, Alex S Flynt, Charles L McCormick
Block ionomer complex (BIC)-siRNA interactions and effectiveness in cell transfection are reported. Aqueous RAFT polymerization was used to prepare a series of hydrophilic-block-cationic copolymers in which the cationic block statistically incorporates increasing amounts of neutral, hydrophilic monomer such that the number of cationic groups remains unchanged but the cationic charge density is diluted along the polymer backbone. Reduced charge density decreases the electrostatic binding strength between copolymers and siRNA with the goal of improving siRNA release after targeted cellular delivery...
October 21, 2016: Polymer Chemistry
https://www.readbyqxmd.com/read/28236743/direct-binding-of-microrna-21-pre-element-with-regorafenib-an-alternative-mechanism-for-anti-colorectal-cancer-chemotherapy
#16
Xiaobing Chen, Bojian Xie, Liang Cao, Feng Zhu, Beibei Chen, Huifang Lv, Xingxing Fan, Lili Han, Liangyu Bie, Xinguang Cao, Xiaokun Shen, Feilin Cao
The Regorafenib is a broad-spectrum kinase inhibitor that has been approved to treat colorectal cancer (CRC). However, evidences have shown that the agent is also implicated in drug interaction with microRNA-21 (miR-21), an oncogenic miRNA which plays a key role in resisting programmed cell death in CRC cells. Here, we supposed that, instead of kinase inhibition, Regorafenib can directly bind to and then stabilize miR-21 pre-element, thus preventing RNase Dicer-meditated cleavage of the pre-element to mature miR-21...
February 10, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28230734/deep%C3%A2-transcriptome%C3%A2-sequencing%C3%A2-of%C3%A2-two%C3%A2-green%C3%A2-algae-chara%C3%A2-vulgaris%C3%A2-and%C3%A2-chlamydomonas%C3%A2-reinhardtii-%C3%A2-provides%C3%A2-no%C3%A2-evidence%C3%A2-of%C3%A2-organellar%C3%A2-rna%C3%A2-editing
#17
A Bruce Cahoon, John A Nauss, Conner D Stanley, Ali Qureshi
Nearly all land plants post-transcriptionally modify specific nucleotides within RNAs, a process known as RNA editing. This adaptation allows the correction of deleterious mutations within the asexually reproducing and presumably non-recombinant chloroplast and mitochondrial genomes. There are no reports of RNA editing in any of the green algae so this phenomenon is presumed to have originated in embryophytes either after the invasion of land or in the now extinct algal ancestor of all land plants. This was challenged when a recent in silico screen for RNA edit sites based on genomic sequence homology predicted edit sites in the green alga Chara vulgaris, a multicellular alga found within the Streptophyta clade and one of the closest extant algal relatives of land plants...
February 20, 2017: Genes
https://www.readbyqxmd.com/read/28203566/increased-spontaneous-recombination-in-rnase-h2-deficient-cells-arises-from-multiple-contiguous-rnmps-and-not-from-single-rnmp-residues-incorporated-by-dna-polymerase-epsilon
#18
Anastasiya Epshtein, Catherine J Potenski, Hannah L Klein
Ribonucleotides can become embedded in DNA from insertion by DNA polymerases, failure to remove Okazaki fragment primers, R-loops that can prime replication, and RNA/cDNA-mediated recombination. RNA:DNA hybrids are removed by RNase H enzymes. Single rNMPs in DNA are removed by RNase H2 and if they remain on the leading strand, can lead to mutagenesis in a Top1-dependent pathway. rNMPs in DNA can also stimulate genome instability, among which are homologous recombination gene conversion events. We previously found that, similar to the rNMP-stimulated mutagenesis, rNMP-stimulated recombination was also Top1-dependent...
June 2016: Microbial Cell
https://www.readbyqxmd.com/read/28182989/6-cyclohexylmethyl-3-hydroxypyrimidine-2-4-dione-as-an-inhibitor-scaffold-of-hiv-reverase-transcriptase-impacts-of-the-3-oh-on-inhibiting-rnase-h-and-polymerase
#19
Jing Tang, Karen A Kirby, Andrew D Huber, Mary C Casey, Juan Ji, Daniel J Wilson, Stefan G Sarafianos, Zhengqiang Wang
3-Hydroxypyrimidine-2,4-dione (HPD) represents a versatile chemical core in the design of inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H and integrase strand transfer (INST). We report herein the design, synthesis and biological evaluation of an HPD subtype (4) featuring a cyclohexylmethyl group at the C-6 position. Antiviral testing showed that most analogues of 4 inhibited HIV-1 in the low nanomolar to submicromolar range, without cytotoxicity at concentrations up to 100 μM...
January 30, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28182633/characterizing-the-coding-region-determinant-binding-protein-crd-bp-microphthalmia-associated-transcription-factor-mitf-mrna-interaction
#20
Gerrit van Rensburg, Sebastian Mackedenski, Chow H Lee
Coding region determinant-binding protein (CRD-BP) binds to the 3'-UTR of microphthalmia-associated transcription factor (MITF) mRNA to prevent its targeted degradation by miR-340. Here, we aim to further understand the molecular interaction between CRD-BP and MITF RNA. Using point mutation in the GXXG motif of each KH domains, we showed that all four KH domains of CRD-BP are important for their physical association with MITF RNA. We mapped the CRD-BP-binding site in the 3'-UTR of MITF RNA from nts 1330-1740 and showed that the 49-nt fragment 1621-1669 is the minimal size MITF RNA for binding...
2017: PloS One
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