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https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#1
Sara Lago, Elena Tosoni, Matteo Nadai, Manlio Palumbo, Sara N Richter
BACKGROUND: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS: Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding...
November 29, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27911493/rna-secondary-structure-prediction
#2
David H Mathews, Douglas H Turner, Richard M Watson
In this unit, protocols are provided for predicting RNA secondary structure with the user-friendly RNAstructure desktop computer program and the RNAstructure Web server. The minimum free energy structure and a set of suboptimal structures with similar free energies are predicted. Prediction of high-affinity oligonucleotide binding sites to a structured RNA target is also presented. © 2016 by John Wiley & Sons, Inc.
December 1, 2016: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/27911399/tools-to-study-the-role-of-architectural-protein-hmgb1-in-the-processing-of-helix-distorting-site-specific-dna-interstrand-crosslinks
#3
Anirban Mukherjee, Karen M Vasquez
High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, such as transcription, DNA replication, and DNA repair. HMGB1 binds to structurally distorted DNA with higher affinity than to canonical B-DNA. For example, we found that HMGB1 binds to DNA interstrand crosslinks (ICLs), which covalently link the two strands of the DNA, cause distortion of the helix, and if left unrepaired can cause cell death. Due to their cytotoxic potential, several ICL-inducing agents are currently used as chemotherapeutic agents in the clinic...
November 10, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27911093/dna-microarray-profiling-highlights-nrf2-mediated-chemoprevention-targeted-by-wasabi-derived-isothiocyanates-in-hepg2-cells
#4
Phoebe Zapanta Trio, Atsuyoshi Kawahara, Shunsuke Tanigawa, Kozue Sakao, De-Xing Hou
6-MSITC and 6-MTITC are sulforaphane (SFN) analogs found in Japanese Wasabi. As we reported previously, Wasabi isothiocyanates (ITCs) are activators of Nrf2-antioxidant response element pathway, and also inhibitors of pro-inflammatory cyclooxygenase-2. This study is the first to assess the global changes in transcript levels by Wasabi ITCs, comparing with SFN, in HepG2 cells. We performed comparative gene expression profiling by treating HepG2 cells with ITCs, followed by DNA microarray analyses using HG-U133 plus 2...
December 2, 2016: Nutrition and Cancer
https://www.readbyqxmd.com/read/27911048/fluorescent-oligonucleotide-probes-for-screening-high-affinity-nucleobase-surrogates
#5
Asmo Aro-Heinilä, Tuomas Lönnberg
Double-helical oligonucleotide probes featuring a single-nucleotide gap opposed by one of the canonical nucleobases and flanked by the fluorescent nucleobase analogue pyrrolocytosine have been synthesized and titrated with PdII chelates of dipicolinamide and its N2,N6-dialkylated derivatives. The fluorometric titrations revealed greatly increased affinity of the PdII chelates for the nucleobases opposing the gap compared to the respective free nucleotides in solution. Owing to the constrained environment of the single-nucleotide gap, the relative stabilities of the various PdII mediated base pairs were also significantly different from those previously reported at monomer level...
December 2, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27907033/normalization-of-patient-identified-plasma-biomarkers-in-smn%C3%AE-7-mice-following-postnatal-smn-restoration
#6
W David Arnold, Sandra Duque, Chitra C Iyer, Phillip Zaworski, Vicki L McGovern, Shannon J Taylor, Katharine M von Herrmann, Dione T Kobayashi, Karen S Chen, Stephen J Kolb, Sergey V Paushkin, Arthur H M Burghes
INTRODUCTION AND OBJECTIVE: Spinal muscular atrophy (SMA) is an autosomal recessive motor neuron disorder. SMA is caused by homozygous loss of the SMN1 gene and retention of the SMN2 gene resulting in reduced levels of full length SMN protein that are insufficient for motor neuron function. Various treatments that restore levels of SMN are currently in clinical trials and biomarkers are needed to determine the response to treatment. Here, we sought to investigate in SMA mice a set of plasma analytes, previously identified in patients with SMA to correlate with motor function...
2016: PloS One
https://www.readbyqxmd.com/read/27906628/role-of-genomic-factors-beyond-thymidylate-synthase-in-the-prediction-of-response-to-5-fluorouracil
#7
Godefridus J Peters, K Smid, E Meijer, C J van Groeningen, L G Leon
5-Fluorouracil (5FU) is still a major drug in combinations regimens for the treatment of colorectal cancer (CRC) both in the adjuvant and palliative setting. 5FU or its oral prodrug capecitabine is usually combined with irinotecan/oxaliplatin and the novel agents bevacizumab/cetuximab. Although this improved the outcome, the overall prognosis in patients with metastasized disease is still relatively poor. Although the target for 5FU, thymidylate synthase was shown to have a predictive value, this could only predict response in a subset of patients...
December 2016: Nucleosides, Nucleotides & Nucleic Acids
https://www.readbyqxmd.com/read/27905914/development-of-a-gene-synthesis-platform-for-the-efficient-large-scale-production-of-small-genes-encoding-animal-toxins
#8
Ana Filipa Sequeira, Joana L A Brás, Catarina I P D Guerreiro, Renaud Vincentelli, Carlos M G A Fontes
BACKGROUND: Gene synthesis is becoming an important tool in many fields of recombinant DNA technology, including recombinant protein production. De novo gene synthesis is quickly replacing the classical cloning and mutagenesis procedures and allows generating nucleic acids for which no template is available. In addition, when coupled with efficient gene design algorithms that optimize codon usage, it leads to high levels of recombinant protein expression. RESULTS: Here, we describe the development of an optimized gene synthesis platform that was applied to the large scale production of small genes encoding venom peptides...
December 1, 2016: BMC Biotechnology
https://www.readbyqxmd.com/read/27905870/transcriptomic-and-proteomic-approach-to-identify-differentially-expressed-genes-and-proteins-in-arabidopsis-thaliana-mutants-lacking-chloroplastic-1-and-cytosolic-fbpases-reveals-several-levels-of-metabolic-regulation
#9
Mauricio Soto-Suárez, Antonio J Serrato, José A Rojas-González, Rocío Bautista, Mariam Sahrawy
BACKGROUND: During the photosynthesis, two isoforms of the fructose-1,6-bisphosphatase (FBPase), the chloroplastidial (cFBP1) and the cytosolic (cyFBP), catalyse the first irreversible step during the conversion of triose phosphates (TP) to starch or sucrose, respectively. Deficiency in cyFBP and cFBP1 isoforms provokes an imbalance of the starch/sucrose ratio, causing a dramatic effect on plant development when the plastidial enzyme is lacking. RESULTS: We study the correlation between the transcriptome and proteome profile in rosettes and roots when cFBP1 or cyFBP genes are disrupted in Arabidopsis thaliana knock-out mutants...
December 1, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/27904776/microrna-195-suppresses-colorectal-cancer-cells-proliferation-via-targeting-fgf2-and-regulating-wnt-%C3%AE-catenin-pathway
#10
Xianxiang Zhang, Ji Xu, Tao Jiang, Guangwei Liu, Dongsheng Wang, Yun Lu
Colorectal cancer (CRC) is a prevalent cancer with high mortality worldwide. This study was aimed to explore the functional effects of microRNA-195 (miR-195) on CRC cells and the underling mechanism involved. quantitative PCR (qPCR) was performed to monitor the expression of miR-195 in CRC tissues and cell lines. SW480 and SW620 cells were transfected with either miR-195 mimic or antisense oligonucleotides (ASO) of miR-195. Then cell viability, cell cycle and the expressions of CyclinB1, CyclinD1 and Cyclin-Dependent Kinase 2 (CDK2) were respectively detected by 3-(4, 5-dimethyl-2-thiazolyl)-2, 5-diphenyltetrazolium bromide (MTT), flow cytometry, qPCR and Western blot...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27903915/max-is-an-epigenetic-sensor-of-5-carboxylcytosine-and-is-altered-in-multiple-myeloma
#11
Dongxue Wang, Hideharu Hashimoto, Xing Zhang, Benjamin G Barwick, Sagar Lonial, Lawrence H Boise, Paula M Vertino, Xiaodong Cheng
The oncogenic transcription factor MYC and its binding partner MAX regulate gene expression by binding to DNA at enhancer-box (E-box) elements 5'-CACGTG-3'. In mammalian genomes, the central E-box CpG has the potential to be methylated at the 5-position of cytosine (5mC), or to undergo further oxidation to the 5-hydroxymethyl (5hmC), 5-formyl (5fC), or 5-carboxyl (5caC) forms. We find that MAX exhibits the greatest affinity for a 5caC or unmodified C-containing E-box, and much reduced affinities for the corresponding 5mC, 5hmC or 5fC forms...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903892/methylation-sensitive-enrichment-of-minor-dna-alleles-using-a-double-strand-dna-specific-nuclease
#12
Yibin Liu, Chen Song, Ioannis Ladas, Mariana Fitarelli-Kiehl, G Mike Makrigiorgos
Aberrant methylation changes, often present in a minor allelic fraction in clinical samples such as plasma-circulating DNA (cfDNA), are potentially powerful prognostic and predictive biomarkers in human disease including cancer. We report on a novel, highly-multiplexed approach to facilitate analysis of clinically useful methylation changes in minor DNA populations. Methylation Specific Nuclease-assisted Minor-allele Enrichment (MS-NaME) employs a double-strand-specific DNA nuclease (DSN) to remove excess DNA with normal methylation patterns...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903889/elasticity-of-the-transition-state-for-oligonucleotide-hybridization
#13
Kevin D Whitley, Matthew J Comstock, Yann R Chemla
Despite its fundamental importance in cellular processes and abundant use in biotechnology, we lack a detailed understanding of the kinetics of nucleic acid hybridization. In particular, the identity of the transition state, which determines the kinetics of the two-state reaction, remains poorly characterized. Here, we used optical tweezers with single-molecule fluorescence to observe directly the binding and unbinding of short oligonucleotides (7-12 nt) to a complementary strand held under constant force. Binding and unbinding rate constants measured across a wide range of forces (1...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903030/-novel-therapeutic-approaches-in-inflammatory-bowel-diseases
#14
Raja Atreya, Markus Friedrich Neurath
Increasing knowledge regarding the immunopathogenesis of IBD has led to the development or approval of novel therapeutic agents for the treatment of Crohn's disease or ulcerative colitis. The new substances for example include antibodies against IL-12 / 23, anti-adhesion molecules and antisense oligonucleotides. The increase of therapeutic options will lead to a change of currently used therapeutic algorithms. Biomarkers to ensure a more individualized therapeutic approach are urgently needed to improve an efficient therapy of IBD patients...
November 2016: Deutsche Medizinische Wochenschrift
https://www.readbyqxmd.com/read/27902930/modulating-micrornas-in-cardiac-surgery-patients-novel-therapeutic-opportunities
#15
REVIEW
Giovanni Biglino, Massimo Caputo, Cha Rajakaruna, Gianni Angelini, Eva van Rooij, Costanza Emanueli
This review focuses on microRNAs (miRs) in cardiac surgery, where they are emerging as potential targets for therapeutic intervention as well as novel clinical biomarkers. Identification of the up/down-regulation of specific miRs in defined groups of cardiac surgery patients can lead to the development of novel strategies for targeted treatment in order to maximise therapeutic results and minimise acute, delayed or chronic complications. MiRs could also be involved in determining the outcome independently of complications, for example in relation to myocardial perfusion and fibrosis...
November 27, 2016: Pharmacology & Therapeutics
https://www.readbyqxmd.com/read/27899652/production-of-dna-minicircles-less-than-250-base-pairs-through-a-novel-concentrated-dna-circularization-assay-enabling-minicircle-design-with-nf-%C3%AE%C2%BAb-inhibition-activity
#16
Thomas Thibault, Jeril Degrouard, Patrick Baril, Chantal Pichon, Patrick Midoux, Jean-Marc Malinge
Double-stranded DNA minicircles of less than 1000 bp in length have great interest in both fundamental research and therapeutic applications. Although minicircles have shown promising activity in gene therapy thanks to their good biostability and better intracellular trafficking, minicircles down to 250 bp in size have not yet been investigated from the test tube to the cell for lack of an efficient production method. Herein, we report a novel versatile plasmid-free method for the production of DNA minicircles comprising fewer than 250 bp...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899568/assembly-of-supramolecular-dna-complexes-containing-both-g-quadruplexes-and-i-motifs-by-enhancing-the-g-repeat-bearing-capacity-of-i-motifs
#17
Yanwei Cao, Shang Gao, Yuting Yan, Michael F Bruist, Bing Wang, Xinhua Guo
The single-step assembly of supramolecular complexes containing both i-motifs and G-quadruplexes (G4s) is demonstrated. This can be achieved because the formation of four-stranded i-motifs appears to be little affected by certain terminal residues: a five-cytosine tetrameric i-motif can bear ten-base flanking residues. However, things become complex when different lengths of guanine-repeats are added at the 3' or 5' ends of the cytosine-repeats. Here, a series of oligomers d(XGiXC5X) and d(XC5XGiX) (X = A, T or none; i < 5) are designed to study the impact of G-repeats on the formation of tetrameric i-motifs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899557/alignment-free-d_2-oligonucleotide-frequency-dissimilarity-measure-improves-prediction-of-hosts-from-metagenomically-derived-viral-sequences
#18
Nathan A Ahlgren, Jie Ren, Yang Young Lu, Jed A Fuhrman, Fengzhu Sun
Viruses and their host genomes often share similar oligonucleotide frequency (ONF) patterns, which can be used to predict the host of a given virus by finding the host with the greatest ONF similarity. We comprehensively compared 11 ONF metrics using several k-mer lengths for predicting host taxonomy from among ∼32 000 prokaryotic genomes for 1427 virus isolate genomes whose true hosts are known. The background-subtracting measure [Formula: see text] at k = 6 gave the highest host prediction accuracy (33%, genus level) with reasonable computational times...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899266/dna-aptamers-against-foki-nuclease-domain-for-genome-editing-applications
#19
Maui Nishio, Daisuke Matsumoto, Yoshio Kato, Koichi Abe, Jinhee Lee, Kaori Tsukakoshi, Ayana Yamagishi, Chikashi Nakamura, Kazunori Ikebukuro
Genome editing with site-specific nucleases (SSNs) can modify only the target gene and may be effective for gene therapy. The main limitation of genome editing for clinical use is off-target effects; excess SSNs in the cells and their longevity can contribute to off-target effects. Therefore, a controlled delivery system for SSNs is necessary. FokI nuclease domain (FokI) is a common DNA cleavage domain in zinc finger nuclease (ZFN) and transcription activator-like effector nuclease. Previously, we reported a zinc finger protein delivery system that combined aptamer-fused, double-strand oligonucleotides and nanoneedles...
November 22, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27898095/efficient-generation-of-orthologous-point-mutations-in-pigs-via-crispr-assisted-ssodn-mediated-homology-directed-repair
#20
Kankan Wang, Xiaochun Tang, Yan Liu, Zicong Xie, Xiaodong Zou, Mengjing Li, Hongming Yuan, Hongsheng Ouyang, Huping Jiao, Daxin Pang
Precise genome editing in livestock is of great value for the fundamental investigation of disease modeling. However, genetically modified pigs carrying subtle point mutations were still seldom reported despite the rapid development of programmable endonucleases. Here, we attempt to investigate single-stranded oligonucleotides (ssODN) mediated knockin by introducing two orthologous pathogenic mutations, p.E693G for Alzheimer's disease and p.G2019S for Parkinson's disease, into porcine APP and LRRK2 loci, respectively...
November 29, 2016: Molecular Therapy. Nucleic Acids
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