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https://www.readbyqxmd.com/read/29165690/the-regulatory-g4-motif-of-the-kirsten-ras-kras-gene-is-sensitive-to-guanine-oxidation-implications-on-transcription
#1
Susanna Cogoi, Annalisa Ferino, Giulia Miglietta, Erik B Pedersen, Luigi E Xodo
KRAS is one of the most mutated genes in human cancer. It is controlled by a G4 motif located upstream of the transcription start site. In this paper, we demonstrate that 8-oxoguanine (8-oxoG), being more abundant in G4 than in non-G4 regions, is a new player in the regulation of this oncogene. We designed oligonucleotides mimicking the KRAS G4-motif and found that 8-oxoG impacts folding and stability of the G-quadruplex. Dimethylsulphate-footprinting showed that the G-run carrying 8-oxoG is excluded from the G-tetrads and replaced by a redundant G-run in the KRAS G4-motif...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29165591/translation-can-affect-the-antisense-activity-of-rnase-h1-dependent-oligonucleotides-targeting-mrnas
#2
Xue-Hai Liang, Joshua G Nichols, Hong Sun, Stanley T Crooke
RNase H1-dependent antisense oligonucleotides (ASOs) can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. Here we show that mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs...
November 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29164876/live-cell-imaging-of-endogenous-rnas-using-pumilio-homology-domain-mutants-principles-and-applications
#3
Hideaki Yoshimura
Recently, dynamic changes in RNA location in space and time in living cells have become a target of interest in biology because of their essential roles in controlling physiological phenomena. To visualize RNA, methods for the fluorescence labeling of RNA in living cells have been developed. For RNA labeling, oligonucleotide-based RNA probes have mainly been used because of their high selectivity for target RNAs. By contrast, protein-based RNA probes have not been used widely because of their lack of design flexibility, although they have various potential advantages compared with nucleotide-based probes, such as controllability of intracellular localization, high detectability, and ease of introduction to cells and transgenic organisms in cell type and tissue specific manner by genetic engineering techniques...
November 22, 2017: Biochemistry
https://www.readbyqxmd.com/read/29163896/fluorogenic-labeling-and-single-base-resolution-analysis-of-5-formylcytosine-in-dna
#4
Chaoxing Liu, Yafen Wang, Wei Yang, Fan Wu, Weiwu Zeng, Zonggui Chen, Jinguo Huang, Guangrong Zou, Xiong Zhang, Shaoru Wang, Xiaocheng Weng, Zhiguo Wu, Yu Zhou, Xiang Zhou
5-Formylcytosine (5fC), which plays an important role in epigenetic functions, has received widespread attention in many related fields. Here, we demonstrate a new design for both the fluorogenic switch-on detection and single-base resolution analysis of 5fC through selectively reacting a reagent with 5fC to yield an intramolecular cyclization nucleobase. The generated product, bearing a similar benzothiazole-iminocoumarin scaffold, is highly fluorescent and enables us to qualitatively and quantitatively detect 5fC moieties in γ-irradiated calf thymus DNA...
November 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29161581/dna-rna-hybrid-substrates-modulate-the-catalytic-activity-of-purified-aid
#5
Hala S Abdouni, Justin J King, Atefeh Ghorbani, Heather Fifield, Lesley Berghuis, Mani Larijani
Activation-induced cytidine deaminase (AID) converts cytidine to uridine at Immunoglobulin (Ig) loci, initiating somatic hypermutation and class switching of antibodies. In vitro, AID acts on single stranded DNA (ssDNA), but neither double-stranded DNA (dsDNA) oligonucleotides nor RNA, and it is believed that transcription is the in vivo generator of ssDNA targeted by AID. It is also known that the Ig loci, particularly the switch (S) regions targeted by AID are rich in transcription-generated DNA/RNA hybrids...
November 18, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/29160746/nucleic-acid-therapies-for-cystic-fibrosis
#6
Shruti Sasaki, Shuling Guo
Nucleic acid therapeutics are an established class of drugs that enable specific targeting of a gene of interest. This diverse family of drugs includes antisense oligonucleotides, siRNAs, and mRNA replacement therapies, which can elicit both gene repression and activation, primarily at the RNA level. Recent advances in medicinal chemistry have increased drug potency and enhanced delivery and distribution to a broad array of tissue and cell types. A key advantage of nucleic acid therapeutics is in their application to monogenic diseases...
November 21, 2017: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29160067/molecular-tension-probes-for-imaging-forces-at-the-cell-surface
#7
Yang Liu, Kornelia Galior, Victor Pui-Yan Ma, Khalid Salaita
Mechanical forces are essential for a variety of biological processes ranging from transcription and translation to cell adhesion, migration, and differentiation. Through the activation of mechanosensitive signaling pathways, cells sense and respond to physical stimuli from the surrounding environment, a process widely known as mechanotransduction. At the cell membrane, many signaling receptors, such as integrins, cadherins and T- or B-cell receptors, bind to their ligands on the surface of adjacent cells or the extracellular matrix (ECM) to mediate mechanotransduction...
November 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/29158840/inorganic-kernel-reconstituted-lipoprotein-biomimetic-nanovehicles-enable-efficient-targeting-trojan-horse-delivery-of-stat3-decoy-oligonucleotide-for-overcoming-trail-resistance
#8
Kai Shi, Jianxiu Xue, Yan Fang, Hongshu Bi, Shan Gao, Dongjuan Yang, Anqi Lu, Yuai Li, Yao Chen, Liyuan Ke
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) can selectively induce apoptosis in a variety of tumor cells, but not most normal cells. Nevertheless, its therapeutic potential is limited due to the frequent occurrence of resistance in tumor cells, especially hepatocellular carcinoma cell lines. Therefore, we investigated the reversal effect of STAT3-decoy oligonucleotides (ODNs) on TRAIL resistance. Methods. Considering that the drawback of poor cellular permeability and rapid degradation in vivo limited ODNs' further clinical applications, we developed a biomimetic calcium phosphate-reconstituted low density lipoprotein nanovehicle (CaP@LDL) that would serve as a "Trojan horse" to carry STAT3-decoy ODNs into tumor cells and then regulate TRAIL-induced apoptosis...
2017: Theranostics
https://www.readbyqxmd.com/read/29157313/calpain-5-gene-expression-in-the-mouse-eye-and-brain
#9
Kellie Schaefer, MaryAnn Mahajan, Anuradha Gore, Stephen H Tsang, Alexander G Bassuk, Vinit B Mahajan
OBJECTIVE: Our objective was to characterize CAPN5 gene expression in the mouse central nervous system. Mouse brain and eye sections were probed with two high-affinity RNA oligonucleotide analogs designed to bind CAPN5 RNA and one scramble, control oligonucleotide. Images were captured in brightfield. RESULTS: CAPN5 RNA probes were validated on mouse breast cancer tumor tissue. In the eye, CAPN5 was expressed in the ganglion cell, inner nuclear and outer nuclear layers of the retina...
November 21, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/29156680/vemurafenib-resistance-via-de-novo-rbm-genes-mutations-and-chromosome-5-aberrations-is-overcome-by-combined-therapy-with-palbociclib-in-thyroid-carcinoma-with-braf-v600e
#10
Zeus A Antonello, Nancy Hsu, Manoj Bhasin, Giovanni Roti, Mukta Joshi, Paul Van Hummelen, Emily Ye, Agnes S Lo, S Ananth Karumanchi, Christine R Bryke, Carmelo Nucera
Purpose: Papillary thyroid carcinoma (PTC) is the most frequent endocrine tumor. BRAF(V600E) represents the PTC hallmark and is targeted with selective inhibitors (e.g. vemurafenib). Although there have been promising results in clinical trials using these inhibitors, most patients develop resistance and progress. Tumor clonal diversity is proposed as one mechanism underlying drug resistance. Here we have investigated mechanisms of primary and secondary resistance to vemurafenib in BRAF(WT/V600E)-positive PTC patient-derived cells with P16(-/-) (CDKN2A(-/-))...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155588/determination-of-equilibrium-constant-and-relative-brightness-in-fret-fcs-by-including-the-third-order-correlations
#11
Lingyi Meng, Shanshan He, Xin Sheng Zhao
Fluorescence correlation spectroscopy (FCS) encodes the information of the equilibrium constant (K), the relative fluorescence brightness of fluorophore (Q), and the forward and backward reaction rate constants (k+ and k-) on a physical or chemical relaxation. However, it has been a long-standing problem to completely resolve the FCS data to get the thermodynamic and kinetic information. Recently, we have solved the problem for fluorescence auto-correlation spectroscopy (FACS). Here, we extend the method to fluorescence cross-correlation spectroscopy (FCCS), which appears when FCS is coupled with fluorescence resonance energy transfer (FRET)...
November 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29153834/precise-editing-at-dna-replication-forks-enables-multiplex-genome-engineering-in-eukaryotes
#12
Edward M Barbieri, Paul Muir, Benjamin O Akhuetie-Oni, Christopher M Yellman, Farren J Isaacs
We describe a multiplex genome engineering technology in Saccharomyces cerevisiae based on annealing synthetic oligonucleotides at the lagging strand of DNA replication. The mechanism is independent of Rad51-directed homologous recombination and avoids the creation of double-strand DNA breaks, enabling precise chromosome modifications at single base-pair resolution with an efficiency of >40%, without unintended mutagenic changes at the targeted genetic loci. We observed the simultaneous incorporation of up to 12 oligonucleotides with as many as 60 targeted mutations in one transformation...
November 15, 2017: Cell
https://www.readbyqxmd.com/read/29153620/targeted-dna-enrichment-and-whole-genome-sequencing-of-neisseria-meningitidis-directly-from-clinical-specimens
#13
Stephen A Clark, Ronan Doyle, Jay Lucidarme, Ray Borrow, Judith Breuer
In England and Wales, approximately one half of all laboratory-confirmed meningococcal disease cases fail to yield a viable invasive isolate, primarily due to the use of antibiotics. Characterisation of non-culture meningococci has been restricted to the detection or sequencing of specific gene targets within clinical specimens. In this study we investigated the ability of the Agilent SureSelectXT kit to facilitate DNA enrichment and genome sequencing of meningococcal DNA within a small panel of blood and CSF specimens...
November 13, 2017: International Journal of Medical Microbiology: IJMM
https://www.readbyqxmd.com/read/29153085/an-ultra-sensitive-fluorescent-turn-on-biosensor-for-glutathione-and-its-application-in-living-cells
#14
Wei Wang, Xiaoshan Hou, Xin Li, Chen Chen, Xiliang Luo
In this work, an effective controlled-release biosensor based on Au nanocages (AuNCs) capped with disulfide-containing DNA molecular gates was developed for ultra-sensitive and highly selective detection of glutathione (GSH). Oligonucleotides containing the S-S bonds were assembled on the surface of the AuNCs by means of electrostatic interactions in order to inhibit the release of fluorescent molecules such as Rhodamine B (RhB) loaded by AuNCs. In the presence of GSH, due to the specific cleavage of S-S bonds in disulfide-containing single-stranded DNAs (ssDNAs) as well as their subsequent departure from the surface of AuNCs, the pores could be opened, and then the dye molecules would be released from AuNCs...
January 15, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29152409/long-adapter-single-strand-oligonucleotide-probes-for-the-massively-multiplexed-cloning-of-kilobase-genome-regions
#15
Lorenzo Tosi, Viswanadham Sridhara, Yunlong Yang, Dongli Guan, Polina Shpilker, Nicola Segata, H Benjamin Larman, Biju Parekkadan
As the catalogue of sequenced genomes and metagenomes continues to grow, massively parallel approaches for the comprehensive and functional analysis of gene products and regulatory elements are becoming increasingly valuable. Current strategies to synthesize or clone complex libraries of DNA sequences are limited by the length of the DNA targets, throughput and cost. Here, we show that long-adapter single-strand oligonucleotide (LASSO) probes can capture and clone thousands of kilobase DNA fragments in a single reaction...
2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/29151323/investigation-of-human-leukocyte-antigen-in-osteoarticular-brucellosis
#16
Sevim Gönen, Murat Dizbay, Oğuz Söylemezoğlu
Background/aim: To determine the relationship between human leukocyte antigen (HLA) antigens and osteoarticular brucellosis by evaluating HLA Class I and II antigens in control subjects and patients developing osteoarticular brucellosis in Turkey.Materials and methods: The study included 28 patients with osteoarticular involvement diagnosed with brucellosis and 100 controls. The HLA Class I and II antigens were studied in isolated DNA samples using sequence-specific oligonucleotide procedure.Results: The mean age of the 28 patients and 100 controls was 42...
November 13, 2017: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/29150963/detection-and-quantification-of-two-parasitic-ciliates-boveria-labialis-and-boveria-subcylindrica-ciliophora-scuticociliatia-by-fluorescence-in-situ-hybridization
#17
Zifeng Zhan, Ju Li, Kuidong Xu
The thigmotrich scuticociliates Boveria labialis and Boveria subcylindrica are obligate parasites that may cause high mortality in cultured sea cucumbers and bivalves. Morphological methods can identify these organisms in active state, but are unable to discern them in resting stages. In aquaculture practice, these parasitic ciliates are hard to eradicate when massive infection occurs in sea cucumbers. Thus, early detection and precaution are crucial for the control of these pathogens. Under such circumstances, fluorescence in situ hybridization (FISH) will serve as a fast way to detect and monitor the occurrence of these parasites...
November 18, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/29149051/molecular-alliance-of-lymantria-dispar-multiple-nucleopolyhedrovirus-and-a-short-unmodified-antisense-oligonucleotide-of-its-anti-apoptotic-iap-3-gene-a-novel-approach-for-gypsy-moth-control
#18
Volodymyr V Oberemok, Kateryna V Laikova, Aleksei S Zaitsev, Maksym N Shumskykh, Igor N Kasich, Nikita V Gal'chinsky, Viktoriya V Bekirova, Valentin V Makarov, Alexey A Agranovsky, Vladimir A Gushchin, Ilya V Zubarev, Anatoly V Kubyshkin, Iryna I Fomochkina, Mikhail V Gorlov, Oleksii A Skorokhod
Baculovirus IAP (inhibitor-of-apoptosis) genes originated by capture of host genes. Unmodified short antisense DNA oligonucleotides (oligoDNAs) from baculovirus IAP genes can down-regulate specific gene expression profiles in both baculovirus-free and baculovirus-infected insects. In this study, gypsy moth (Lymantria dispar) larvae infected with multiple nucleopolyhedrovirus (LdMNPV), and LdMNPV-free larvae, were treated with oligoDNA antisense to the RING (really interesting new gene) domain of the LdMNPV IAP-3 gene...
November 17, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29148741/controlling-association-and-separation-of-gold-nanoparticles-with-computationally-designed-zinc-coordinating-proteins
#19
Matthew J Eibling, Christopher M MacDermaid, Zhaoxia Qian, Christopher J Lanci, So-Jung Park, Jeffery G Saven
Functionalization of nanoparticles with biopolymers has yielded a wide range of structured and responsive hybrid materials. DNA provides the ability to program length and recognition using complementary oligonucleotide sequences. Nature more often leverages the versatility of proteins, however, where structure, assembly, and recognition are more subtle to engineer. Herein, a protein was computationally designed to present multiple Zn(2+) coordination sites and cooperatively self-associate to form an antiparallel helical homodimer...
November 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29147499/nano-microvehicles-for-efficient-delivery-and-bio-sensing-at-the-cellular-level
#20
S Campuzano, B Esteban-Fernández de Ávila, P Yáñez-Sedeño, J M Pingarrón, J Wang
A perspective review of recent strategies involving the use of nano/microvehicles to address the key challenges associated with delivery and (bio)sensing at the cellular level is presented. The main types and characteristics of the different nano/microvehicles used for these cellular applications are discussed, including fabrication pathways, propulsion (catalytic, magnetic, acoustic or biological) and navigation strategies, and relevant parameters affecting their propulsion performance and sensing and delivery capabilities...
October 1, 2017: Chemical Science
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