keyword
MENU ▼
Read by QxMD icon Read
search

oligonucleotide

keyword
https://www.readbyqxmd.com/read/28534065/tailoring-high-density-oligonucleotide-arrays-for-transcript-profiling-of-different-arabidopsis-thaliana-accessions-using-a-sequence-based-approach
#1
Anastassia Boudichevskaia, Hieu Xuan Cao, Renate Schmidt
Excluding polymorphic probes from GeneChip (®) transcript profiling experiments via a sequence-based approach results in improved detection of differentially expressed genes in developing seeds of Arabidopsis thaliana accessions Col-0 and C24. GeneChip(®) arrays represent a powerful tool for transcript profiling experiments. The ATH1 GeneChip(®) has been designed based on the sequence of the Arabidopsis thaliana reference genome Col-0, hence the features on the array exactly match the sequences of Col-0 transcripts...
May 22, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28533404/repression-of-phosphatidylinositol-transfer-protein-%C3%AE-ameliorates-the-pathology-of-duchenne-muscular-dystrophy
#2
Natassia M Vieira, Janelle M Spinazzola, Matthew S Alexander, Yuri B Moreira, Genri Kawahara, Devin E Gibbs, Lillian C Mead, Sergio Verjovski-Almeida, Mayana Zatz, Louis M Kunkel
Duchenne muscular dystrophy (DMD) is a progressive muscle wasting disease caused by X-linked inherited mutations in the DYSTROPHIN (DMD) gene. Absence of dystrophin protein from the sarcolemma causes severe muscle degeneration, fibrosis, and inflammation, ultimately leading to cardiorespiratory failure and premature death. Although there are several promising strategies under investigation to restore dystrophin protein expression, there is currently no cure for DMD, and identification of genetic modifiers as potential targets represents an alternative therapeutic strategy...
May 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28533357/tlr9-expression-and-secretion-of-lif-by-prostate-cancer-cells-stimulates-accumulation-and-activity-of-polymorphonuclear-mdscs
#3
Haejung Won, Dayson Moreira, Chan Gao, Priyanka Duttagupta, Xingli Zhao, Edwin Manuel, Don Diamond, Yate-Ching Yuan, Zheng Liu, Jeremy Jones, Massimo D'Apuzzo, Sumanta Pal, Marcin Kortylewski
Proinflammatory signals promote prostate tumorigenesis and progression, but their origins and downstream effects remain unclear. We recently demonstrated that the expression of an innate immune receptor, TLR9, by prostate cancer cells is critical for their tumor-propagating potential. We investigated whether cancer cell-intrinsic TLR9 signaling alters composition of the prostate tumor microenvironment. We generated Ras/Myc (RM9) and Myc-driven (Myc-CaP) prostate cancer cells expressing the tetracycline-inducible gene Tlr9 (Tlr9(ON) ) or the control LacZ (LacZ(ON) )...
May 22, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28533173/targeting-human-telomerase-rna-component-using-antisense-oligonucleotide-induces-rapid-cell-death-and-increases-ato-induced-apoptosis-in-apl-cells
#4
Leila Asghari-Kia, Davood Bashash, Ava Safaroghli-Azar, Majid Momeny, Mohsen Hamidpour, Seyed H Ghaffari
The impressive advances carried out in designing pharmacological strategies with the aim of telomerase inhibition in cancers emerged a consensus that telomerase-targeted therapies could be exciting prospect in repertoire of future cancer strategies. The results of the present study indicated that targeting telomerase using an oligonucleotide-based molecule against human telomerase RNA template (hTR ASODN) reduced the survival rate of NB4 cells and induced a caspase-3-dependent apoptosis. Our finding was even noticeable in the synergistic experiments, where we found an enhanced reduction in the viability of the cells after short-term treatment with ATO in combination with the inhibitor...
May 19, 2017: European Journal of Pharmacology
https://www.readbyqxmd.com/read/28532670/syntheses-of-prodrug-type-phosphotriester-oligonucleotides-responsive-to-intracellular-reducing-environment-for-improvement-of-cell-membrane-permeability-and-nuclease-resistance
#5
Junsuke Hayashi, Yusuke Samezawa, Yosuke Ochi, Shun-Ichi Wada, Hidehito Urata
We synthesized prodrug-type phosphotriester (PTE) oligonucleotides containing the six-membered cyclic disulfide moiety by using phosphoramidite chemistry. Prodrug-type oligonucleotides named "Reducing-Environment-Dependent Uncatalyzed Chemical Transforming (REDUCT) PTE oligonucleotides" were converted into natural oligonucleotides under cytosol-mimetic reductive condition. Furthermore, the REDUCT PTE oligonucleotides were robust to nuclease digestion and exhibited good cell membrane permeability.
May 11, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28531214/suspected-lynch-syndrome-associated-msh6-variants-a-functional-assay-to-determine-their-pathogenicity
#6
Hellen Houlleberghs, Anne Goverde, Jarnick Lusseveld, Marleen Dekker, Marco J Bruno, Fred H Menko, Arjen R Mensenkamp, Manon C W Spaander, Anja Wagner, Robert M W Hofstra, Hein Te Riele
Lynch syndrome (LS) is a hereditary cancer predisposition caused by inactivating mutations in DNA mismatch repair (MMR) genes. Mutations in the MSH6 DNA MMR gene account for approximately 18% of LS cases. Many LS-associated sequence variants are nonsense and frameshift mutations that clearly abrogate MMR activity. However, missense mutations whose functional implications are unclear are also frequently seen in suspected-LS patients. To conclusively diagnose LS and enroll patients in appropriate surveillance programs to reduce morbidity as well as mortality, the functional consequences of these variants of uncertain clinical significance (VUS) must be defined...
May 22, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28531137/synthesis-and-excellent-duplex-stability-of-oligonucleotides-containing-2-amino-lna-functionalized-with-galactose-units
#7
Rajesh Kumar, Annika Ries, Jesper Wengel
A convenient method for the preparation of oligonucleotides containing internally-attached galactose and triantennary galactose units has been developed based on click chemistry between 2'-N-alkyne 2'-amino-LNA nucleosides and azido-functionalized galactosyl building blocks. The synthesized oligonucleotides show excellent binding affinity and selectivity towards complementary DNA/RNA strands with an increase in the melting temperature of up to +23.5 °C for triply-modified variants.
May 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28530287/microfluidic-self-assembly-of-folate-targeted-monomolecular-sirna-lipid-nanoparticles
#8
R Krzysztoń, B Salem, D J Lee, G Schwake, E Wagner, J O Rädler
Non-viral delivery of nucleic acids for therapies based on RNA interference requires a rational design and optimal self-assembly strategies. Nucleic acid particles need to be small, stable and functional in terms of selective cell uptake and controlled release of encapsulated nucleic acids. Here we report on small (∼38 nm) monomolecular nucleic acid/lipid particles (mNALPs) that contain single molecules of short double-stranded oligonucleotides covered by a tight, highly curved lipid bilayer. The particles consist of DOPE, DOTAP, DOPC and DSPE-PEG(2000) and are assembled with 21 bp double-stranded DNA or small interfering RNA by solvent exchange on a hydrodynamic-focusing microfluidic chip...
May 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28528550/isotachophoretic-fluorescence-in-situ-hybridization-of-intact-bacterial-cells
#9
Sui Ching Phung, Joan Marc Cabot, Mirek Macka, Shane M Powell, Rosanne M Guijt, Michael C Breadmore
A counter-pressure assisted capillary isotachophoresis method in combination with a sieving matrix and ionic spacer was used to perform in-line fluorescence in situ hybridization (FISH) of bacterial cells. A high concentration of sieving matrix (1.8% w/v HEC) was introduced at one end of the capillary and the bacterial cells were suspended in the spacer electrolyte for injection. Using a 2 min injection with 18 psi counter-pressure, 50% of the cells injected into the capillary were hybridized with the fluorescently labelled oligonucleotide and the excess unhybridized probe was separated from the hybridized cells-probe complexes in a two stage ITP method...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28528145/uv-induced-electron-transfer-between-triethylamine-and-5-bromo-2-deoxyuridine-a-puzzle-concerning-the-photochemical-debromination-of-labeled-dna
#10
Paweł Wityk, Magdalena Zdrowowicz, Justyna Wiczk, Janusz Rak
5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding in the labeled DNA is dramatically changed due to the photoinduced electron transfer (PET) between the photoexcited BrdU and the ground state TEA...
May 11, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28527284/-new-multiplex-pcr-for-species-specific-diagnosis-of-human-candidiasis
#11
Liliana Torcoroma García, Liany Johanna Luna, Tania Katherine Velasco, Beatriz Elena Guerra
INTRODUCTION: Candidiases is a group of opportunistic infections caused by yeasts belonging to the genus Candida. Candida albicans is the most prevalent species in both superficial and deep infections, however, the clinical importance of non-albicans Candida has increased during the last decade, driving an urgent need for diagnostic tests that allow for species-level resolution and selection of the optimum therapeutic approach. OBJECTIVE: To design and to optimize a new multiplex PCR assay for the simultaneous identification of the five most relevant species of Candida involved in human candidiasis etiology...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28524768/anti-microrna-targeting-using-peptide-based-nanocomplexes-to-inhibit-differentiation-of-human-pancreatic-stellate-cells
#12
Jonas Schnittert, Praneeth R Kuninty, Tomasz F Bystry, Roland Brock, Gert Storm, Jai Prakash
AIM: To develop novel peptide-based nanocomplexes (NCs) for delivery of anti-miRNA oligonucleotides to human-derived pancreatic stellate cells (hPSCs), precursors of cancer-associated fibroblasts. MATERIALS & METHODS: NCs of anti-miRNA oligonucleotides and cell-penetrating peptides (different variants) were formed and characterized. The effects of anti-miR-199a delivery on hPSC differentiation and 3D heterospheroid formation were investigated. RESULTS: Dimeric cell-penetrating peptide based NCs (NC-2) showed 130-fold higher uptake by hPSCs compared with monomer-based NCs (NC-1) and tenfold higher uptake compared with general fibroblasts and different pancreatic tumor cells...
May 19, 2017: Nanomedicine
https://www.readbyqxmd.com/read/28524214/-possible-treatments-for-infantile-spinal-atrophy
#13
S I Pascual-Pascual, M Garcia-Romero
The new treatments of spinal muscular atrophy (SMA) due by SMN1 gene deletions are reviewed. There are several ways to increase the protein SMN, its activity and persistence in the tissues. Neuroprotective drugs as olesoxime or riluzole, and drugs acting by epigenetic mechanisms, as histone deacetylase inhibitors, have shown positive effects in preclinical studies but no clear efficacy in clinical trials. They might give in the future added benefits when used associated to other genetic modifying drugs. The best improvements in murine models of SMA and in clinical trials have been reached with antisense oligonucleotides, drugs that modify the splicing of SMN2, and they are expected to get better in the near future...
May 17, 2017: Revista de Neurologia
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#14
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28522268/design-and-synthesis-of-novel-photoinduced-electron-transfer-based-hybridization-probes
#15
Chika Yokoyama, Kosuke Nakamoto, Yoshihito Ueno
Photoinduced electron transfer (PeT)-based hybridization probe is a linear and quencher-free oligonucleotide (ON) probe for DNA or RNA detection. In this report, we designed and synthesized novel adenosine analogues for PeT-based hybridization probe. In particular, the analogue containing a piperazinomethyl moiety showed effective quenching property under physiological conditions. When the probe containing the analogue was hybridized with a complementary DNA or RNA, the fluorescence increased 3- or 4-fold, respectively, compared to the single-stranded state...
May 6, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28522225/genetic-screening-of-spinal-muscular-atrophy-using-a-real-time-modified-cop-pcr-technique-with-dried-blood-spot-dna
#16
Mawaddah Ar Rochmah, Nur Imma Fatimah Harahap, Emma Tabe Eko Niba, Kenta Nakanishi, Hiroyuki Awano, Ichiro Morioka, Kazumoto Iijima, Toshio Saito, Kayoko Saito, Poh San Lai, Yasuhiro Takeshima, Atsuko Takeuchi, Yoshihiro Bouike, Maya Okamoto, Hisahide Nishio, Masakazu Shinohara
BACKGROUND: Spinal muscular atrophy (SMA) is a common neuromuscular disorder caused by mutations in SMN1. More than 95% of SMA patients carry homozygous SMN1 deletion. SMA is the leading genetic cause of infant death, and has been considered an incurable disease. However, a recent clinical trial with an antisense oligonucleotide drug has shown encouraging clinical efficacy. Thus, early and accurate detection of SMN1 deletion may improve prognosis of many infantile SMA patients. METHODS: A total of 88 DNA samples (37 SMA patients, 12 carriers and 39 controls) from dried blood spots (DBS) on filter paper were analyzed...
May 15, 2017: Brain & Development
https://www.readbyqxmd.com/read/28521066/optochemical-control-of-biological-processes-in-cells-and-animals
#17
Nicholas Ankenbruck, Taylor Courtney, Yuta Naro, Alexander Deiters
Achieving precise control of biological function represents a crucial tool for studying the mechanisms of cellular processes. Naturally, these processes occur in a strict spatially and temporally regulated fashion. In order to generate accurate models, the tools used to study these processes must also operate with high spatiotemporal resolution. To this end, the use of light as a conditional stimulus has found extensive applications for the activation and deactivation of small molecules, proteins, peptides, and oligonucleotides...
May 18, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28520986/chemical-ligation-of-oligonucleotides-using-an-electrophilic-phosphorothioester
#18
Hideto Maruyama, Ryota Oikawa, Mayu Hayakawa, Shono Takamori, Yasuaki Kimura, Naoko Abe, Genichiro Tsuji, Akira Matsuda, Satoshi Shuto, Yoshihiro Ito, Hiroshi Abe
We developed a new approach for chemical ligation of oligonucleotides using the electrophilic phosphorothioester (EPT) group. A nucleophilic phosphorothioate group on oligonucleotides was converted into the EPT group by treatment with Sanger's reagent (1-fluoro-2,4-dinitrobenzene). EPT oligonucleotides can be isolated, stored frozen, and used for the ligation reaction. The reaction of the EPT oligonucleotide and an amino-modified oligonucleotide took place without any extra reagents at pH 7.0-8.0 at room temperature, and resulted in a ligation product with a phosphoramidate bond with a 39-85% yield...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28520401/identification-of-galnac-conjugated-antisense-oligonucleotide-metabolites-using-an-untargeted-and-generic-approach-based-on-high-resolution-mass-spectrometry
#19
Christophe Husser, Andreas Brink, Manfred Zell, Martina B Müller, Erich Koller, Simone Schadt
Antisense oligonucleotides linked by phosphorothioates are an important class of therapeutics under investigation in various pharmaceutical companies. Antisense oligonucleotides may be coupled to high-affinity ligands (triantennary N-acetyl ga-lactosamine = GalNAc) for hepatocyte-specific asialoglycoprotein receptors (ASGPR) to enhance uptake to hepatocytes and to increase potency. Since disposition and biotransformation of GalNAc-conjugated oligonucleotides is different from unconjugated oligonucleotides, appropriate analytical methods are required to identify main cleavage sites and degradation products of GalNAc conjugated and unconjugated oligonucleotides in target cells...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28518172/super-resolution-microscopy-with-dna-paint
#20
Joerg Schnitzbauer, Maximilian T Strauss, Thomas Schlichthaerle, Florian Schueder, Ralf Jungmann
Super-resolution techniques have begun to transform biological and biomedical research by allowing researchers to observe structures well below the classic diffraction limit of light. DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) offers an easy-to-implement approach to localization-based super-resolution microscopy, owing to the use of DNA probes. In DNA-PAINT, transient binding of short dye-labeled ('imager') oligonucleotides to their complementary target ('docking') strands creates the necessary 'blinking' to enable stochastic super-resolution microscopy...
June 2017: Nature Protocols
keyword
keyword
62632
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"