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Results: 34
Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis.
Lovorka Stojic, Aaron TL Lun, Jasmin Mangei, Patrice Mascalchi, Valentina Quarantotti, Alexis R Barr, Chris Bakal, John C Marioni, Fanni Gergely, Duncan T Odom
Sep 05, 2018
A computational platform for high-throughput analysis of RNA sequences and modifications by mass spectrometry.
Samuel Wein, Byron Andrews, Timo Sachsenberg, Helena Santos-Rosa, Oliver Kohlbacher, Tony Kouzarides, Benjamin A Garcia, Hendrik Weisser
Apr 14, 2020
The field of epitranscriptomics continues to reveal how post-transcriptional modification of RNA affects a wide variety of biological phenomena. A pivotal challenge in this area is the identification of modified RNA residues...
Repeat DNA-PAINT suppresses background and non-specific signals in optical nanoscopy.
Alexander H Clowsley, William T Kaufhold, Tobias Lutz, Anna Meletiou, Lorenzo Di Michele, Christian Soeller
Jan 21, 2021
Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides.
Alice LB Pyne, Agnes Noy, Kavit HS Main, Victor Velasco-Berrelleza, Michael M Piperakis, Lesley A Mitchenall, Fiorella M Cugliandolo, Joseph G Beton, Clare EM Stevenson, Bart W Hoogenboom, Andrew D Bates, Anthony Maxwell, Sarah A Harris
Feb 16, 2021
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of...
Oligonucleotide-based systems
There is an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte...
Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution.
John M Atack, Lucy A Weinert, Alexander W Tucker, Asma U Husna, Thomas M Wileman, Nazreen F Hadjirin, Ngo T Hoa, Julian Parkhill, Duncan J Maskell, Patrick J Blackall, Michael P Jennings
Dec 06, 2018
Alleles Animals DNA Methylation DNA Modification Methylases DNA Bacterial Epigenesis Genetic Escherichia coli Gene Expression Regulation Bacterial genetic variation Genome Bacterial Methyltransferases Microsatellite Repeats Oligonucleotides Phenotype Regulon Streptococcal Infections Streptococcus suis Swine
Hypoxia-induced neutrophil survival is mediated by HIF-1alpha-dependent NF-kappaB activity.
Sarah R Walmsley, Cristin Print, Neda Farahi, Carole Peyssonnaux, Randall S Johnson, Thorsten Cramer, Anastasia Sobolewski, Alison M Condliffe, Andrew S Cowburn, Nicola Johnson, Edwin R Chilvers
Mar 13, 2020
Neutrophils are key effector cells of the innate immune response and are required to migrate and function within adverse microenvironmental conditions. These inflammatory sites are characterized by low levels of oxygen and...
Animals Apoptosis Blotting Western Cell Survival Chemokine CCL4 Cytokines DNA Primers DNA-Binding Proteins Enzyme-Linked Immunosorbent Assay Gliotoxin Humans Hypoxia Hypoxia-Inducible Factor 1 Hypoxia-Inducible Factor 1 alpha Subunit Macrophage Inflammatory Proteins Mice Mice Knockout Mixed Function Oxygenases NF-kappa B p50 Subunit Neutrophils Nuclear Proteins Oligonucleotide Array Sequence Analysis Oligonucleotides Polymerase Chain Reaction Protein Binding Repressor Proteins Sesquiterpenes Transcription Factors
Huntingtin-lowering strategies for Huntington's disease.
INTRODUCTION: Huntington's disease (HD) is an incurable, autosomal dominant neurodegenerative disease caused by an abnormally long polyglutamine tract in the huntingtin protein. Because this mutation causes disease via...
Transcriptional networks controlling the cell cycle.
Martin Bonke, Mikko Turunen, Maria Sokolova, Anna Vähärautio, Teemu Kivioja, Minna Taipale, Mikael Björklund, Jussi Taipale
Nov 04, 2020
In this work, we map the transcriptional targets of 107 previously identified Drosophila genes whose loss caused the strongest cell-cycle phenotypes in a genome-wide RNA interference screen and mine the resulting data...
Animals CDC2 Protein Kinase Cell Cycle Cell Line Cell Size Chromatin Immunoprecipitation Cluster Analysis Drosophila Feedback Physiological Flow Cytometry Gene Expression Profiling Gene Regulatory Networks Microarray Analysis Mitosis Oligonucleotides Phosphorylation RNA Interference Sequence Analysis RNA
Amputation-induced reactive oxygen species are required for successful Xenopus tadpole tail regeneration.
Nick R Love, Yaoyao Chen, Shoko Ishibashi, Paraskevi Kritsiligkou, Robert Lea, Yvette Koh, Jennifer L Gallop, Karel Dorey, Enrique Amaya
Jun 22, 2020
Understanding the molecular mechanisms that promote successful tissue regeneration is critical for continued advancements in regenerative medicine. Vertebrate amphibian tadpoles of the species Xenopus laevis and Xenopus...
Amputation Surgical Animals Animals Genetically Modified antioxidants Cell Proliferation Enzyme Inhibitors Fibroblast Growth Factors Gene Expression Regulation Hydrogen Peroxide Larva NADPH Oxidases Oligonucleotides Antisense Reactive Oxygen Species Regeneration Tail Time Factors Wnt Proteins Wnt Signaling Pathway Xenopus Proteins Xenopus laevis beta Catenin
xMAN
BACKGROUND: The ability to rapidly map millions of oligonucleotide fragments to a reference genome is crucial to many high throughput genomic technologies. RESULTS: We propose an intuitive and efficient algorithm, titled extreme...
Liquid-crystalline ordering of antimicrobial peptide-DNA complexes controls TLR9 activation.
Nathan W Schmidt, Fan Jin, Roberto Lande, Tine Curk, Wujing Xian, Calvin Lee, Loredana Frasca, Daan Frenkel, Jure Dobnikar, Michel Gilliet, Gerard CL Wong
Jul 13, 2015
Oligonucleotide-based systems
There is an increasing number of applications that have been developed for oligonucleotide-based biosensing systems in genetics and biomedicine. Oligonucleotide-based biosensors are those where the probe to capture the analyte...
RNA Docking and Local Translation Regulate Site-Specific Axon Remodeling In Vivo
CE Holt, H-W Wong, Q Lin, F Stroehl, CG Roque, JM Cioni, R Cagnetta, B Turner-Bridger, R Laine, WA Harris, CF Kaminski
Jul 28, 2017
FRAP RNA labeling RNA localization RNA trafficking axon branching Axon guidance local protein synthesis Mitochondria neural wiring Retinotectal projection β-actin Actins Animals Anisomycin Axons Biotin Blastomeres Carbocyanines Cycloheximide Deoxyuracil Nucleotides Embryo Nonmammalian Gene Expression Regulation Developmental In Vitro Techniques Luminescent Proteins Mitochondria Morpholinos Oligonucleotides Antisense Organ Culture Techniques Protein Synthesis Inhibitors RNA Retina Xenopus laevis
A Platform for Site-Specific DNA-Antibody Bioconjugation by Using Benzoylacrylic-Labelled Oligonucleotides.
Juraj Konč, Libby Brown, Daniel R Whiten, Yukun Zuo, Peter Ravn, David Klenerman, Gonçalo JL Bernardes
Sep 28, 2021
Many bioconjugation strategies for DNA oligonucleotides and antibodies suffer limitations, such as site-specificity, stoichiometry and hydrolytic instability of the conjugates, which makes them unsuitable for biological...
Regulation of chemotropic guidance of nerve growth cones by microRNA.
Liang Han, Zhexing Wen, Rachel C Lynn, Marie-Laure Baudet, Christine E Holt, Yukio Sasaki, Gary J Bassell, James Q Zheng
Nov 16, 2011
Structural requirements for PACSIN/Syndapin operation during zebrafish embryonic notochord development.
Melissa A Edeling, Subramaniam Sanker, Takaki Shima, PK Umasankar, Stefan Höning, Hye Y Kim, Lance A Davidson, Simon C Watkins, Michael Tsang, David J Owen, Linton M Traub
May 11, 2020
PACSIN/Syndapin proteins are membrane-active scaffolds that participate in endocytosis. The structure of the Drosophila Syndapin N-terminal EFC domain reveals a crescent shaped antiparallel dimer with a high affinity for...
Amino Acid Sequence Animals Carrier Proteins Cell Movement Embryo Nonmammalian Embryonic Development HeLa Cells Humans Liposomes Molecular Sequence Data Notochord Oligonucleotides Antisense Phenotype Protein Binding Protein Structure Tertiary Structure-Activity Relationship Zebrafish Zebrafish Proteins
A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH.
Nicolas Wicker, Annaïck Carles, Ian G Mills, Maija Wolf, Abhi Veerakumarasivam, Henrik Edgren, Fabrice Boileau, Bohdan Wasylyk, Jack A Schalken, David E Neal, Olli Kallioniemi, Olivier Poch
Jun 16, 2011
An improved cucumber mosaic virus-based vector for efficient decoying of plant microRNAs.
Monobody adapter for functional antibody display on nanoparticles for adaptable targeted delivery applications.
C Albert, L Bracaglia, A Koide, J DiRito, T Lysyy, L Harkins, C Edwards, O Richfield, J Grundler, K Zhou, E Denbaum, G Ketavarapu, T Hattori, S Perincheri, J Langford, A Feizi, D Haakinson, SA Hosgood, ML Nicholson, JS Pober, WM Saltzman, S Koide, GT Tietjen
Nov 15, 2022
Vascular endothelial cells (ECs) play a central role in the pathophysiology of many diseases. The use of targeted nanoparticles (NPs) to deliver therapeutics to ECs could dramatically improve efficacy by providing elevated and...
Cationic surfactant mediated hybridization and hydrophobization of DNA molecules at the liquid/liquid interface and their phase transfer
Murali Sastry, Ashavani Kumar, Mrunalini Pattarkine, Vidya Ramakrishnan, Krishna N. Ganesh
Jan 01, 0001
Hybridization of complementary oligonucleotides mediated by a cationic surfactant at the water/hexane interface leads to hydrophobic, double-helical DNA which may be readily phase transferred to the organic phase and cast into...
Cationic surfactant hybridization DNA water/hexane interface Substrate Hydrophobic Oligonucleotides Analytical, Diagnostic and Therapeutic Techniques and Equipment Biochemical and Biomolecular Engineering Biology and Biomimetic Materials biomaterials Biomedical Biomedical Engineering and Bioengineering Bioresource and Agricultural Engineering Biotechnology Business Administration, Management, and Operations Computational Biology Food Biotechnology Food Microbiology food processing health economics Medical Biotechnology Medical Molecular Biology Medical Pharmacology Molecular Biology Molecular, Cellular, and Tissue Engineering Molecular, Genetic, and Biochemical Nutrition Molecular genetics nanomedicine Nanoscience and Nanotechnology Nanotechnology Nanotechnology Fabrication Pharmacy and Pharmaceutical Sciences
Published by: Harrisburg University of Science and Technology
Targeting non-coding RNA family members with artificial endonuclease XNAzymes.
Non-coding RNAs (ncRNAs) offer a wealth of therapeutic targets for a range of diseases. However, secondary structures and high similarity within sequence families make specific knockdown challenging. Here, we engineer a series...
Differential uptake, kinetics and mechanisms of intracellular trafficking of next-generation antisense oligonucleotides across human cancer cell lines.
Emily Linnane, Paul Davey, Pei Zhang, Sanyogitta Puri, Mark Edbrooke, Elisabetta Chiarparin, Alexey S Revenko, A Robert Macleod, Jim C Norman, Sarah J Ross
Jan 06, 2020
Antisense oligonucleotides (ASOs) modulate cellular target gene expression through direct binding to complementary RNA. Advances in ASO chemistry have led to the development of phosphorothioate (PS) ASOs with constrained-ethyl...
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