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Results: 96
Molecular basis of infantile reversible cytochrome c oxidase deficiency myopathy.
Rita Horvath, John P Kemp, Helen AL Tuppen, Gavin Hudson, Anders Oldfors, Suely KN Marie, Ali-Reza Moslemi, Serenella Servidei, Elisabeth Holme, Sara Shanske, Gittan Kollberg, Parul Jayakar, Angela Pyle, Harold M Marks, Elke Holinski-Feder, Mena Scavina, Maggie C Walter, Jorida Coku, Andrea Günther-Scholz, Paul M Smith, Robert McFarland, Zofia MA Chrzanowska-Lightowlers, Robert N Lightowlers, Michio Hirano, Hanns Lochmüller, Robert W Taylor, Patrick F Chinnery, Mar Tulinius, Salvatore DiMauro
Mar 07, 2019
Childhood-onset mitochondrial encephalomyopathies are usually severe, relentlessly progressive conditions that have a fatal outcome. However, a puzzling infantile disorder, long known as 'benign cytochrome c oxidase deficiency...
Freiburg RNA tools
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, Rolf Backofen
Nov 06, 2018
The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver...
Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.
Double-stranded RNA (dsRNA) is a potent proinflammatory signature of viral infection. Long cytosolic dsRNA is recognized by MDA5. The cooperative assembly of MDA5 into helical filaments on dsRNA nucleates the assembly of a...
AGS ATPase Aicardi-Goutières syndrome DExD/H-box RNA helicase RIG-I-like receptor RLR SF2 helicases SMS Singleton-Merten syndrome cryo-EM Cryoelectron Microscopy helical reconstruction innate immune pattern recognition nucleic acid sensing superfamily 2 helicases Adenosine Triphosphate Cryoelectron Microscopy HEK293 Cells Humans Hydrolysis Hydrophobic and Hydrophilic Interactions Interferon-Induced Helicase IFIH1 Interferon-beta Molecular Docking Simulation Mutation Nucleic Acid Conformation Protein Conformation RNA Double-Stranded Signal Transduction Structure-Activity Relationship
2'-Alkynylnucleotides
Marius M Haugland, Afaf H El-Sagheer, Rachel J Porter, Javier Peña, Tom Brown, Edward A Anderson, Janet E Lovett
Jan 26, 2018
Electron paramagnetic resonance (EPR) spectroscopy is a powerful method to elucidate molecular structure through the measurement of distances between conformationally well-defined spin labels. Here we report a sequence-flexible...
Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.
The mapping between biological genotypes and phenotypes plays an important role in evolution, and understanding the properties of this mapping is crucial to determine the outcome of evolutionary processes. One of the most...
Structural biology of multicomponent assemblies in DNA double-strand-break repair through non-homologous end joining.
The transposable elements of the Drosophila melanogaster euchromatin
Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker
Jun 17, 2011
Structural and functional analysis of four non-coding Y RNAs from Chinese hamster cells
Quirino Alves de Lima Neto, Francisco Ferreira Duarte Junior, Paulo Sérgio Alves Bueno, Flavio Augusto Vicente Seixas, Madzia Pauline Kowalski, Eyemen Kheir, Torsten Krude, Maria Aparecida Fernandez
Sep 29, 2016
BACKGROUND: The genes coding for Y RNAs are evolutionarily conserved in vertebrates. These non-coding RNAs are essential for the initiation of chromosomal DNA replication in vertebrate cells. However thus far, no information is...
Insights into POT1 structural dynamics revealed by cryo-EM.
Telomeres are protein-DNA complexes that protect the ends of linear eukaryotic chromosomes. Mammalian telomeric DNA consists of 5'-(TTAGGG)n-3' double-stranded repeats, followed by up to several hundred bases of a 3'...
Controlling aggregation of cholesterol-modified DNA nanostructures.
Alexander Ohmann, Kerstin Göpfrich, Himanshu Joshi, Rebecca F Thompson, Diana Sobota, Neil A Ranson, Aleksei Aksimentiev, Ulrich F Keyser
Oct 08, 2019
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...
Nucleosome plasticity is a critical element of chromatin liquid-liquid phase separation and multivalent nucleosome interactions.
Stephen E Farr, Esmae J Woods, Jerelle A Joseph, Adiran Garaizar, Rosana Collepardo-Guevara
Mar 24, 2021
MDA5 disease variant M854K prevents ATP-dependent structural discrimination of viral and cellular RNA.
Functions of the 5' and 3' ends of calicivirus genomes.
Caliciviruses Norovirus RNA secondary structures RNA–protein interactions 3' Untranslated Regions 5' Untranslated Regions Animals Caliciviridae Conserved Sequence Genome Viral Host-Pathogen Interactions Humans Models Biological Nucleic Acid Conformation Promoter Regions Genetic RNA Viral Transcription Genetic Virus Replication
Archaeal fibrillarin-Nop5 heterodimer 2'-O-methylates RNA independently of the C/D guide RNP particle.
Miglė Tomkuvienė, Janina Ličytė, Ingrida Olendraitė, Zita Liutkevičiūtė, Béatrice Clouet-d'Orval, Saulius Klimašauskas
Feb 12, 2019
Archaeal fibrillarin (aFib) is a well-characterized S-adenosyl methionine (SAM)-dependent RNA 2'-O-methyltransferase that is known to act in a large C/D ribonucleoprotein (RNP) complex together with Nop5 and L7Ae proteins and a...
Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiří Šponer
Feb 15, 2019
G-quadruplexes are the most important noncanonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other...
Optical Voltage Sensing Using DNA Origami.
Elisa A Hemmig, Clare Fitzgerald, Christopher Maffeo, Lisa Hecker, Sarah E Ochmann, Aleksei Aksimentiev, Philip Tinnefeld, Ulrich F Keyser
May 01, 2018
We explore the potential of DNA nanotechnology for developing novel optical voltage sensing nanodevices that convert a local change of electric potential into optical signals. As a proof-of-concept of the sensing mechanism, we...
DNA nanotechnology coarse-grained simulations nanocapillary optical voltage measurements single-molecule FRET Biosensing Techniques DNA Electricity Electrodes Equipment Design Fluorescence Resonance Energy Transfer Fluorescent Dyes Ion Transport NANOSTRUCTURES Nanotechnology Nucleic Acid Conformation
Discovery of frameshifting in Alphavirus 6K resolves a 20-year enigma.
BACKGROUND: The genus Alphavirus includes several potentially lethal human viruses. Additionally, species such as Sindbis virus and Semliki Forest virus are important vectors for gene therapy, vaccination and cancer research...
Amino Acid Sequence Animals Base Sequence Cell Line Conserved Sequence Cricetinae Fluorescent Antibody Technique Frameshifting Ribosomal Gene Order Immunoprecipitation Isotope Labeling Mass Spectrometry Molecular Sequence Data Nucleic Acid Conformation RNA Viral Semliki forest virus Viral Structural Proteins Virion
Short inverted repeats contribute to localized mutability in human somatic cells.
Xueqing Zou, Sandro Morganella, Dominik Glodzik, Helen Davies, Yilin Li, Michael R Stratton, Serena Nik-Zainal
Sep 05, 2018
Selected repetitive sequences termed short inverted repeats (SIRs) have the propensity to form secondary DNA structures called hairpins. SIRs comprise palindromic arm sequences separated by short spacer sequences that form the...
DNA-Tile Structures Induce Ionic Currents through Lipid Membranes.
Kerstin Göpfrich, Thomas Zettl, Anna EC Meijering, Silvia Hernández-Ainsa, Samet Kocabey, Tim Liedl, Ulrich F Keyser
Sep 07, 2016
Dimerisation of HIV-2 genomic RNA is linked to efficient RNA packaging, normal particle maturation and viral infectivity.
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