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  • ribozyme
  • Utilizing synchrotron x-ray scattering at the Biophysics Collaborative Access Team (Bio-CAT) beamline 18-ID at the Argonne Advanced Photon Source (APS), researchers investigated the unique folding behavior of ribozyme , which is an RNA that acts as a catalyst. (phys.org)
  • The native structure of ribozyme was found to be important for this cooperation, with small alterations in the ribozyme architecture determining the entire folding pattern. (phys.org)
  • We have combined recent technological advances in time-resolved hydroxyl radical (·OH) footprinting ( 24 ) and analysis ( 25 ) with automated kinetic and structural modeling ( 26 ) to construct folding landscapes for the T. thermophila ribozyme under a variety of different conditions. (pnas.org)
  • We use a hidden-Markov-model (HMM) analysis to construct a model of the Mg2+-dependent folding dynamics of the ribozyme Diels-Alderase from single-molecule FRET data. (fu-berlin.de)
  • Catalysis
  • Conformational transitions of RNA play fundamental roles in the processes of RNA refolding and annealing, in the catalysis of chemical reactions by ribozymes, and in the regulation of gene expression by riboswitches. (ibs.fr)
  • nucleic acid
  • Using tools from synthetic biology and nucleic acid nanotechnology (specifically, toehold mediated strand displacement), we have demonstrated and are further developing an alternative approach to direct and control 5' to 3' sequential RNA folding. (jbsdonline.com)
  • riboswitch
  • RNAs are synthesized exclusively in a 5' to 3' direction and it is well established that many (particularly long noncoding, but also riboswitch) RNAs begin to fold before the transcript is fully synthesized. (jbsdonline.com)
  • Methods
  • The presented techniques include powerful tools with a long tradition in RNA research as well as more advanced, novel methods, thus the methods span multiple disciplines, including molecular biology, biochemistry, biophysics, and computational biology. (springer.com)
  • Practical and authoritative, RNA Folding: Methods and Protocols serves as a vital reference for researchers attempting to gain insights into the secrets of this astounding macromolecule. (springer.com)
  • Thermodynamic
  • Thermodynamic folding software ( mfold [ 7 ], ViennaRNA Package [ 8 ]) includes the possibility to constrain the set of allowed base pairs or to force individual nucleotides to be paired. (biomedcentral.com)
  • Simulations and thermodynamic experiments implicate linkage between folding and protonation in nucleobase p K a shifting. (biochemsoctrans.org)
  • vivo
  • Although changes in folding environment and severely destabilizing mutations are not likely to occur in vivo , their use as a tool to perturb the RNA folding landscape in vitro yields significant insight into the folding mechanism. (pnas.org)
  • ligand
  • The RNA refolding upon ligand binding can be conveniently studied by real-time multi-dimensional NMR spectroscopy. (ibs.fr)
  • Transcription
  • Small RNAs are known to regulate diverse gene expression processes including translation, transcription, and splicing. (nih.gov)
  • Among small RNAs, the microRNAs (miRNAs) of 17 to 27 nucleotides (nts) undergo biogeneses including primary transcription, RNA excision and folding, nuclear export, cytoplasmic processing, and then bioactivity as regulatory agents. (nih.gov)
  • Base Pairs
  • The sparsification method exploits two properties of the input: the number of subsequence Z with the endpoints belonging to the optimal folding set and the maximum number base-pairs L . These sparsity properties satisfy \(0 \le L \le n / 2\) and \(n \le Z \le n^2 / 2\) , and the method reduces the algorithmic running time to O ( LZ ). (biomedcentral.com)
  • The RNA polymers having a long and rigid stem accumulate, whereas a polymer with stem length less than 4 base pairs shows depletion. (pnas.org)
  • viruses
  • Segmented RNA viruses are ubiquitous pathogens, which include influenza viruses and rotaviruses. (elifesciences.org)
  • This kind of difference can explain the ability of various strains of bacteria to reject infectious RNA from another strain's viruses (phage). (blogspot.com)
  • Human parechovirus 1 is an example of such viruses that contains 60 short regions of ordered RNA density making identical contacts with the protein shell. (aalto.fi)
  • double-stranded
  • Genomes of rotaviruses (RVs), and other pathogens of the Reoviridae family, comprise nine to twelve double-stranded (ds)RNA segments, co-packaged into each infectious virion. (elifesciences.org)
  • Such measurements emphasize the crucial contribution of the double-stranded parts of RNA for thermal separation and selection under a temperature gradient. (pnas.org)
  • Footprinting
  • We distinguish the contribution of the electrostatic environment, initial conformational ensemble, and macromolecular stability on the folding mechanism of a large RNA using a combination of time-resolved "Fast Fenton" hydroxyl radical footprinting and exhaustive kinetic modeling. (pnas.org)
  • Multifold ( https://pypi.python.org/pypi/multifold ) - According to the authors:"MultifFold is a Python based tool package for RNA footprinting data analysis. (wordpress.com)
  • It accepts RNA footprinting data generated from SHAPE-Seq, PARS and DMS-Seq technologies. (wordpress.com)
  • It could handle RNA footprinting data generated from gene isoforms or overlapped transcripts. (wordpress.com)
  • hairpin
  • The V protein unfolded the ATP-hydrolysis domain of MDA5 via a β-hairpin motif and recognized a structural motif of MDA5 that is normally buried in the conserved helicase fold. (sciencemag.org)
  • mutations
  • Examining the effects of mutations and solvent ionic strength on folding shows that the folding transition state is compact and electrostatically stabilized like the native state, but without substantial native tertiary contacts. (jbsdonline.com)
  • virion
  • The data are consistent with RNA packaging signals playing essential roles in virion assembly. (aalto.fi)
  • accumulate
  • We demonstrated that in such temperature gradients one could accumulate many-fold DNA by combining thermophoresis and convection ( 5 ). (pnas.org)
  • mRNA
  • The graphic shows the minimum-free-energy folding of the mRNA for catalase in Staphylococcus epidermidis strain RP62A (left) and Pseudomonas putida strain GB-1 (on the right). (blogspot.com)
  • As a result, the potential for purine-pyrimidine hydrogen bonding is considerably less in the Staph version of the mRNA than in the Pseudomonas version, and you can easily see this by comparing the two RNAs shown below. (blogspot.com)
  • Function
  • RNA is a unique biopolymer that can carry both genetic information and catalytic function. (jbsdonline.com)
  • It makes explicit use of the conceptual separation of the "folding grammar" defining the search space and the actual energy evaluation, which allows constraints to be interleaved in a natural way between recursion steps and evaluation of the standard energy function. (biomedcentral.com)
  • Linkage between protonation and co-operativity of folding may drive p K a shifting and provide for enhanced function in RNA. (biochemsoctrans.org)
  • Cells
  • RNA is one of two types of nucleic acids found in all cells. (phys.org)
  • Rothemund further adds, "The payoff is that unlike DNA origami, which are expensive and have to be made outside of cells, RNA origami should be able to be grown cheaply in large quantities, simply by growing bacteria with genes for them. (eurekalert.org)
  • uncover
  • Further work to uncover the entire RNA interaction network in rotaviruses would also accelerate the design of new vaccines and may help us to develop antiviral drugs to treat infections. (elifesciences.org)