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Angewandte Chemie, Volume 137, Issue 9, February 24, 2025.The SARS‐CoV‐2 frameshift element pseudoknot plays a crucial role in viral replication. Using various techniques, especially NMR spectroscopy and in vitro frameshift assays, we have developed and optimized chemical probes that serve as fundamental structures for potential inhibitors targeting viral RNAs.
Betül Ceylan +19 more
wiley +2 more sources
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage
Nature Chemical Biology, 2016 The field of small self-cleaving nucleolytic ribozymes has been invigorated by the recent discovery of the twister, twister-sister, pistol and hatchet ribozymes.
A. Ren +7 more
semanticscholar +1 more source
Exploring the Potential and Advancements of Circular RNA Therapeutics
Exploration, EarlyView.Given the remarkable advantages in terms of stability, sustained expression profile, safety, wide range of druggable targets, scalable and cost‐effective manufacturing capabilities, circRNA is currently undergoing intensive investigation for various therapeutic applications such as vaccines, protein replacement, genetic disease treatment, gene therapy,
Lei Wang +6 more
wiley +1 more source
Lifting Prediction to Alignment of RNA Pseudoknots [PDF]
Journal of Computational Biology, 2009 Prediction and alignment of RNA pseudoknot structures are NP-hard. Nevertheless, several efficient prediction algorithms by dynamic programming have been proposed for restricted classes of pseudoknots. We present a general scheme that yields an efficient alignment algorithm for arbitrary such classes.
Möhl, Mathias +2 more
openaire +6 more sources
A twist in the tail : SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication [PDF]
, 2011 The RNA structure and long-range interactions of the SL9266 cis-acting replication element located within the NS5B coding region of hepatitis C virus (HCV) were determined using selective 2′-hydroxyl acylation analysed by primer extension.
Andrew Tuplin +56 more
core +3 more sources
Small synthetic molecule-stabilized RNA pseudoknot as an activator for –1 ribosomal frameshifting
Nucleic Acids Research, 2018 Programmed –1 ribosomal frameshifting (−1PRF) is a recoding mechanism to make alternative proteins from a single mRNA transcript. −1PRF is stimulated by cis-acting signals in mRNA, a seven-nucleotide slippery sequence and a downstream secondary structure
Saki Matsumoto +4 more
semanticscholar +1 more source
An algebraic language for RNA pseudoknots comparison [PDF]
BMC Bioinformatics, 2019 RNA secondary structure comparison is a fundamental task for several studies, among which are RNA structure prediction and evolution. The comparison can currently be done efficiently only for pseudoknot-free structures due to their inherent tree representation.In this work, we introduce an algebraic language to represent RNA secondary structures with ...
Michela Quadrini +2 more
openaire +5 more sources
jViz.RNA 4.0-Visualizing pseudoknots and RNA editing employing compressed tree graphs.
PLoS ONE, 2019 Previously, we have introduced an improved version of jViz.RNA which enabled faster and more stable RNA visualization by employing compressed tree graphs.
Boris Shabash, Kay C Wiese
doaj +1 more source
An adaptive defect weighted sampling algorithm to design pseudoknotted RNA secondary structures
Frontiers in Genetics, 2016 Computational design of RNA sequences that fold into targeted secondary structures hasmany applications in biomedicine, nanotechnology and synthetic biology.
Kasra Zandi +3 more
doaj +1 more source
Nop9 binds the central pseudoknot region of 18S rRNA
Nucleic Acids Research, 2017 The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional ...
B. Wang, K. Ye
semanticscholar +1 more source