Results 1 to 10 of about 14,795 (267)
Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles [PDF]
Nature Communications, 2021 Development of Cas12a for human therapeutics and diagnostics may significantly benefit from, or even require, chemical modification of its guide RNA. Here the authors show that the noncanonical 5′ pseudoknot structure of the AsCas12a crRNA guide can be ...
Eman A. Ageely +7 more
doaj +3 more sources
Nature Communications, 2021 The RNA pseudoknot of SARS-CoV-2 promotes -1 programmed ribosomal frameshifting. Here the authors use single molecule force spectroscopy to study the folding of this pseudoknot, showing that it forms at least two different pseudoknot conformers with ...
Krishna Neupane +8 more
doaj +2 more sources
Scientific Reports, 2022 Pepino mosaic virus (PepMV) is a potexvirus of the family Alphaflexiviridae within the order of Tymovirales that threatens tomato production worldwide.
René C. L. Olsthoorn +2 more
doaj +2 more sources
Salt-Dependent RNA Pseudoknot Stability: Effect of Spatial Confinement
Frontiers in Molecular Biosciences, 2021 Macromolecules, such as RNAs, reside in crowded cell environments, which could strongly affect the folded structures and stability of RNAs. The emergence of RNA-driven phase separation in biology further stresses the potential functional roles of ...
Chenjie Feng +4 more
doaj +2 more sources
Shapify: Paths to SARS-CoV-2 frameshifting pseudoknot.
PLoS Computational Biology, 2023 Multiple coronaviruses including MERS-CoV causing Middle East Respiratory Syndrome, SARS-CoV causing SARS, and SARS-CoV-2 causing COVID-19, use a mechanism known as -1 programmed ribosomal frameshifting (-1 PRF) to replicate.
Luke Trinity +4 more
doaj +2 more sources
Methods and Protocols, 2022 Obtaining valuable clues for noncoding RNA (ribonucleic acid) subsequences remains a significant challenge, acknowledging that most of the human genome transcribes into noncoding RNA parts related to unknown biological operations.
Christos Andrikos +5 more
doaj +2 more sources
NMR Studies of Genomic RNA in 3′ Untranslated Region Unveil Pseudoknot Structure that Initiates Viral RNA Replication in SARS-CoV-2 [PDF]
JACS AuIn the 3′ untranslated region of the SARS-CoV-2 virus RNA genome, genomic RNA replication is initiated in the highly conserved region called 3′PK, containing three stem structures (P1pk, P2, and P5).
Takako Ohyama +3 more
openalex +2 more sources
PseudoknotVisualizer: Visualization of pseudoknots on three-dimensional RNA structures. [PDF]
PLoS Computational BiologyWe introduce the PseudoknotVisualizer, a specialized software designed to identify and visualize pseudoknots within RNA three-dimensional structures. Typically, RNA secondary structures containing pseudoknots can be decomposed into multiple pseudoknot ...
Takumi Otagaki +3 more
doaj +2 more sources
Nature Communications, 2021 Exoribonuclease-resistant RNAs (xrRNAs) are RNA elements that block the exoribonucleolytic degradation of RNA. Here the authors show how a long-range pseudoknot length modulates the Mg2+-dependence of flaviviral xrRNA’s folding, conformational dynamics ...
Xiaolin Niu +6 more
doaj +2 more sources
New models and algorithms for RNA pseudoknot order assignment
International Journal of Applied Mathematics and Computer Science, 2020 The pseudoknot is a specific motif of the RNA structure that highly influences the overall shape and stability of a molecule. It occurs when nucleotides of two disjoint single-stranded fragments of the same chain, separated by a helical fragment ...
Zok Tomasz +5 more
doaj +2 more sources