Spontaneous base flipping helps drive Nsp15’s preferences in double stranded RNA substrates
Nature CommunicationsCoronaviruses evade detection by the host immune system with the help of the endoribonuclease Nsp15, which regulates levels of viral double stranded RNA by cleaving 3′ of uridine (U).
Zoe M. Wright +11 more
doaj +1 more source
How Large is the Universe of RNA-Like Motifs? A Clustering Analysis of RNA Graph Motifs Using Topological Descriptors [PDF]
arXivWe introduce a computational topology-based approach with unsupervised machine-learning algorithms to estimate the database size and content of RNA-like graph topologies. Specifically, we apply graph theory enumeration to generate all 110,667 possible 2D dual graphs for vertex numbers ranging from 2 to 9.
arxiv
Produção e caracterização de um antissoro policlonal para detecção de ds-RNA [PDF]
, 1998 A maioria dos vírus fitopatogénicos contém no seu genoma ácido ribonucleico monocatenário(ss-RNA). Este ácido nucleico viral tem capacidade de replicação no interior das células vegetais,dando origem a uma forma replicativa de ácido nucleico bicatenário (
Carvalho, Miguel +2 more
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Single molecule pull down of double strand RNA binding proteins [PDF]
, 2015 RNA molecules are transcribed as single stranded naturally, but with most of them forming in to structures composed of duplex regions, loop, bulge or mismatches. RNAs with double stranded regions, or known as double-strand RNAs (dsRNAs).
Wang, Xinlei
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RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching [PDF]
arXivThe growing significance of RNA engineering in diverse biological applications has spurred interest in developing AI methods for structure-based RNA design. While diffusion models have excelled in protein design, adapting them for RNA presents new challenges due to RNA's conformational flexibility and the computational cost of fine-tuning large ...
arxiv
In situ probe and inhibitory RNA synthesis using streamlined gene cloning with Gibson assembly
STAR Protocols, 2022 Summary: The synthesis of single-stranded riboprobes or double-stranded RNAs for in situ hybridization and gene knockdowns often use vectors that require time-consuming plasmid restriction digests and inefficient gel purifications.
Andrew Wolff +3 more
doaj
Parametric analysis of RNA folding [PDF]
arXiv, 2009 We extend recent methods for parametric sequence alignment to the parameter space for scoring RNA folds. This involves the construction of an RNA polytope. A vertex of this polytope corresponds to RNA secondary structures with common branching. We use this polytope and its normal fan to study the effect of varying three parameters in the free energy ...
arxiv
Molecular Cloning and Analysis of Tomato Blackring Virus [PDF]
, 1985 Tomato blackring virus RNA was reverse transcribed into single-strand complementary DNA. The RNA template was removed by alkaline hydrolysis, and the cDNA was transcribed into a double-stranded structure.
Lochead, Susan Milne
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Targeted dsRNA-mediated suppression of Phytophthora infestans infection via Avr3a
Applied Biological ChemistryPhytophthora infestans (P. infestans) is a highly destructive oomycete that causes the late blight in Solanaceous crops, such as potatoes and tomatoes, reducing crop yield. Although many pesticides are used to control P.
Hyeonmin Lee +4 more
doaj +1 more source
Suppression of Argonaute 2 Transcript Levels in Du182A Cells [PDF]
, 2018 RNA interference (RNAi) uses double-stranded RNA (dsRNA) molecules to degrade and suppress the transcript level of a complementary mRNA target1.
Featherston, Kyah +2 more
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