Computational protocol: Extensive terminal and asymmetric processing of small RNAs from rRNAs, snoRNAs, snRNAs, and tRNAs

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Protocol publication

[…] To ensure minimum structural disruptions in mutated tRNA (LysTTT) sequences, the RNAs were folded by Vienna RNA Package (), and then manually inspected using VARNA (). Wild-type and mutated tRNA sequences were constructed using mirVana miRNA Probe Construction kit (Ambion, Austin, TX, USA). Briefly, wild-type or mutated tRNA DNA oligos were synthesized (IDT, IA, USA) and annealed to a shorter DNA oligo harboring T7 promoter sequence. The partial double-stranded DNA was filled in by Klenow polymerase and then subjected to in vitro transcription by T7 RNA polymerase. Synthesized RNA was purified by Trizol (Invitrogen), before performing in vitro cleavage assays. […]

Pipeline specifications

Software tools ViennaRNA, VARNA
Application RNA structure analysis
Organisms Mus musculus, Homo sapiens