Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

ABSTRACT: RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicab

SUBMITTER: Strobel EJ 

PROVIDER: S-EPMC5499547 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature