Abstract:
:RNA folds during transcription in the cell. Compared to most in vitro studies where the focus is generally on Mg(2+)-initiated refolding of fully synthesized transcripts, cotranscriptional RNA folding studies better replicate how RNA folds in a cellular environment. Unique aspects of cotranscriptional folding include the 5'- to 3'-polarity of RNA, the transcriptional speed, pausing properties of the RNA polymerase, the effect of the transcriptional complex and associated factors, and the effect of RNA-binding proteins. Identifying strategic pause sites can reveal insights on the folding pathway of the nascent transcript. Structural mapping of the paused transcription complexes identifies important folding intermediates along these pathways. Oligohybridization assays and the appearance of the catalytic activity of a ribozyme either in trans or in cis can be used to monitor cotranscriptional folding under a wide range of conditions. In our laboratory, these methodologies have been applied to study the folding of three highly conserved RNAs (RNase P, SRP, and tmRNA), several circularly permuted forms of a bacterial RNase P RNA, a riboswitch (thiM), and an aptamer-activated ribozyme (glmS).
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Wong TN,Pan Tdoi
10.1016/S0076-6879(09)68009-5subject
Has Abstractpub_date
2009-01-01 00:00:00pages
167-93eissn
0076-6879issn
1557-7988pii
S0076-6879(09)68009-5journal_volume
468pub_type
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