Structural dynamics of a single-stranded RNA–helix junction using NMR

Authors

Catherine D. Eichhorn, University of MichiganFollow
Hashim M. Al-Hashimi, Duke UniversityFollow

Document Type

Article

Date of this Version

2014

Citation

RNA 20:782–791

Comments

© 2014 Eichhorn and Al-Hashimi

http://www.rnajournal.org/cgi/doi/10.1261/rna.043711.113.

Abstract

Many regulatory RNAs contain long single strands (ssRNA) that adjoin secondary structural elements. Here, we use NMR spectroscopy to study the dynamic properties of a 12-nucleotide (nt) ssRNA tail derived from the prequeuosine riboswitch linked to the 3′ end of a 48-nt hairpin. Analysis of chemical shifts, NOE connectivity, ¹³C spin relaxation, and residual dipolar coupling data suggests that the first two residues (A25 and U26) in the ssRNA tail stack onto the adjacent helix and assume an ordered conformation. The following U26-A27 step marks the beginning of an A₆-tract and forms an acute pivot point for substantial motions within the tail, which increase toward the terminal end. Despite substantial internal motions, the ssRNA tail adopts, on average, an A-form helical conformation that is coaxial with the helix. Our results reveal a surprising degree of structural and dynamic complexity at the ssRNA–helix junction, which involves a fine balance between order and disorder that may facilitate efficient pseudoknot formation on ligand recognition.