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

Journal Article (Journal Article)

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, (13)C 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.

Full Text

Duke Authors

Cited Authors

  • Eichhorn, CD; Al-Hashimi, HM

Published Date

  • June 2014

Published In

Volume / Issue

  • 20 / 6

Start / End Page

  • 782 - 791

PubMed ID

  • 24742933

Pubmed Central ID

  • PMC4024633

Electronic International Standard Serial Number (EISSN)

  • 1469-9001

Digital Object Identifier (DOI)

  • 10.1261/rna.043711.113


  • eng

Conference Location

  • United States