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RNA. 2014 Jun;20(6):782-91. doi: 10.1261/rna.043711.113. Epub 2014 Apr 17.

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

Author information

1
Chemical Biology Doctoral Program, University of Michigan, Ann Arbor, Michigan 48109, USA.
2
Department of Biochemistry, Duke University Medical Center, Durham, North Carolina 27710, USA.

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, (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.

KEYWORDS:

RNA dynamics; ligand recognition; prequeuosine riboswitch; residual dipolar couplings; spin relaxation

PMID:
24742933
PMCID:
PMC4024633
DOI:
10.1261/rna.043711.113
[Indexed for MEDLINE]
Free PMC Article

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