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

Publication ,  Journal Article
Eichhorn, CD; Al-Hashimi, HM
Published in: RNA
June 2014

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.

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Published In

RNA

DOI

EISSN

1469-9001

Publication Date

June 2014

Volume

20

Issue

6

Start / End Page

782 / 791

Location

United States

Related Subject Headings

  • Riboswitch
  • RNA
  • Nucleic Acid Conformation
  • Magnetic Resonance Spectroscopy
  • Ligands
  • Developmental Biology
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology
 

Citation

APA
Chicago
ICMJE
MLA
NLM
Eichhorn, C. D., & Al-Hashimi, H. M. (2014). Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA, 20(6), 782–791. https://doi.org/10.1261/rna.043711.113
Eichhorn, Catherine D., and Hashim M. Al-Hashimi. “Structural dynamics of a single-stranded RNA-helix junction using NMR.RNA 20, no. 6 (June 2014): 782–91. https://doi.org/10.1261/rna.043711.113.
Eichhorn CD, Al-Hashimi HM. Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA. 2014 Jun;20(6):782–91.
Eichhorn, Catherine D., and Hashim M. Al-Hashimi. “Structural dynamics of a single-stranded RNA-helix junction using NMR.RNA, vol. 20, no. 6, June 2014, pp. 782–91. Pubmed, doi:10.1261/rna.043711.113.
Eichhorn CD, Al-Hashimi HM. Structural dynamics of a single-stranded RNA-helix junction using NMR. RNA. 2014 Jun;20(6):782–791.

Published In

RNA

DOI

EISSN

1469-9001

Publication Date

June 2014

Volume

20

Issue

6

Start / End Page

782 / 791

Location

United States

Related Subject Headings

  • Riboswitch
  • RNA
  • Nucleic Acid Conformation
  • Magnetic Resonance Spectroscopy
  • Ligands
  • Developmental Biology
  • 3101 Biochemistry and cell biology
  • 0601 Biochemistry and Cell Biology