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Protocol for the Solid-phase Synthesis of Oligomers of RNA Containing a 2'-O-thiophenylmethyl Modification and Characterization via Circular Dichroism
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Solution Structure of Poly(UG) RNA.

Cristian A Escobar1, Riley J Petersen1, Marco Tonelli2

  • 1Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.

Journal of Molecular Biology
|November 4, 2023
PubMed
Summary
This summary is machine-generated.

Researchers determined the solution structure of free poly(UG) (pUG) RNA, revealing a compact, left-handed quadruplex structure. This "pUG fold" is consistent with the structure bound to a ligand, suggesting it

Keywords:
NMRQuadruplexRNASAXSpoly(UG)

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Area of Science:

  • Molecular Biology
  • Structural Biology
  • RNA Biology

Background:

  • Poly(UG) (pUG) RNAs are abundant eukaryotic sequences involved in gene silencing.
  • Previous studies determined the crystal structure of pUG RNA bound to N-methyl mesoporphyrin IX (NMM).
  • The structure of free pUG RNA remained unknown.

Purpose of the Study:

  • To determine the solution structure of free poly(UG) RNA.
  • To investigate the structural basis of the pUG fold and its stability.

Main Methods:

  • Nuclear Magnetic Resonance (NMR) spectroscopy
  • Small and Wide-Angle X-ray Scattering (SAXS/WAXS)
  • Site-specific deoxyribose modifications to aid NMR signal assignment

Main Results:

  • The solution structure of free (GU)12 RNA was determined using NMR-SAXS-WAXS.
  • A compact, left-handed quadruplex structure with a Z-form backbone, termed the 'pUG fold', was identified.
  • The determined structure is consistent with the crystal structure of NMM-bound pUG RNA, indicating the fold is unaltered by ligand binding.

Conclusions:

  • The pUG fold is a stable structural motif of free pUG RNA.
  • The solution structure provides conformational details not resolved by crystallography.
  • These findings explain how the pUG fold can form within longer RNA molecules.