1XV6

The solution structure of 2',5'-linked 3'-O-(2-methoxyethyl)-RNA hairpin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 30 
  • Selection Criteria: all calculated structures submitted 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex

Plevnik, M.Gdaniec, Z.Plavec, J.

(2005) Nucleic Acids Res. 33: 1749-1759

  • DOI: 10.1093/nar/gki318

  • PubMed Abstract: 
  • The isomerization of phosphodiester functionality of nucleic acids from 3',5'- to a less common 2',5'-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conf ...

    The isomerization of phosphodiester functionality of nucleic acids from 3',5'- to a less common 2',5'-linkage influences the complex interplay of stereoelectronic effects that drive pseudorotational equilibrium of sugar rings and thus affect the conformational propensities for compact or more extended structures. The present study highlights the subtle balance of non-covalent forces at play in structural equilibrium of 2',5'-linked RNA analogue, 3'-O-(2-methoxyethyl) substituted dodecamer *CG*CGAA*U*U*CG*CG, 3'-MOE-2',5'-RNA, where all cytosines and uracils are methylated at C5. The NMR and UV spectroscopic studies have shown that 3'-MOE-2',5'-RNA adopts both hairpin and duplex secondary structures, which are involved in a dynamic exchange that is slow on the NMR timescale and exhibits strand and salt concentration as well as pH dependence. Unusual effect of pH over a narrow physiological range is observed for imino proton resonances with exchange broadening observed at lower pH and relatively sharp lines observed at higher pH. The solution structure of 3'-MOE-2',5'-RNA hairpin displays a unique and well-defined loop, which is stabilized by Watson-Crick A5.*U8 base pair and by n --> pi* stacking interactions of O4' lone-pair electrons of A6 and *U8 with aromatic rings of A5 and *U7, respectively. In contrast, the stem region of 3'-MOE-2',5'-RNA hairpin is more flexible. Our data highlight the important feature of backbone modifications that can have pronounced effects on interstrand association of nucleic acids.


    Organizational Affiliation

    Slovenian NMR Center, National Institute of Chemistry Hajdrihova 19, PO Box, 660, SI-1001 Ljubljana, Slovenia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*(C2L)P*(G2L)P*(C2L)P*(G2L)P*(A2L)P*(A2L)P*(U2L)P*(U2L)P*(C2L)P*(G2L)P*(C2L)P*(G2L))-2'A12N/A
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
A2L
Query on A2L
A
RNA LINKINGC13 H20 N5 O8 PA
U2L
Query on U2L
A
RNA LINKINGC13 H21 N2 O10 PU
G2L
Query on G2L
A
RNA LINKINGC13 H20 N5 O9 PG
C2L
Query on C2L
A
RNA LINKINGC13 H22 N3 O9 PC
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 30 
  • Selection Criteria: all calculated structures submitted 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-04-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance