PDBsum entry 1xv6

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PDB id:
Name: RNA
Title: The solution structure of 2',5'-linked 3'-o-(2- methoxyethyl)-RNA hairpin
Structure: 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'. Chain: a. Synonym: 2'-moe RNA. Engineered: yes
Source: Synthetic: yes. Other_details: solid phase synthesis, phosphoramidite chemistry
NMR struc: 30 models
Authors: M.Plevnik,Z.Gdaniec,J.Plavec
Key ref: M.Plevnik et al. (2005). Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex. Nucleic Acids Res, 33, 1749-1759. PubMed id: 15788747
27-Oct-04     Release date:   05-Apr-05    


Nucleic Acids Res 33:1749-1759 (2005)
PubMed id: 15788747  
Solution structure of a modified 2',5'-linked RNA hairpin involved in an equilibrium with duplex.
M.Plevnik, Z.Gdaniec, J.Plavec.
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.
  Selected figure(s)  
Figure 5.
Overview of the interresidual NOEs in the 2',5'-RNA hairpin loop. Sequential and long-range NOE connectivities are shown by solid and dotted lines, respectively.
Figure 6.
Solution structure of 3'-MOE-2',5'-RNA hairpin. (a) Superposition of the 30 final structures based on the loop residues A5-*U8. The heavy atoms without MOE groups have been superimposed. The loop residues are colored blue (A) and red (*U). Stem residues are coloured green. (b) Stereoview of a single representative structure of the 2',5'-linked RNA hairpin loop. All atoms without MOE groups are displayed.
  The above figures are reprinted from an Open Access publication published by Oxford University Press: Nucleic Acids Res (2005, 33, 1749-1759) copyright 2005.  
  Figures were selected by an automated process.