2LVY

Solution Structure of a RNA Duplex Containing a 2'-O-Pivaloyloxymethyl Modification

• PDB DOI: https://doi.org/10.2210/pdb2LVY/pdb
• NAKB: 2LVY
• BMRB: 18593

• Classification: RNA
• Mutation(s): No 


• Deposited: 2012-07-13 Released: 2013-04-10 
• Deposition Author(s): Baraguey, C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure.

Baraguey, C., Lescrinier, E., Lavergne, T., Debart, F., Herdewijn, P., Vasseur, J.J.

(2013) Org Biomol Chem 11: 2638-2647

• PubMed: 23455628 
• DOI: https://doi.org/10.1039/c3ob27005j
• Primary Citation of Related Structures:  
  2LVY


• PubMed Abstract: 
  

  The pivaloyloxymethyl (PivOM) group is a biolabile 2'-O-ribose protection that is under development in a prodrug-based approach for siRNA applications. Besides an expected cellular uptake, nucleic acid sequences carrying PivOM showed also increased nuclease resistance and, in most cases, an affinity for complementary RNA. The r(CGCU*ACGC)dT:r(GCGUAGCG)dT model duplex containing a single modified residue (U*) was synthesized and its solution structure was determined by NMR. The duplex showed a maintained A-RNA helix. In U*, both 2'-O-acetal ester side chain and ring pucker presented a notable rigid conformation. The PivOM moiety was oriented with the carbonyl group turned outside the minor groove and with trans, -ac and -ac torsion angles around the C2'-O2', O2'-CA and CA-OB1 bonds respectively. Gauche effects and dipolar interactions between the PivOM and the backbone appeared to be the predominant factors influencing the PivOM conformation and the orientation of the two supplementary H acceptors suggested that hydration could also play a role in the duplex stability.

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Organizational Affiliation: 

IBMM UMR 5742 CNRS-UM1-UM2 Université Montpellier II, Place Eugene Bataillon, 34095 Montpellier Cedex 05, France. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.81 kDa 
• Atom Count: 384 
• Modelled Residue Count: 18 
• Deposited Residue Count: 18 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3')	A	9	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3')	B	9	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-10 
Deposition Author(s): Baraguey, C.

Revision History  

• Version 1.0: 2013-04-10
  Type: Initial release