2LVY

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

Summary for 2LVY

• Entry DOI: 10.2210/pdb2lvy/pdb
• NMR Information: BMRB: 18593
• Descriptor: RNA (5'-R(*CP*GP*CP*(UPV)P*AP*CP*GP*CP*T)-3'), RNA (5'-R(*GP*CP*GP*UP*AP*GP*CP*GP*T)-3') (2 entities in total)
• Functional Keywords: rna, modification
• Total number of polymer chains: 2
• Total formula weight: 5805.68

Authors

Baraguey, C. (deposition date: 2012-07-13, release date: 2013-04-10, Last modification date: 2024-05-01)

Primary citation

Baraguey, C.,Lescrinier, E.,Lavergne, T.,Debart, F.,Herdewijn, P.,Vasseur, J.J.
The biolabile 2'-O-pivaloyloxymethyl modification in an RNA helix: an NMR solution structure.
Org.Biomol.Chem., 11:2638-2647, 2013

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.

PubMed: 23455628
DOI: 10.1039/c3ob27005j

Experimental method

SOLUTION NMR