6CXZ

RNA octamer containing 2'-F, 4'-Calpha-Me U.

Summary for 6CXZ

• Entry DOI: 10.2210/pdb6cxz/pdb
• Related: 5VR4
• Descriptor: RNA (5'-R(*CP*GP*AP*AP*(U4M)P*UP*CP*G)-3'), CACODYLATE ION, COBALT HEXAMMINE(III), ... (4 entities in total)
• Functional Keywords: rna, oligonucleotide, modified base
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 5383.26

Authors

Harp, J.M.,Egli, M. (deposition date: 2018-04-04, release date: 2018-08-29, Last modification date: 2023-10-04)

Primary citation

Harp, J.M.,Guenther, D.C.,Bisbe, A.,Perkins, L.,Matsuda, S.,Bommineni, G.R.,Zlatev, I.,Foster, D.J.,Taneja, N.,Charisse, K.,Maier, M.A.,Rajeev, K.G.,Manoharan, M.,Egli, M.
Structural basis for the synergy of 4'- and 2'-modifications on siRNA nuclease resistance, thermal stability and RNAi activity.
Nucleic Acids Res., 46:8090-8104, 2018

PubMed Abstract: Chemical modification is a prerequisite of oligonucleotide therapeutics for improved metabolic stability, uptake and activity, irrespective of their mode of action, i.e. antisense, RNAi or aptamer. Phosphate moiety and ribose C2'/O2' atoms are the most common sites for modification. Compared to 2'-O-substituents, ribose 4'-C-substituents lie in proximity of both the 3'- and 5'-adjacent phosphates. To investigate potentially beneficial effects on nuclease resistance we combined 2'-F and 2'-OMe with 4'-Cα- and 4'-Cβ-OMe, and 2'-F with 4'-Cα-methyl modification. The α- and β-epimers of 4'-C-OMe-uridine and the α-epimer of 4'-C-Me-uridine monomers were synthesized and incorporated into siRNAs. The 4'α-epimers affect thermal stability only minimally and show increased nuclease stability irrespective of the 2'-substituent (H, F, OMe). The 4'β-epimers are strongly destabilizing, but afford complete resistance against an exonuclease with the phosphate or phosphorothioate backbones. Crystal structures of RNA octamers containing 2'-F,4'-Cα-OMe-U, 2'-F,4'-Cβ-OMe-U, 2'-OMe,4'-Cα-OMe-U, 2'-OMe,4'-Cβ-OMe-U or 2'-F,4'-Cα-Me-U help rationalize these observations and point to steric and electrostatic origins of the unprecedented nuclease resistance seen with the chain-inverted 4'β-U epimer. We used structural models of human Argonaute 2 in complex with guide siRNA featuring 2'-F,4'-Cα-OMe-U or 2'-F,4'-Cβ-OMe-U at various sites in the seed region to interpret in vitro activities of siRNAs with the corresponding 2'-/4'-C-modifications.

PubMed: 30107495
DOI: 10.1093/nar/gky703

Experimental method

X-RAY DIFFRACTION (1.5 Å)