6BGB

Crystal Structure of the 16mer GCAGNCUUAAGUCUGC containing BrPh 7-triazolyl-8-aza-7-deazaadenosine

Summary for 6BGB

• Entry DOI: 10.2210/pdb6bgb/pdb
• Related: 4NFO 4NFP 4NFQ
• Descriptor: (5'-R(*GP*CP*AP*GP*(A7C)P*CP*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3') (2 entities in total)
• Functional Keywords: duplex, structural classification, synthetic, rna
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 15966.41

Authors

Fisher, A.J.,Beal, P.A.,Mumbleau, M.M. (deposition date: 2017-10-27, release date: 2017-12-06, Last modification date: 2024-03-13)

Primary citation

Suter, S.R.,Ball-Jones, A.,Mumbleau, M.M.,Valenzuela, R.,Ibarra-Soza, J.,Owens, H.,Fisher, A.J.,Beal, P.A.
Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications.
Org. Biomol. Chem., 15:10029-10036, 2017

PubMed Abstract: SiRNAs can cause unintended gene silencing due to miRNA-like effects because of the similarity in function of an siRNA guide strand and a miRNA. Here we evaluate the effect on miRNA-like off targeting of introducing the adenosine derivative 7-EAA and triazoles prepared from 7-EAA at different positions in an siRNA guide strand. We find that a sterically demanding triazole placed in the RNA duplex major groove at position six of the guide strand dramatically reduces miRNA-like off targeting potency. A high-resolution structure of an RNA duplex bearing a novel, major-groove localized triazole is reported, which suggests that modified triazoles could be disrupting the hAgo2-guide-target RNA ternary complex. Five different triazole modifications were tested at the guide strand 6-position for effects on on-target and miRNA-like off target knockdown potency. A 7-EAA triazole bearing a benzylamine substituent displayed on-target knockdown activity as potent as the native siRNA, while having an IC against a miRNA-like off target >100-fold higher. Melting temperature studies revealed no obvious correlation between potency in knockdown assays and a modification's effect on duplex stability. These results, along with known structures of hAgo2-guide-target ternary complexes, are used to rationalize the effect of 7-EAA triazoles on miRNA-like off target effects.

PubMed: 29164215
DOI: 10.1039/c7ob02654d

Experimental method

X-RAY DIFFRACTION (1.65 Å)