2Q1R

Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A mismatch.

Summary for 2Q1R

• Entry DOI: 10.2210/pdb2q1r/pdb
• Descriptor: RNA (5'-R(*CP*GP*CP*GP*AP*AP*UP*UP*AP*GP*CP*G)-3'), MAGNESIUM ION (3 entities in total)
• Functional Keywords: g-a mismatch, rna, rnai
• Total number of polymer chains: 1
• Total formula weight: 3899.97

Authors

Li, F.,Pallan, P.S. (deposition date: 2007-05-25, release date: 2007-10-30, Last modification date: 2024-04-03)

Primary citation

Li, F.,Pallan, P.S.,Maier, M.A.,Rajeev, K.G.,Mathieu, S.L.,Kreutz, C.,Fan, Y.,Sanghvi, J.,Micura, R.,Rozners, E.,Manoharan, M.,Egli, M.
Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme.
Nucleic Acids Res., 35:6424-6438, 2007

PubMed Abstract: Short interfering RNA (siRNA) duplexes are currently being evaluated as antisense agents for gene silencing. Chemical modification of siRNAs is widely expected to be required for therapeutic applications in order to improve delivery, biostability and pharmacokinetic properties. Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the RNA-protein effector complexes (RNA-induced silencing complex or RISC). We have studied the in vitro activity in HeLa cells of siRNA duplexes against firefly luciferase with substitutions in the guide strand of U for the apolar ribo-2,4-difluorotoluyl nucleotide (rF) [Xia, J. et al. (2006) ACS Chem. Biol., 1, 176-183] as well as of C for rF. Whereas an internal rF:A pair adjacent to the Ago2 ('slicer' enzyme) cleavage site did not affect silencing relative to the native siRNA duplex, the rF:G pair and other mismatches such as A:G or A:A were not tolerated. The crystal structure at atomic resolution determined for an RNA dodecamer duplex with rF opposite G manifests only minor deviations between the geometries of rF:G and the native U:G wobble pair. This is in contrast to the previously found, significant deviations between the geometries of rF:A and U:A pairs. Comparison between the structures of the RNA duplex containing rF:G and a new structure of an RNA with A:G mismatches with the structures of standard Watson-Crick pairs in canonical duplex RNA leads to the conclusion that local widening of the duplex formed by the siRNA guide strand and the targeted region of mRNA is the most likely reason for the intolerance of human Ago2 (hAgo2), the RISC endonuclease, toward internal mismatch pairs involving native or chemically modified RNA. Contrary to the influence of shape, the thermodynamic stabilities of siRNA duplexes with single rF:A, A:A, G:A or C:A (instead of U:A) or rF:G pairs (instead of C:G) show no obvious correlation with their activities. However, incorporation of three rF:A pairs into an siRNA duplex leads to loss of activity. Our structural and stability data also shed light on the role of organic fluorine as a hydrogen bond acceptor. Accordingly, UV melting (T(M)) data, osmotic stress measurements, X-ray crystallography at atomic resolution and the results of semi-empirical calculations are all consistent with the existence of weak hydrogen bonds between fluorine and the H-N1(G) amino group in rF:G pairs of the investigated RNA dodecamers.

PubMed: 17881374
DOI: 10.1093/nar/gkm664

Experimental method

X-RAY DIFFRACTION (1.12 Å)