3S7C

Crystal structure of a 2'-azido-uridine-modified RNA

Summary for 3S7C

• Entry DOI: 10.2210/pdb3s7c/pdb
• Related: 3DVZ 3S8U
• Descriptor: Ecoli 23 S rRNA Sarcin Ricin loop (2 entities in total)
• Functional Keywords: hairpin rna, rna labelling, 2'-azido-uridine, rna
• Total number of polymer chains: 1
• Total formula weight: 8770.27

Authors

Ennifar, E.,Micura, R. (deposition date: 2011-05-26, release date: 2012-04-11, Last modification date: 2023-09-13)

Primary citation

Fauster, K.,Hartl, M.,Santner, T.,Aigner, M.,Kreutz, C.,Bister, K.,Ennifar, E.,Micura, R.
2'-Azido RNA, a Versatile Tool for Chemical Biology: Synthesis, X-ray Structure, siRNA Applications, Click Labeling.
Acs Chem.Biol., 7:581-589, 2012

PubMed Abstract: Chemical modification can significantly enrich the structural and functional repertoire of ribonucleic acids and endow them with new outstanding properties. Here, we report the syntheses of novel 2'-azido cytidine and 2'-azido guanosine building blocks and demonstrate their efficient site-specific incorporation into RNA by mastering the synthetic challenge of using phosphoramidite chemistry in the presence of azido groups. Our study includes the detailed characterization of 2'-azido nucleoside containing RNA using UV-melting profile analysis and CD and NMR spectroscopy. Importantly, the X-ray crystallographic analysis of 2'-azido uridine and 2'-azido adenosine modified RNAs reveals crucial structural details of this modification within an A-form double helical environment. The 2'-azido group supports the C3'-endo ribose conformation and shows distinct water-bridged hydrogen bonding patterns in the minor groove. Additionally, siRNA induced silencing of the brain acid soluble protein (BASP1) encoding gene in chicken fibroblasts demonstrated that 2'-azido modifications are well tolerated in the guide strand, even directly at the cleavage site. Furthermore, the 2'-azido modifications are compatible with 2'-fluoro and/or 2'-O-methyl modifications to achieve siRNAs of rich modification patterns and tunable properties, such as increased nuclease resistance or additional chemical reactivity. The latter was demonstrated by the utilization of the 2'-azido groups for bioorthogonal Click reactions that allows efficient fluorescent labeling of the RNA. In summary, the present comprehensive investigation on site-specifically modified 2'-azido RNA including all four nucleosides provides a basic rationale behind the physico- and biochemical properties of this flexible and thus far neglected type of RNA modification.

PubMed: 22273279
DOI: 10.1021/cb200510k

Experimental method

X-RAY DIFFRACTION (1.1 Å)