6ZXZ

Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification

Summary for 6ZXZ

• Entry DOI: 10.2210/pdb6zxz/pdb
• Descriptor: Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification, POTASSIUM ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: ribosome, modification, rna
• Biological source: synthetic construct
• Total number of polymer chains: 3
• Total formula weight: 25718.62

Authors

Ennifar, E. (deposition date: 2020-07-30, release date: 2020-12-16, Last modification date: 2024-01-31)

Primary citation

Himmelstoss, M.,Erharter, K.,Renard, E.,Ennifar, E.,Kreutz, C.,Micura, R.
2'- O -Trifluoromethylated RNA - a powerful modification for RNA chemistry and NMR spectroscopy.
Chem Sci, 11:11322-11330, 2020

PubMed Abstract: New RNA modifications are needed to advance our toolbox for targeted manipulation of RNA. In particular, the development of high-performance reporter groups facilitating spectroscopic analysis of RNA structure and dynamics, and of RNA-ligand interactions has attracted considerable interest. To this end, fluorine labeling in conjunction with F-NMR spectroscopy has emerged as a powerful strategy. Appropriate probes for RNA previously focused on single fluorine atoms attached to the 5-position of pyrimidine nucleobases or at the ribose 2'-position. To increase NMR sensitivity, trifluoromethyl labeling approaches have been developed, with the ribose 2'-SCF modification being the most prominent one. A major drawback of the 2'-SCF group, however, is its strong impact on RNA base pairing stability. Interestingly, RNA containing the structurally related 2'-OCF modification has not yet been reported. Therefore, we set out to overcome the synthetic challenges toward 2'-OCF labeled RNA and to investigate the impact of this modification. We present the syntheses of 2'-OCF adenosine and cytidine phosphoramidites and their incorporation into oligoribonucleotides by solid-phase synthesis. Importantly, it turns out that the 2'-OCF group has only a slight destabilizing effect when located in double helical regions which is consistent with the preferential C3'-endo conformation of the 2'-OCF ribose as reflected in the (H1'-H2') coupling constants. Furthermore, we demonstrate the exceptionally high sensitivity of the new label in F-NMR analysis of RNA structure equilibria and of RNA-small molecule interactions. The study is complemented by a crystal structure at 0.9 Å resolution of a 27 nt hairpin RNA containing a single 2'-OCF group that well integrates into the minor groove. The new label carries high potential to outcompete currently applied fluorine labels for nucleic acid NMR spectroscopy because of its significantly advanced performance.

PubMed: 34094374
DOI: 10.1039/d0sc04520a

Experimental method

X-RAY DIFFRACTION (2.44 Å)