DSSR-PyMOL cartoon-block schematics: PDB entry 7qp2

PDB-id

7qp2; SNAP-derived features in text and JSON formats

Class

RNA

Method

X-ray (0.9 Å)

Summary

1-deazaguanosine modified-RNA sarcin ricin loop

Reference

Bereiter R, Renard E, Breuker K, Kreutz C, Ennifar E, Micura R (2022): "1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis." J.Am.Chem.Soc., 144, 10344-10352. doi: 10.1021/jacs.2c01877.

Abstract

Atomic mutagenesis is the key to advance our understanding of RNA recognition and RNA catalysis. To this end, deazanucleosides are utilized to evaluate the participation of specific atoms in these processes. One of the remaining challenges is access to RNA-containing 1-deazaguanosine (c₁G). Here, we present the synthesis of this nucleoside and its phosphoramidite, allowing first time access to c₁G-modified RNA. Thermodynamic analyses revealed the base pairing parameters for c₁G-modified RNA. Furthermore, by NMR spectroscopy, a c₁G-triggered switch of Watson-Crick into Hoogsteen pairing in HIV-2 TAR RNA was identified. Additionally, using X-ray structure analysis, a guanine-phosphate backbone interaction affecting RNA fold stability was characterized, and finally, the critical impact of an active-site guanine in twister ribozyme on the phosphodiester cleavage was revealed. Taken together, our study lays the synthetic basis for c₁G-modified RNA and demonstrates the power of the completed deazanucleoside toolbox for RNA atomic mutagenesis needed to achieve in-depth understanding of RNA recognition and catalysis.