8FEP

16mer self-complementary duplex RNA with two continuous native U:U pairs

This is a non-PDB format compatible entry.

Summary for 8FEP

• Entry DOI: 10.2210/pdb8fep/pdb
• Descriptor: RNA 16mer (2 entities in total)
• Functional Keywords: rna, duplexes, uu pairs
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 5060.02

Authors

Fang, Z.,Szostak, J.W. (deposition date: 2022-12-06, release date: 2024-01-24, Last modification date: 2024-02-21)

Primary citation

Ding, D.,Fang, Z.,Kim, S.C.,O'Flaherty, D.K.,Jia, X.,Stone, T.B.,Zhou, L.,Szostak, J.W.
Unusual Base Pair between Two 2-Thiouridines and Its Implication for Nonenzymatic RNA Copying.
J.Am.Chem.Soc., 146:3861-3871, 2024

PubMed Abstract: 2-Thiouridine (sU) is a nucleobase modification that confers enhanced efficiency and fidelity both on modern tRNA codon translation and on nonenzymatic and ribozyme-catalyzed RNA copying. We have discovered an unusual base pair between two 2-thiouridines that stabilizes an RNA duplex to a degree that is comparable to that of a native A:U base pair. High-resolution crystal structures indicate similar base-pairing geometry and stacking interactions in duplexes containing sU:sU compared to those with U:U pairs. Notably, the C═O···H-N hydrogen bond in the U:U pair is replaced with a C═S···H-N hydrogen bond in the sU:sU base pair. The thermodynamic stability of the sU:sU base pair suggested that this self-pairing might lead to an increased error frequency during nonenzymatic RNA copying. However, competition experiments show that sU:sU base-pairing induces only a low level of misincorporation during nonenzymatic RNA template copying because the correct A:sU base pair outcompetes the slightly weaker sU:sU base pair. In addition, even if an sU is incorrectly incorporated, the addition of the next base is greatly hindered. This strong stalling effect would further increase the effective fidelity of nonenzymatic RNA copying with sU. Our findings suggest that sU may enhance the rate and extent of nonenzymatic copying with only a minimal cost in fidelity.

PubMed: 38293747
DOI: 10.1021/jacs.3c11158

Experimental method

X-RAY DIFFRACTION (1.55 Å)