5AY3

Crystal structure of RNA duplex containing C-C base pairs

Summary for 5AY3

• Entry DOI: 10.2210/pdb5ay3/pdb
• Descriptor: RNA (5'-R(*GP*GP*AP*CP*UP*(CBR)P*GP*A*CP*UP*CP*C)-3') (2 entities in total)
• Functional Keywords: rna, x-ray analysis, metallo base pair, ag(i)
• Biological source: synthetic construct
• Total number of polymer chains: 2
• Total formula weight: 7700.42

Authors

Kondo, J.,Tada, Y.,Dairaku, T.,Saneyoshi, H.,Okamoto, I.,Tanaka, Y.,Ono, A. (deposition date: 2015-08-06, release date: 2015-10-21, Last modification date: 2024-03-20)

Primary citation

Kondo, J.,Tada, Y.,Dairaku, T.,Saneyoshi, H.,Okamoto, I.,Tanaka, Y.,Ono, A.
High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like CSilver(I)C Metallo-Base Pairs
Angew.Chem.Int.Ed.Engl., 54:13323-13326, 2015

PubMed Abstract: Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices.

PubMed: 26448329
DOI: 10.1002/anie.201507894

Experimental method

X-RAY DIFFRACTION (1.2 Å)