5AY3: Crystal Structure Of Rna Duplex Containing C-c Base Pairs

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.
PDB ID: 5AY3Download
MMDB ID: 133551
PDB Deposition Date: 2015/8/6
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 1.2  Å
Source Organism:
Biological Unit for 5AY3: dimeric; determined by author and by software (PISA)
Molecular Components in 5AY3
Label Count Molecule
Nucleotide(1 molecule)
RNA (5'-r(*gp*gp*ap*cp*up*(cbr)p*gp*a*cp*up*cp*c)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB