5KGV: Structural Impact Of Single Ribonucleotides In Dna

Single ribonucleotide intrusions represent the most common nonstandard nucleotide type found incorporated in genomic DNA, yet little is known of their structural impact. This lesion incurs genomic instability in addition to affecting the physical properties of the DNA. To probe for structural and dynamic effects of single ribonucleotides in various sequence contexts-AxC, CxG, and GxC, where x=rG or dG-we report the structures of three single-ribonucleotide-containing DNA duplexes and the corresponding DNA controls. The lesion subtly and locally perturbs the structure asymmetrically on the 3' side of the lesion in both the riboguanosine-containing and the complementary strand of the duplex. The perturbations are mainly restricted to the sugar and phosphodiester backbone. The ribose and 3'-downstream deoxyribose units are predominately in N-type conformation; backbone torsion angles and/or zeta of the ribonucleotide or upstream deoxyribonucleotide are affected. Depending on the flanking sequences, the C2'-OH group forms hydrogen bonds with the backbone, 3'-neighboring base, and/or sugar. Interestingly, even in similar purine-rG-pyrimidine environments (A-rG-C and G-rG-C), a riboguanosine unit affects DNA in a distinct manner and manifests different hydrogen bonds, which makes generalizations difficult.
PDB ID: 5KGVDownload
MMDB ID: 142321
PDB Deposition Date: 2016/6/13
Updated in MMDB: 2016/11
Experimental Method:
solution nmr
Source Organism:
Biological Unit for 5KGV: dimeric; determined by author
Molecular Components in 5KGV
Label Count Molecule
Nucleotides(2 molecules)
Dna/rna (5'-d(*ap*tp*gp*gp*a)-r(p*g)-d(p*cp*tp*c)-3')
Molecule annotation
DNA (5'-d(*gp*ap*gp*cp*tp*cp*cp*ap*t)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB