2M43: Dna Containing A Cluster Of 8-oxo-guanine And Abasic Site Lesion: Alpha Anomer (ap6, 8og 14)

Clustered DNA damage sites are caused by ionizing radiation. They are much more difficult to repair than are isolated single lesions, and their biological outcomes in terms of mutagenesis and repair inhibition are strongly dependent on the type, relative position and orientation of the lesions present in the cluster. To determine whether these effects on repair mechanism could be due to local structural properties within DNA, we used (1)H NMR spectroscopy and restrained molecular dynamics simulation to elucidate the structures of three DNA duplexes containing bistranded clusters of lesions. Each DNA sequence contained an abasic site in the middle of one strand and differed by the relative position of the 8-oxoguanine, staggered on either the 3' or the 5' side of the complementary strand. Their repair by base excision repair protein Fpg was either complete or inhibited. All the studied damaged DNA duplexes adopt an overall B-form conformation and the damaged residues remain intrahelical. No striking deformations of the DNA chain have been observed as a result of close proximity of the lesions. These results rule out the possibility that differential recognition of clustered DNA lesions by the Fpg protein could be due to changes in the DNA's structural features induced by those lesions and provide new insight into the Fpg recognition process.
PDB ID: 2M43Download
MMDB ID: 116440
PDB Deposition Date: 2013/1/29
Updated in MMDB: 2014/04
Experimental Method:
solution nmr
Source Organism:
Biological Unit for 2M43: dimeric; determined by author
Molecular Components in 2M43
Label Count Molecule
Nucleotides(2 molecules)
DNA (5'-d(*cp*gp*cp*tp*cp*(orp)p*cp*ap*cp*gp*c)-3')
Molecule annotation
DNA (5'-d(*gp*cp*(8og)p*tp*gp*gp*gp*ap*gp*cp*g)-3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB