2M3P

DNA containing a cluster of 8-oxo-guanine and abasic site lesion: alpha anomer

Summary for 2M3P

• Entry DOI: 10.2210/pdb2m3p/pdb
• Related: 2M3Y 2M40 2M43 2M44
• NMR Information: BMRB: 18973
• Descriptor: DNA (5'-D(*CP*GP*CP*TP*CP*(ORP)P*CP*AP*CP*GP*C)-3'), DNA (5'-D(*GP*CP*GP*TP*GP*GP*GP*AP*(8OG)P*CP*G)-3') (2 entities in total)
• Functional Keywords: dna lesion cluster, 8-oxo-guanine, abasic site, dna
• Total number of polymer chains: 2
• Total formula weight: 6633.28

Authors

Zalesak, J.,Jourdan, M.,Lourdin, M.,Constant, J. (deposition date: 2013-01-25, release date: 2014-01-08, Last modification date: 2024-05-01)

Primary citation

Zalesak, J.,Lourdin, M.,Krejc, L.,Constant, J.F.,Jourdan, M.
Structure and dynamics of DNA duplexes containing a cluster of mutagenic 8-oxoguanine and abasic site lesions.
J.Mol.Biol., 426:1524-1538, 2014

PubMed Abstract: 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.

PubMed: 24384094
DOI: 10.1016/j.jmb.2013.12.022

Experimental method

SOLUTION NMR