PDBsum entry 2n4m

DNA

PDB id: 2n4m

Contents

DNA/RNA

PDB id:

2n4m

Name:

DNA

Title:

Base-displaced intercalated structure of the n-(2'deoxyguanosin-8-yl)- 3-aminobenzanthrone DNA adduct

Structure:

DNA (5'-d( Gp Tp Gp Cp (4E9)p Tp Gp Tp Tp Tp Gp T)-3'). Chain: a. Engineered: yes. DNA (5'-d( Ap Cp Ap Ap Ap Cp Ap Cp Gp Cp Ap C)-3'). Chain: b. Engineered: yes

Source:

Synthetic: yes. Synthetic: yes

NMR struc:

10 models

Authors:

D.A.Politica,M.P.Stone,C.K.Malik,A.K.Basu

Key ref:

D.A.Politica et al. (2015). Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct. Chem Res Toxicol, 28, 2253-2266. PubMed id: 26641105 DOI: 10.1021/acs.chemrestox.5b00277

Date:

23-Jun-15 Release date: 06-Jul-16

DNA/RNA chains

G-T-G-C-4E9-T-G-T-T-T-G-T 12 bases

A-C-A-A-A-C-A-C-G-C-A-C 12 bases

DOI no: 10.1021/acs.chemrestox.5b00277

Chem Res Toxicol 28:2253-2266 (2015)

PubMed id: 26641105

Base-Displaced Intercalated Structure of the N-(2'-Deoxyguanosin-8-yl)-3-aminobenzanthrone DNA Adduct.

D.A.Politica, C.K.Malik, A.K.Basu, M.P.Stone.

ABSTRACT

3-Nitrobenzanthrone (3-NBA), an environmental mutagen found in diesel exhaust and a suspected carcinogen, undergoes metabolic reduction followed by reaction with DNA to form aminobenzanthrone (ABA) adducts, with the major alkylation product being N-(2'-deoxyguanosin-8-yl)-3-aminobenzanthrone (C8-dG-ABA). Site-specific synthesis of the C8-dG-ABA adduct in the oligodeoxynucleotide 5'-d(GTGCXTGTTTGT)-3':5'-d(ACAAACACGCAC)-3'; X = C8-dG-ABA adduct, including codons 272-275 of the p53 gene, has allowed for investigation into the structural and thermodynamic properties of this adduct. The conformation of the C8-dG-ABA adduct was determined using NMR spectroscopy and was refined using molecular dynamics (MD) calculations restrained by experimentally determined interproton distance restraints obtained from NOE experiments. The refined structure revealed that the C8-dG-ABA adduct formed a base-displaced intercalated conformation. The adducted guanine was shifted into the syn conformation about the glycosidic bond. The 5'- and 3'-neighboring base pairs remained intact. While this facilitated π-stacking interactions between the ABA moiety and neighboring bases, the thermal melting temperature (Tm) of the adduct-containing duplex showed a decrease of 11 °C as compared to the corresponding unmodified oligodeoxynucleotide duplex. Overall, in this sequence, the base-displaced intercalated conformation of the C8-dG-ABA lesion bears similarity to structures of other arylamine C8-dG adducts. However, in this sequence, the base-displaced intercalated conformation for the C8-dG-ABA adduct differs from the conformation of the N(2)-dG-ABA adduct reported by de los Santos and co-workers, in which it is oriented in the minor groove toward the 5' end of the duplex, with the modified guanine remaining in the anti conformation about the glyosidic torsion angle, and the complementary base remaining within the duplex. The results are discussed in relationship to differences between the C8-dG-ABA and N(2)-dG-ABA adducts with respect to susceptibility to nucleotide excision repair (NER).