PDBsum entry 2knk

DNA

PDB id: 2knk

Contents

DNA/RNA

Ligands

TME

PDB id:

2knk

Name:

DNA

Title:

Structure of the trimethylene n2-dg:n2-dg interstrand cross-link in 5'-cpg-3' sequence context

Structure:

DNA (5'-d( Ap Gp Gp Cp Gp Cp Cp T)-3'). Chain: a, b. Engineered: yes

Source:

Synthetic: yes

NMR struc:

1 models

Authors:

H.Huang,P.A.Dooley,C.M.Harris,T.M.Harris,M.P.Stone

Key ref:

H.Huang et al. (2009). Differential base stacking interactions induced by trimethylene interstrand DNA cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts. Chem Res Toxicol, 22, 1810-1816. PubMed id: 19916525

Date:

26-Aug-09 Release date: 29-Sep-09

DNA/RNA chains

A-G-G-C-G-C-C-T 8 bases

A-G-G-C-G-C-C-T 8 bases

Chem Res Toxicol 22:1810-1816 (2009)

PubMed id: 19916525

Differential base stacking interactions induced by trimethylene interstrand DNA cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts.

H.Huang, P.A.Dooley, C.M.Harris, T.M.Harris, M.P.Stone.

ABSTRACT

Synthetically derived trimethylene interstrand DNA cross-links have been used as surrogates for the native cross-links that arise from the 1,N(2)-deoxyguanosine adducts derived from alpha,beta-unsaturated aldehydes. The native enal-mediated cross-linking occurs in the 5'-CpG-3' sequence context but not in the 5'-GpC-3' sequence context. The ability of the native enal-derived 1,N(2)-dG adducts to induce interstrand DNA cross-links in the 5'-CpG-3' sequence as opposed to the 5'-GpC-3' sequence is attributed to the destabilization of the DNA duplex in the latter sequence context. Here, we report higher accuracy solution structures of the synthetically derived trimethylene cross-links, which are refined from NMR data with the AMBER force field. When the synthetic trimethylene cross-links are placed into either the 5'-CpG-3' or the 5'-GpC-3' sequence contexts, the DNA duplex maintains B-DNA geometry with structural perturbations confined to the cross-linked base pairs. Watson-Crick hydrogen bonding is conserved throughout the duplexes. Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5'-CpG-3' sequence. In contrast, the stacking at the cross-linked base pairs in the 5'-GpC-3' sequence is greatly perturbed. The pi-stacking interactions between the cross-linked and the neighbor base pairs are reduced. This is consistent with remarkable chemical shift perturbations of the C(5) H5 and H6 nucleobase protons that shifted downfield by 0.4-0.5 ppm. In contrast, these chemical shift perturbations in the 5'-CpG-3' sequence are not remarkable, consistent with the stacked structure. The differential stacking of the base pairs at the cross-linking region probably explains the difference in stabilities of the trimethylene cross-links in the 5'-CpG-3' and 5'-GpC-3' sequence contexts and might, in turn, account for the sequence selectivity of the interstrand cross-link formation induced by the native enal-derived 1,N(2)-dG adducts.