Nucleic Acids Research 2015-04-20

Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA.

Nathan E Price, Michael J Catalano, Shuo Liu, Yinsheng Wang, Kent S Gates

Index: Nucleic Acids Res. 43 , 3434-41, (2015)

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Abstract

A new type of interstrand DNA-DNA cross-link between abasic (Ap) sites and 2'-deoxyadenosine (dA) residues was recently reported, but the chemical structure and properties of this lesion were not rigorously established. Here we characterized the nucleoside cross-link remnant released by enzymatic digestion of duplex DNA containing the dA-Ap cross-link. A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N(6)-amino group of dA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the synthetic material 6: matched the authentic cross-link remnant released by enzymatic digestion of cross-linked DNA. These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA. Both the nucleoside cross-link remnant 6: and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.