Use of a DNA film on a self-assembled monolayer for investigating the physical process of DNA damage induced by core electron ionization

Abstract

Purpose: A novel two-layer sample composed of a deoxyribonucleic acid (DNA) film and self-assembled monolayer (SAM) was prepared on an inorganic surface to mimic the processes in which DNA is damaged by soft X-ray irradiation.

Materials and methods: A mercaptopropyltrimethoxysilane (MPTS) SAM was formed on a sapphire surface, then oligonucleotide (OGN) molecules were adsorbed on the MPTS-SAM. The thicknesses and chemical states of the layers were determined by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) around the phosphorus (P) and sulfur (S) K-edges. To induce the damage to the OGN molecules, the sample was irradiated with synchrotron soft X-rays. The chemical state of the OGN molecules before and after irradiation was examined by NEXAFS around the nitrogen (N) K-edge region.

Results: The thickness of the MPTS-OGN layer was approximately 7.7 nm. The S atom of the OGN molecules was located at the bottom of the OGN layer. The peak shape of the N K-edge NEXAFS spectra of the MPTS-OGN layers clearly changed following irradiation.

Conclusions: The MPTS-OGN layer formed on the sapphire surface. The chemical states and the structure of the interface were elucidated using synchrotron soft X-rays. The OGN molecules adsorbed on the MPTS films decomposed upon exposure to soft X-ray irradiation.

Keywords:

• DNA damage
• chromatin structure
• self-assembled monolayer
• synchrotron X-ray
• X-ray photoelectron spectroscopy
• near-edge X-ray absorption fine structure

Acknowledgements

We would like to thank the staff at KEK-PF and the SPring-8 for their assistance throughout the experiments.

Disclosure statement

The authors report no conflicts of interest. The authors alone are response for the content and writing of the paper.

Funding information

This work was supported by a Japan Society for the Promotion of Science KAKENHI Grant-in-Aid for Young Scientists (B) 25740020. The experiments were conducted with the approval of the Photon Factory (Proposal No. 2013G707) and SPring-8 (Proposal No. 2014A3812).