Photon Factory Activity Report 2016 #34 (2017)

BL-27A/2015G673

Fluorescence XAFS measurements of DNA film immobilized on organic SAM
Ayumi Narita1,*, 2 Mitsunori Honda2, Kentaro Fujii3, Akinari Yokoya3, Yuji Baba2, Iwao
Shimoyama 1NIMS GREEN, 1-1 Namiki, Tsukuba, Ibaraki
305-0047, Japan
2
JAEA
MSRC,
2-4,
Shirakata,
Tokai,
Ibaraki319-1195,
Japan
3
QST, 2-4, Shirakata, Tokai, Ibaraki 319-1195, Japan
1Introduction
Monochromatic soft X-rays have been used as a probeto control the initial process of DNA damage induction.
Fujii et al. reported that yields of radiation damage inDNA including strand breaks and oxidative lesions ofnucleobases depend strongly on the soft X-ray energy
tuned around K-edges of DNA constituent atoms, namely
carbon (280 eV), nitrogen (400 eV) or oxygen (530 eV).
They used the thin layer samples of DNA dropped anddried on an inorganic substrate. The chemical state of thethin layer DNA is substantially different from that in vivo
DNA which twines round histone proteins. In ourprevious study[1], to simulate in vivo DNA, we suggesteda new model of the DNA sample using self-assembled
monolayer (SAM). The obtained results showed that theDNA molecules were strongly immobilized on the SAM.
In this report, to understand the chemical state ofimmobilized DNA in solution, fluorescence XAFS weremeasured.
2 Experiment
We used mercaptopropyltrimetoxisilane (MPTS)
molecules (HS(CH2)3Si(OCH3)3) as an organic SAM on
sapphire C-planes. MPTS molecules have thiol group(SH) and silicon alkoxide (Si(OCH3)3) at the respective
terminal sites of the alkyl backbone. Oligonucleotide(OGN) molecules were used as a DNA sample.
Five samples were prepared and showed in Table 1.
Sample (a) is an OGN thick film as a reference sample.
For sample (b), the OGN molecules were dissolved in 10mM Tris-HCl solution. Sample (c) was prepared bydropped 100 µM OGN solution, then the surface waswashed by supersonic waves. As sample (d) and (e),MPTS molecules were adsorbed on sapphire by
immersing the substrate in 10% ethanol solution. Then,
100 µM OGN solution was dropped on the MPTS film.
Only sample (d) was dried in air. The samples were
measured by NEXAFS (near edge X-ray absorption finestructure).
Table 1: Prepared samples
Sample(a)
(b)
(c)
(d)
(e)

Oligonucleotide thick film
100µM oligonucleotide solution
Oligonucleotide thin film on sapphire
100μM oligonucleotide/MPTS/Sapphire (dry)
100μM oligonucleotide/MPTS/Sapphire (wet)3 Results and Discussion
P K-edge fluorescence NEXAFS spectra show in
Fig.1. Observed peaks (i) and (ii) originate from P 1s to6e, and to 9a1+7e orbital, respectively[2]. The presence of3peak (i) indicates PO4 , thus, phosphoric acid in OGN
molecules.

Compared with the film and solution sample, for example(a) and (b), the peak energy was not shifted. Moreover,the same results were obtained in the case of the MPTS
film existing or not, such as (a) and (d). These results
suggest that the chemical state of the phosphoric acid in
OGN molecules is stable and is not affected by theambient environment. Concerning the spectrum of (c), thepeak intensity is low than that of other samples. In
previous study, we proposed that the OGN molecules areimmobilized on the MPTS-SAM through chemical bonds.
The sample (c) was prepared by dropped the OGN
solution on sapphire surface without MPTS film.
Therefore, the peaks were not observed because the OGN
molecules were not immobilized on the surface. Insummary, it is suggested that the chemical state ofphosphorous atoms in OGN molecules immobilized on
MPTS film is chemically stable, and the OGN molecules
were adsorbed on the MPTS film strongly.

Fig.1: P K-edge NEXAFS spectra of OGN samples.
Acknowledgement
This work was supported by JSPS KAKENHIGrant Number 25740020.
References[1] K. Fujii, N. Shikazono and A. Yokoya, J.
Phys. Chem. B, 113, 16007 (2009).
[2] A. Narita, K. Fujii, A. Yokoya, Y. Baba, I.
Shimoyama, Photon Factory Activity Report 2013 #31(2014) B.
[3] G. Küper, R. Chauvistré, J. Hormes, F. Frick, M.
Jansen, B. Lüer, and E. Hartmann, Chem. Phys. 165,
405 (1992).
*NARITA.Ayumi@nims.go.jp