Structural changes of nucleic acid base in aqueous solution as observed in X-ray absorption near edge structure (XANES)
Graphical abstract
Introduction
DNA lesions caused by ionizing radiations are an important cause of significant biological effects such as cell death and mutations. Lesions on nucleobases are known to play an essential role in these biological effects. The DNA lesions can be induced indirectly by reactive oxygen species such as OH, which is produced by irradiated water molecules surrounding the DNA molecule (indirect effect, see review by O’Neill and Fielden [1]). The DNA lesions can also be induced directly by the interaction of ionizing radiation with the DNA molecule (direct effect), the extent of which is shown to be almost equivalent to that of the indirect effect (see review by Becker and Sevilla [2]). The physicochemical mechanism of the direct effect has been studied extensively (see review by Bernhard and Close [3]), but there still exists an open subject, in particular, for base lesions [3].
The monochromatized soft X-rays obtained from a synchrotron radiation source have been used to study the direct radiation effect and thereby specify the primary reactive atomic species (e.g. C, N, and O) in DNA (see review by Yokoya et al. [4]). Noticing that N atoms are contained only in nucleobases, we have recently examined a selective excitation of nucleobases by measuring X-ray absorption spectra of nucleotides near the N K-edge [5]. Furthermore, since the characteristic binding energies of 1s electrons of identical atomic species differ depending on their bonding sites, it should be possible to specify the primary site of energy deposition by the use of X-rays for a particular excitation of the 1s electron to an unoccupied orbital [6]. We remark, therefore, that a detailed measurement of the X-ray absorption near edge structure (XANES) of DNA and nucleotides should provide an opportunity to investigate the primary deposition of radiation energy onto a specified atomic site in nucleobases.
In the present Letter, we report on the nitrogen K-edge XANES of adenine-containing nucleotides, adenosine 5′-monophosphate (AMP), and adenosine 5′-triphosphate (ATP) in aqueous solutions (Figure 1—1 and 2). The difference in the XANES spectra for AMP and ATP is shown and discussed in terms of a core-level chemical shift of nitrogen atoms caused by protonation in acidic solution, which identifies particular absorption peaks of XANES as the 1s electron excitations of specific N sites in AMP and ATP.
Section snippets
Experimental
The experiments were done at the beam line BL-23SU of the synchrotron radiation facility SPring-8 in Japan. The experimental setup is essentially identical to that reported in Ref. [5]. The aqueous solution of nucleotides is introduced into a vacuum chamber as a laminar flow through an orifice with a diameter of 20 μm using a liquid microjet technique. The pressure of the vacuum chamber is typically 1 × 10−2 Pa when the liquid sample is introduced. The liquid jet is intersected with a focused beam
Results
Figure 2 shows the total electron yields for AMP and ATP in aqueous solutions as a function of photon energy. The pH values of these solutions were 8.3 for AMP and 2.9 for ATP. The peak structures above the photon energy of 399 eV in the total electron yields are assignable to the excitation and ionization of nitrogen K-shell electrons in adenine moiety of AMP and ATP. The background electron yield is mainly due to the photoionization of L-shell electrons of oxygen atoms in water and K-shell
Discussion
Let us discuss the origin of the difference between the XANES spectra of AMP and ATP. First, the geometrical structures of adenine, AMP, and ATP molecules in the gas phase and in the aqueous solution are summarized as a basis of discussion. Second, the peaks observed in the XANES spectra for AMP and ATP are assigned with reference to a theoretical calculation for adenine in the gas phase [10], which is the constituent base of AMP and ATP. Finally, the spectral difference between AMP and ATP is
Conclusions
The XANES spectra of AMP and ATP in aqueous solution and film samples, measured using synchrotron radiation, are analyzed by comparison with that of gas phase adenine in previous reports. The intense peak at 399.7 eV is identified as transitions of the 1s electrons of N1, N3, N7 atoms to the π∗ orbitals, and the weak peak at 401.9 eV as that from N9 and N6′ atoms to the π∗ orbitals.
The difference between the XANES spectra of ATP and AMP is ascribed to the protonation of the N1 atom in the adenine
Acknowledgments
This work is supported financially by a Grant-in-Aid for Scientific Research (A) from the Japan Society of Promotion of Science No. 21241017. The experiments at SPring-8 are carried out under approval of Japan Synchrotron Radiation Research Institute (JASRI) Proposal Review Committee for proposal numbers of 2011B3810 and 2012A3810. We thank G. Harries for a critical reading of the manuscript.
References (23)
- et al.
Adv. Radiat. Biol.
(1993) - et al.
Adv. Radiat. Biol.
(1993) - et al.
Chem. Phys. Lett.
(2010) - et al.
Nucl. Instrum. Methods Phys. Res. B
(2003) Chem. Phys.
(2008)- et al.
Chem. Phys. Lett.
(1989) - et al.
Inorg. Chim. Acta
(1992) - et al.
- et al.
NEXAFS Spectroscopy
(1992)
Phys. Rev. A
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Nitrogen containing functional groups of biochar: An overview
2020, Bioresource TechnologyCitation Excerpt :By comparing the spectra of samples with the spectra of standard compounds, N-functional groups such as pyridinic-N (399.8 eV), pyridonic-N (401.1 eV), pyrrolic-N (402.6–403.5 eV) and pyridinic-N-oxide groups (405.0 eV) were identified in the study carried out by Jia et al. (2002b). In addition, some studies have also carried out the determination of N-functional groups such as tertiary amine-N (401.9 eV), amide-N (399.5 eV), and nitrile-N (287.2 eV) by XANES (Lenardi et al., 2000; Shimada et al., 2014). The N-functional groups present in biochars from different biomass types can be seen in Table 1.
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