Photoionization of DNA and RNA Bases, Nucleosides and Nucleotides Through a Combination of One- and Two-photon Pathways upon 266 nm Nanosecond Laser Excitation¶

Crespo‐Hernández, Carlos E.; Arce, Rafael

doi:10.1562/0031-8655(2002)0760259podarb2.0.co2

Cited by 5 publications

(2 citation statements)

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“…It is thus in no way guaranteed that calculations will converge fast upon increasing model size toward DNA. Experimentally, the oxidation of nucleic acid components has been straightforwardly studied by photoelectron (PE) spectroscopy. − However, here again the gas phase and cluster systems are not directly linked to the real DNA in its native environment. Ionization parameters of solvated nucleic acid fragments could be estimated only indirectly .…”

Section: Introductionmentioning

confidence: 99%

Modeling Photoionization of Aqueous DNA and Its Components

2015

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Radiation damage to DNA is usually considered in terms of UVA and UVB radiation. These ultraviolet rays, which are part of the solar spectrum, can indeed cause chemical lesions in DNA, triggered by photoexcitation particularly in the UVB range. Damage can, however, be also caused by higher energy radiation, which can ionize directly the DNA or its immediate surroundings, leading to indirect damage. Thanks to absorption in the atmosphere, the intensity of such ionizing radiation is negligible in the solar spectrum at the surface of Earth. Nevertheless, such an ionizing scenario can become dangerously plausible for astronauts or flight personnel, as well as for persons present at nuclear power plant accidents. On the beneficial side, ionizing radiation is employed as means for destroying the DNA of cancer cells during radiation therapy. Quantitative information about ionization of DNA and its components is important not only for DNA radiation damage, but also for understanding redox properties of DNA in redox sensing or labeling, as well as charge migration along the double helix in nanoelectronics applications. Until recently, the vast majority of experimental and computational data on DNA ionization was pertinent to its components in the gas phase, which is far from its native aqueous environment. The situation has, however, changed for the better due to the advent of photoelectron spectroscopy in liquid microjets and its most recent application to photoionization of aqueous nucleosides, nucleotides, and larger DNA fragments. Here, we present a consistent and efficient computational methodology, which allows to accurately evaluate ionization energies and model photoelectron spectra of aqueous DNA and its individual components. After careful benchmarking, the method based on density functional theory and its time-dependent variant with properly chosen hybrid functionals and polarizable continuum solvent model provides ionization energies with accuracy of 0.2-0.3 eV, allowing for faithful modeling and interpretation of DNA photoionization. The key finding is that the aqueous medium is remarkably efficient in screening the interactions within DNA such that, unlike in the gas phase, ionization of a base, nucleoside, or nucleotide depends only very weakly on the particular DNA context. An exception is the electronic interaction between neighboring bases which can lead to sequence-specific effects, such as a partial delocalization of the cationic hole upon ionization enabled by presence of adjacent bases of the same type.

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Section: Introductionmentioning

confidence: 99%

Modeling Photoionization of Aqueous DNA and Its Components

2015

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“…The binding of DNA bases to the surface of AuNPs can affect the interaction of photoelectrons with DNA and their accessibility to different UMOs, and thus offset the preferential release of Cyt that is observed for electrons with higher energy. Lastly, it is worth noting that Ade and Gua are major products arising from UV photolysis of the corresponding nucleosides and other derivatives under conditions of both single- and two-photon excitation in aqueous solution. − Although a similar mechanism of base release involving LEEs may be invoked, it is nevertheless a minor reaction in the case of UV–visible photolysis of AuNPs and DNA in view of the low yield of base release products in the absence of AuNPs (<10%; Table ).…”

Section: Discussionmentioning

confidence: 99%

Electron-Induced Damage by UV Photolysis of DNA Attached to Gold Nanoparticles

Huwaidi,

Robert,

Kumari

et al. 2024

Chem. Res. Toxicol.

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Photolysis of DNA attached to gold nanoparticles (AuNPs) with ultraviolet (UV) photons induces DNA damage. The release of nucleobases (Cyt, Gua, Ade, and Thy) from DNA was the major reaction (99%) with an approximately equal release of pyrimidines and purines. This reaction contributes to the formation of abasic sites in DNA. In addition, liquid chromatography-mass spectrometry/MS (LC-MS/MS) analysis revealed the formation of reduction products of pyrimidines (5,6-dihydrothymidine and 5,6-dihydro-2′-deoxyuridine) and eight 2′,3′- and 2′,5′-dideoxynucleosides. In contrast, there was no evidence of the formation of 5-hydroxymethyluracil and 8-oxo-7,8-dihydroguanine, which are common oxidation products of thymine and guanine, respectively. Using appropriate filters, the main photochemical reactions were found to involve photoelectrons ejected from AuNPs by UV photons. The contribution of “hot” conduction band electrons with energies below the photoemission threshold was minor. The mechanism for the release of free nucleobases by photoelectrons is proposed to take place by the initial formation of transient molecular anions of the nucleobases, followed by dissociative electron attachment at the C1′-N glycosidic bond connecting the nucleobase to the sugar–phosphate backbone. This mechanism is consistent with the reactivity of secondary electrons ejected by X-ray irradiation of AuNPs attached to DNA, as well as the reactions of various nucleic acid derivatives irradiated with monoenergetic very-low-energy electrons (∼2 eV). These studies should help us to understand the chemistry of nanoparticles that are exposed to UV light and that are used as scaffolds and catalysts in molecular biology, curative agents in photodynamic therapy, and components of sunscreens and cosmetics.

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