Quantum Yield of DNA Strand Breaks under Photoexcitation of a Molecular Ruby.

Photodynamic therapy (PDT) used for treating cancer relies on the generation of highly reactive oxygen species, for example, singlet oxygen 1 O2 , by light-induced excitation of a photosensitizer (PS) in the presence of molecular oxygen, inducing DNA damage in close proximity of the PS. Although many precious metal complexes have been explored as PS for PDT and received clinical approval, only recently, the potential of photoactive complexes of non-noble metals as PS has been discovered. Using the DNA origami technology that can absolutely quantify DNA strand break cross sections, we assessed the potential of the luminescent transition metal complex [Cr(ddpd)2 ]3+ (ddpd=N,N'-dimethyl-N,N'-dipyridine-2-ylpyridine-2,6-diamine) to damage DNA in an air-saturated aqueous environment upon UV/Vis illumination. The quantum yield for strand breakage, that is, the ratio of DNA strand breaks to the number of absorbed photons, was determined to 1-4 %, indicating efficient transformation of photons into DNA strand breaks by [Cr(ddpd)2 ]3+ .

Plasmonic reactivity of halogen thiophenols on gold nanoparticles studied by SERS and XPS.

Localized surface plasmon resonances on noble metal nanoparticles (NPs) can efficiently drive reactions of adsorbed ligand molecules and provide versatile opportunities in chemical synthesis. The driving forces of these reactions are typically elevated temperatures, hot charge carriers, or enhanced electric fields. In the present work, dehalogenation of halogenated thiophenols on the surface of AuNPs has been studied by surface enhanced Raman scattering (SERS) as a function of the photon energy to track the kinetics and identify reaction products. Reaction rates are found to be surprisingly similar for different halothiophenols studied here, although the bond dissociation energies of the C-X bonds differ significantly. Complementary information about the electronic properties at the AuNP surface, namely, work-function and valence band states, has been determined by x-ray photoelectron spectroscopy of isolated AuNPs in the gas-phase. In this way, it is revealed how the electronic properties are altered by the adsorption of the ligand molecules, and we conclude that the reaction rates are mainly determined by the plasmonic properties of the AuNPs. SERS spectra reveal differences in the reaction product formation for different halogen species, and, on this basis, the possible reaction mechanisms are discussed to approach an understanding of opportunities and limitations in the design of catalytical systems with plasmonic NPs.

Low-Energy (5-20 eV) Electron-Induced Single and Double Strand Breaks in Well-Defined DNA Sequences.

Ionizing radiation is used in cancer radiation therapy to effectively damage the DNA of tumors. The main damage is due to generation of highly reactive secondary species such as low-energy electrons (LEEs). The accurate quantification of DNA radiation damage of well-defined DNA target sequences in terms of absolute cross sections for LEE-induced DNA strand breaks is possible by the DNA origami technique; however, to date, it is possible only for DNA single strands. In the present work DNA double strand breaks in the DNA sequence 5'-d(CAC)4/5'-d(GTG)4 are compared with DNA single strand breaks in the oligonucleotides 5'-d(CAC)4 and 5'-d(GTG)4 upon irradiation with LEEs in the energy range from 5 to 20 eV. A maximum of strand break cross section was found around 7 and 10 eV independent of the DNA sequence, indicating that dissociative electron attachment is the underlying mechanism of strand breakage and confirming previous studies using plasmid DNA.

The electronic structure of the metal-organic interface of isolated ligand coated gold nanoparticles.

Light induced electron transfer reactions of molecules on the surface of noble metal nanoparticles (NPs) depend significantly on the electronic properties of the metal-organic interface. Hybridized metal-molecule states and dipoles at the interface alter the work function and facilitate or hinder electron transfer between the NPs and ligand. X-ray photoelectron spectroscopy (XPS) measurements of isolated AuNPs coated with thiolated ligands in a vacuum have been performed as a function of photon energy, and the depth dependent information of the metal-organic interface has been obtained. The role of surface dipoles in the XPS measurements of isolated ligand coated NPs is discussed and the binding energy of the Au 4f states is shifted by around 0.8 eV in the outer atomic layers of 4-nitrothiophenol coated AuNPs, facilitating electron transport towards the molecules. Moreover, the influence of the interface dipole depends significantly on the adsorbed ligand molecules. The present study paves the way towards the engineering of the electronic properties of the nanoparticle surface, which is of utmost importance for the application of plasmonic nanoparticles in the fields of heterogeneous catalysis and solar energy conversion.

Folding DNA into origami nanostructures enhances resistance to ionizing radiation.

We report experimental results on damage induced by ionizing radiation to DNA origami triangles which are commonly used prototypes for scaffolded DNA origami nanostructures. We demonstrate extreme stability of DNA origami upon irradiation, which is caused by (i) the multi-row design holding the shape of the origami even after severe damage to the scaffold DNA and (ii) the reduction of damage to the scaffold DNA due to the protective effect of the folded structure. With respect to damage induced by ionizing radiation, the protective effect of the structure is superior to that of a naturally paired DNA double helix. Present results allow estimating the stability of scaffolded DNA origami nanostructures in applications such as nanotechnology, pharmacy or in singulo molecular studies where they are exposed to ionizing radiation from natural and artificial sources. Additionally, possibilities are opened for scaffolded DNA use in the design of radiation-resistant and radio-sensitive materials.

Kinetics of molecular decomposition under irradiation of gold nanoparticles with nanosecond laser pulses-A 5-Bromouracil case study.

Laser illuminated gold nanoparticles (AuNPs) efficiently absorb light and heat up the surrounding medium, leading to versatile applications ranging from plasmonic catalysis to cancer photothermal therapy. Therefore, an in-depth understanding of the thermal, optical, and electron induced reaction pathways is required. Here, the electrophilic DNA nucleobase analog 5-Bromouracil (BrU) has been used as a model compound to study its decomposition in the vicinity of AuNPs illuminated with intense ns laser pulses under various conditions. The plasmonic response of the AuNPs and the concentration of BrU and resulting photoproducts have been tracked by ultraviolet and visible (UV-Vis) spectroscopy as a function of the irradiation time. A kinetic model has been developed to determine the reaction rates of two parallel fragmentation pathways of BrU, and their dependency on laser fluence and adsorption on the AuNP have been evaluated. In addition, the size and the electric field enhancement of the decomposed AuNPs have been determined by atomic force microscopy and finite domain time difference calculations, respectively. A minor influence of the direct photoreaction and a strong effect of the heating of the AuNPs have been revealed. However, due to the size reduction of the irradiated AuNPs, a trade-off between laser fluence and plasmonic response of the AuNPs has been observed. Hence, the decomposition of the AuNPs might be limiting the achievable temperatures under irradiation with several laser pulses. These findings need to be considered for an efficient design of catalytic plasmonic systems.

Length and Energy Dependence of Low-Energy Electron-Induced Strand Breaks in Poly(A) DNA.

The DNA in living cells can be effectively damaged by high-energy radiation, which can lead to cell death. Through the ionization of water molecules, highly reactive secondary species such as low-energy electrons (LEEs) with the most probable energy around 10 eV are generated, which are able to induce DNA strand breaks via dissociative electron attachment. Absolute DNA strand break cross sections of specific DNA sequences can be efficiently determined using DNA origami nanostructures as platforms exposing the target sequences towards LEEs. In this paper, we systematically study the effect of the oligonucleotide length on the strand break cross section at various irradiation energies. The present work focuses on poly-adenine sequences (d(A4), d(A8), d(A12), d(A16), and d(A20)) irradiated with 5.0, 7.0, 8.4, and 10 eV electrons. Independent of the DNA length, the strand break cross section shows a maximum around 7.0 eV electron energy for all investigated oligonucleotides confirming that strand breakage occurs through the initial formation of negative ion resonances. When going from d(A4) to d(A16), the strand break cross section increases with oligonucleotide length, but only at 7.0 and 8.4 eV, i.e., close to the maximum of the negative ion resonance, the increase in the strand break cross section with the length is similar to the increase of an estimated geometrical cross section. For d(A20), a markedly lower DNA strand break cross section is observed for all electron energies, which is tentatively ascribed to a conformational change of the dA20 sequence. The results indicate that, although there is a general length dependence of strand break cross sections, individual nucleotides do not contribute independently of the absolute strand break cross section of the whole DNA strand. The absolute quantification of sequence specific strand breaks will help develop a more accurate molecular level understanding of radiation induced DNA damage, which can then be used for optimized risk estimates in cancer radiation therapy.

Role of Valence Band States and Plasmonic Enhancement in Electron-Transfer-Induced Transformation of Nitrothiophenol.

Hot-electron-induced reactions are more and more recognized as a critical and ubiquitous reaction in heterogeneous catalysis. However, the kinetics of these reactions is still poorly understood, which is also due to the complexity of plasmonic nanostructures. We determined the reaction rates of the hot-electron-mediated reaction of 4-nitrothiophenol (NTP) on gold nanoparticles (AuNPs) using fractal kinetics as a function of the laser wavelength and compared them with the plasmonic enhancement of the system. The reaction rates can be only partially explained by the plasmonic response of the NPs. Hence, synchrotron X-ray photoelectron spectroscopy (XPS) measurements of isolated NTP-capped AuNP clusters have been performed for the first time. In this way, it was possible to determine the work function and the accessible valence band states of the NP systems. The results show that besides the plasmonic enhancement, the reaction rates are strongly influenced by the local density of the available electronic states of the system.

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks - Influence of the DNA Sequence and Substrate.

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF2 as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7-2.3×10-16  cm2 . The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.

Vacuum-UV induced DNA strand breaks - influence of the radiosensitizers 5-bromouracil and 8-bromoadenine.

Radiation therapy is a basic part of cancer treatment. To increase the DNA damage in carcinogenic cells and preserve healthy tissue at the same time, radiosensitizing molecules such as halogenated nucleobase analogs can be incorporated into the DNA during the cell reproduction cycle. In the present study 8.44 eV photon irradiation induced single strand breaks (SSB) in DNA sequences modified with the radiosensitizer 5-bromouracil (5BrU) and 8-bromoadenine (8BrA) are investigated. 5BrU was incorporated in the 13mer oligonucleotide flanked by different nucleobases. It was demonstrated that the highest SSB cross sections were reached, when cytosine and thymine were adjacent to 5BrU, whereas guanine as a neighboring nucleobase decreases the activity of 5BrU indicating that competing reaction mechanisms are active. This was further investigated with respect to the distance of guanine to 5BrU separated by an increasing number of adenine nucleotides. It was observed that the SSB cross sections were decreasing with an increasing number of adenine spacers between guanine and 5BrU until the SSB cross sections almost reached the level of a non-modified DNA sequence, which demonstrates the high sequence dependence of the sensitizing effect of 5BrU. 8BrA was incorporated in a 13mer oligonucleotide as well and the strand breaks were quantified upon 8.44 eV photon irradiation in direct comparison to a non-modified DNA sequence of the same composition. No clear enhancement of the SSB yield of the modified in comparison to the non-modified DNA sequence could be observed. Additionally, secondary electrons with a maximum energy of 3.6 eV were generated when using Si as a substrate giving rise to further DNA damage. A clear enhancement in the SSB yield can be ascertained, but to the same degree for both the non-modified DNA sequence and the DNA sequence modified with 8BrA.

The Physico-Chemical Basis of DNA Radiosensitization: Implications for Cancer Radiation Therapy.

High-energy radiation is used in combination with radiosensitizing therapeutics to treat cancer. The most common radiosensitizers are halogenated nucleosides and cisplatin derivatives, and recently also metal nanoparticles have been suggested as potential radiosensitizing agents. The radiosensitizing action of these compounds can at least partly be ascribed to an enhanced reactivity towards secondary low-energy electrons generated along the radiation track of the high-energy primary radiation, or to an additional emission of secondary reactive electrons close to the tumor tissue. This is referred to as physico-chemical radiosensitization. In this Concept article we present current experimental methods used to study fundamental processes of physico-chemical radiosensitization and discuss the most relevant classes of radiosensitizers. Open questions in the current discussions are identified and future directions outlined, which can lead to optimized treatment protocols or even novel therapeutic concepts.

Sensitizing DNA Towards Low-Energy Electrons with 2-Fluoroadenine.

2-Fluoroadenine ((2F) A) is a therapeutic agent, which is suggested for application in cancer radiotherapy. The molecular mechanism of DNA radiation damage can be ascribed to a significant extent to the action of low-energy (<20 eV) electrons (LEEs), which damage DNA by dissociative electron attachment. LEE induced reactions in (2F) A are characterized both isolated in the gas phase and in the condensed phase when it is incorporated into DNA. Information about negative ion resonances and anion-mediated fragmentation reactions is combined with an absolute quantification of DNA strand breaks in (2F) A-containing oligonucleotides upon irradiation with LEEs. The incorporation of (2F) A into DNA results in an enhanced strand breakage. The strand-break cross sections are clearly energy dependent, whereas the strand-break enhancements by (2F) A at 5.5, 10, and 15 eV are very similar. Thus, (2F) A can be considered an effective radiosensitizer operative at a wide range of electron energies.