Probing DNA Radiation Damage by DNA Nanotechnology

• Applicant: Professor Dr. Ilko Bald
• Subject Area: Physical Chemistry of Molecules, Liquids and Interfaces, Biophysical Chemistry ; Physical Chemistry of Solids and Surfaces, Material Characterisation
• Term: from 2012 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 230710387

The damage of DNA by electromagnetic or particle radiation is a pivotal process occurring for instance during tumor radiation therapy. In radiotherapy radiosensitizers such as halogenated nucleosides are applied to sensitize the tumour tissue towards radiation. But the DNA is damaged only to a small extent by the primary high-energy radiation. Most of the damage occurs due to low-energy secondary particles such as electrons. In the meantime it is well-established that electrons with kinetic energy below 12 eV can damage DNA via the dissociative electron attachment mechanism. However, the underlying processes are only well-understood for simple model compounds such as single nucleobases. The influence of the DNA sequence on the DNA strand breakage and the effect of radiosensitizers was suggested within preliminary experiments, but could not be investigated systematically due to a lack of suitable analytical tools. In the previous project of the applicant a novel technique for the determination of DNA strand break yields in oligonucleotides of defined sequence was established. The key aspects of this technique are the arrangement of the target oligonucleotide sequences on DNA origami nanostructures and the detection of electron-induced strand breaks by atomic force microscopy (AFM). In this way, multiple DNA sequences can be compared within a single irradiation experiment, and absolute cross sections for strand breakage are directly accessible. In the present proposal cross sections for electron induced strand breakage will be determined for DNA sequences, which are modified with clinically established and potential radiosensitizers. By comparison with non-modified sequences enhancement factors will be determined at different electron energies. The molecular structure of the radiosensitizers will be modified systematically to reveal damage mechanisms and to be able to stimulate the development of novel radiosensitizers. Furthermore, the influence of an aqueous environment on the DNA damage will be studied. Gold nanoparticles are used as a source of photoelectrons, which can damage the DNA in solution. The influence of the solvent will on the one hand be studied by determination of strand break yields using the DNA origami technique and AFM and by comparison with vacuum experiments. On the other hand damage products can be detected using surface-enhanced Raman scattering. In this way complementary information about radiation induced chemical changes in aqueous environment will be obtained. This is a novel approach to explore damage mechanisms in increasingly complex systems and the final goal is to reveal the physico-chemical basis of DNA radiosensitization.

• DFG Programme: Research Grants