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Accessing radiation damage to biomolecules on the nanoscale by particle-scattering simulations
(2023)
Radiation damage to DNA plays a central role in radiation therapy to cure cancer. The physico-chemical and biological processes involved encompass huge time and spatial scales. To obtain a comprehensive understanding on the nano and the macro scale is a very challenging tasks for experimental techniques alone. Therefore particle-scattering simulations are often applied to complement measurements and aide their interpretation, to help in the planning of experiments, to predict their outcome and to test damage models. In the last years, powerful multipurpose particle-scattering framework based on the Monte-Carlo simulation (MCS) method, such as Geant4 and Geant4-DNA, were extended by user friendly interfaces such as TOPAS and TOPAS-nBio. This shifts their applicability from the realm of dedicated specialists to a broader range of scientists. In the present review we aim to give an overview over MCS based approaches to understand radiation interaction on a broad scale, ranging from cancerous tissue, cells and their organelles including the nucleus, mitochondria and membranes, over radiosensitizer such as metallic nanoparticles, and water with additional radical scavenger, down to isolated biomolecules in the form of DNA, RNA, proteins and DNA-protein complexes. Hereby the degradation of biomolecules by direct damage from inelastic scattering processes during the physical stage, and the indirect damage caused by radicals during the chemical stage as well as some parts of the early biological response is covered. Due to their high abundance the action of hydroxyl radicals (•OH) and secondary low energy electrons (LEE) as well as prehydrated electrons are covered in additional detail. Applications in the prediction of DNA damage, DNA repair processes, cell survival and apoptosis, influence of radiosensitizer on the dose distribution within cells and their organelles, the study of linear energy transfer (LET), the relative biological effectiveness (RBE), ion beam cancer therapy, microbeam radiation therapy (MRT), the FLASH effect, and the radiation induced bystander effect are reviewed.
Numerous new tin catalysts that enable the synthesis of cyclic polylactides with broad variation in their molecular mass were recently developed. The abundance of cyclics in matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectra is, however, frequently reported to greatly exceed that of linears. Thus, the MALDI ionization behavior of various end-capped linear poly(L-lactide)s and one cyclic poly(L-lactide) was investigated and compared.
Neat compounds and various blends of cyclic and linear species were prepared and studied under identical conditions with regard to sample preparation and instrumental condition, except for the laser power. For this purpose, two different MALDI-TOF mass spectrometers were applied.
Our results reveal that cyclics indeed show a slightly better ionization in MALDI, although their ionization as a neat compound seems to be less effective than that of linear polylactides. The ionization of most linear polylactides investigated does not depend on the end group structure. However, linear polylactides containing 12-bromododecyl end groups reveal an unexpected saturation effect that is not caused by fragmentation of the polymer or the end group, or by electronic saturation of the detector digitizer. Furthermore, polylactides with a 2-bromoethyl end group did not show such a saturation effect.
An overestimation of cyclic species in MALDI-TOF mass spectra of poly(L-lactide)s must be considered, but the commonly assumed peak suppression of linear polymers in mixtures of both structures can be excluded.