Super-Resolution Radiation Biology: From Bio-Dosimetry towards Nano-Studies of DNA Repair Mechanisms

Past efforts in radiobiology, radio-biophysics, epidemiology and clinical research strongly contributed to the current understanding of ionizing radiation effects on biological materials like cells and tissues. It is well accepted that the most dangerous, radiation induced damages of DNA in the cell nucleus are double strand breaks, as their false rearrangements cause dysfunction and tumor cell proliferation. Therefore, cells have developed highly efficient and adapted ways to repair lesions of the DNA double strand. To better understand the mechanisms behind DNA strand repair, a variety of fluorescence microscopy based approaches are routinely used to study radiation responses at the organ, tissue and cellular level. Meanwhile, novel super-resolution fluorescence microscopy techniques have rapidly evolved and become powerful tools to study biological structures and bio-molecular (re-)arrangements at the nano-scale. In fact, recent investigations have increasingly demonstrated how super-resolution microscopy can be applied to the analysis of radiation damage induced chromatin arrangements and DNA repair protein recruitment in order to elucidate how spatial organization of damage sites and repair proteins contribute to the control of repair processes. In this chapter, we would like to start with some fundamental aspects of ionizing radiation, their impact on biological materials, and some standard radiobiology assays. We conclude by introducing the concept behind super-resolution radiobiology using single molecule localization microscopy (SMLM) and present promising results from recent studies that show an organized architecture of damage sites and their environment. Persistent homologies of repair clusters indicate a correlation between repair cluster topology and repair pathway at a given damage locus. This overview over recent investigations may motivate radiobiologists to consider chromatin architecture and spatial repair protein organization for the understanding of DNA repair processes.

Where Quantum Biochemistry Meets Structural Bioinformatics: Excited Conformationally-Tautomeric States of the Classical A·T DNA Base Pair

This Chapter summarizes recent quantum-chemical (QM) investigations of the novel conformational and tautomeric states on the potential energy hypersurface of the classical A·T/A·U nucleobase pairs. For the first time, it was observed 28 local minima for each base pair excluding enantiomers - planar, non-planar base pairs and structures with wobble geometry. Considered excited conformationally-tautomeric states of the classical A·T DNA base pair have been revealed in the Nucleic Acid Database by structural bioinformatics. These data shed light on the biological significance of the unusual A·T/A·U nucleobase pairs for the functioning of the nucleic acids at the quantum level.