Networks and Islands of Genome Nano-architecture and Their Potential Relevance for Radiation Biology

Combinatorial Oligonucleotide FISH (COMBO-FISH): Computer Designed Probe Sets for Microscopy Research of Chromatin in Cell Nuclei

“…In combination with super-resolution localization microscopy and novel tools of data evaluation and interpretation by geometric and topological algorithms [61][62][63][64] COMBO-FISH probes offer new perspectives in understanding the reaction of chromatin as a system as a whole during gene expression, proliferation, or stress response [47].…”

“…COMBO-FISH probes carrying one fluorochrome molecule at one end of each oligonucleotide are ideal nano-probes for Single Molecule Localization Microscopy [23,24,43] (SMLM) in order to analyze chromatin structure and architecture on the nano-scale in subchromosomal regions of cell nuclei [32,[43][44][45][46][47].…”

Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment

“…657 The molecular dynamics and macromolecular organization must follow the chemical and physical laws of atomic and molecular binding, thermodynamics, electrodynamics, and physical chemistry within a limited volume. 663 Exposure to UV or ionizing radiation, such as X-rays, γ-rays, high-energy electrons or protons, high-energy particles or ions, etc,. causes chromatin damage of different types, for instance, base modifications, single-strand breaks (SSBs), and especially double-strand breaks (DSBs) of different complexity.…”

“…Such networks characteristically rearranged themselves depending on cell fate 661 and under environmental stress such as exposure to ionizing irradiation, thereby interacting with epigenetic pathways and response loops. 663 In order to obtain quantitative parameters for networks and network dynamics, super-resolution SMLM 664 is used as a method for accurate (to within ten nanometers) registration of the coordinates of fluorescence labels of specific DNA sequences/chromatin domains and proteins. The major advantage of SMLM depends on this registration process, which results in a map of molecule coordinates without primarily processing an image.…”

“…Although sometimes ATP-supported, it seems that this trafficking works somehow self-propelled and drives and governs the system perfectly . The molecular dynamics and macromolecular organization must follow the chemical and physical laws of atomic and molecular binding, thermodynamics, electrodynamics, and physical chemistry within a limited volume …”