Lipiec, E. | Search bioRxiv

bioRxiv2026

Nanoscale insights into chromatin integrity molecular rearrangements upon DNA damage response

DNA Double Strand Breaks (DSBs) threaten genomic stability, leading to cell death, chromosomal rearrangements, and cancer-driving mutations. Therefore, the effective repair mechanisms are essential for maintaining genomic stability and ensuring cellular survival across diverse organisms. At the core of this process lies chromatin integrity, which facilitates the local DNA conformational changes, regulating accessibility to repair proteins and other biomolecules. To deepen our understanding of the DNA damage response pathway, the local molecular mechanisms regulating the interplay between DNA damage formation and alterations in chromatin conformation must be investigated at the nanoscale level. Here, we integrated atomic force microscope-infrared spectroscopy (AFM-IR) and confocal fluorescence microscopy to explore local chemical modifications in DNA structure and chromatin integrity in metaphase chromosomes and chromosomal aberrations isolated from cells treated with the chemotherapeutic agent, bleomycin. Our findings reveal changes in secondary protein structures, indicating the engagement of DNA repair proteins with high {beta}-sheet content. Nanospectroscopic mapping resolved the alterations in DNA condensation along the chromosomes. Moreover, we observed global DNA demethylation, particularly the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), correlating with increased DSBs. We conclude that these transitions in protein conformation and DNA methylation correlate with chromatin relaxation and enhanced accessibility for the repair protein.

biophysics↗

bioRxiv2018

DNA structure change induced by guanosine radicals -- a theoretical and spectroscopic study

Proton radiation therapy is one of the newest and most promising methods used in modern oncology. Nonetheless, the dissemination of that method may result challenging. This is partially due to the fact that the mechanism of DNA damage induced by protons, which is one of the ways proton radiation interacts with tissues, has not been fully understood yet. It is well known that ionizing radiation especially ions such as protons may directly damage DNA but it also causes the formation of radicals, which may lead to even more serious damage of the DNA sugar-backbone than direct interaction with charged ion. In this article we focus on the influence of guanine radicals on the DNA structure, namely the conformation and stability of the DNA strand. We present the theoretical results of the optimization calculations of DNA structures with guanine radical-adenine pairs as well as calculated Raman spectra. By combining theoretical calculations with the experimental spectra we were able to explain molecular modifications of the DNA sugar-backbone affected by guanine radicals formed upon radiation exposure, which lead to spectral changes between spectra of control and irradiated DNA. Thus we established a pathway of the formation of DNA damage caused by protons.

biophysics↗