DNA damage – a novel method to measure the rate of single-stranded breaks from fragmenting dsDNA in nanochannels – theory and modeling

Abstract: Damage to DNA can cause death to an individual cell and serious harm to the host organism. Photosensitized reactions are one cause of DNA damage. It can lead to destructive chemical reactions targeted to a base of the DNA as well as a breakage along one or both of the DNA strands. Due to this, quantifying and understanding photosensitized driven DNA damage is an important topic of research. From experimental data of fragmenting fluorescently stained linear double-stranded DNA in nanochannels, we will extract the non-observable single-stranded cleavage rate (nicking rate) from observable times of double-stranded cleaves (cuts), which lets us quantify the rate of DNA damage. To do this, we present a new probabilistic model that connects the cutting rate to the time of cuts. We present two distinct models for the cutting rate, the first one is analytical and the second is based on simulations. We find through validation on synthetic data with known nicking rates that using the cutting rate from the simulation-based model yields more accurate estimates of the nicking rate compared to using the cutting rate from the analytical model. In addition, we manage to estimate the nicking rate for three experimental data sets with varying illumination strength. From these estimates, we conclude that the nicking rate, as expected, increases with increasing illumination strength. We hope that this study will serve as proof of concept for our new methodology to estimate the nicking rate and provide a good starting point for other studies which want to add to the knowledge of nicking rate estimation under different conditions.