Double-strand breaks quantification by statistical length analysis of DNA fragments imaged with AFM. (July 2022)

• Record Type: Journal Article
• Authors: Sofińska, Kamila; Cieśla, Michał; Barbasz, Jakub; Wilkosz, Natalia; Lipiec, Ewelina; Szymoński, Marek; Białas, Piotr
• Is Part Of: Measurement. Volume 198(2022)
• Publication Date: 2022-07
• Subjects: Double-strand breaks -- DSB -- DNA -- AFM imaging -- Bleomycin -- DNA conformation -- DNA damage -- DNA lesions -- Statistical analysis; Weights and measures -- Periodicals; Measurement -- Periodicals; Measurement; Weights and measures; Periodicals; 530.8
• DOI: 10.1016/j.measurement.2022.111362
• Languages: English
• ISSNs: 0263-2241

Abstract

Graphical abstract: Highlights: A statistics-based approach for the quantification of the double-strand breaks (DSBs) number. DSBs are introduced in the DNA molecule via the interaction with the anticancer chemotherapeutic drug – bleomycin. The number of DSBs in the DNA molecule are determined based on AFM images of DNA fragments. The quantification of DSBs based only on the fraction of uncut DNA plasmids is presented. The numerical procedure allowing to correct the obtained value of DSBs that considers missing short fragments of DNA strands is proposed. Abstract: DNA, a molecule carrying our genome, is constantly exposed to various endogenous and exogenous damaging factors. These factors may lead to the formation of single- or double-strand breaks. Recently, an atomic force microscopy emerged as an attractive tool for determination of the length of DNA fragments deposited at surfaces, allowing quantification of double-strand breaks (DSBs). In spite of this, the length of objects provided via AFM is strictly related to the image spatial resolution, which in consequence leads to underestimation of DSBs quantity. To correct this deficiency, we provide here a novel methodology based on statistics of DNA fragments length. This approach allows for highly accurate determination of the DSBs number. Moreover, we provide the software that enables to automatically calculate the number of DSBs according to the described methodology. Finally, the method is applied for characterization of the DNA plasmid fragmentation by bleomycin - an anticancer chemotherapeutic drug.