AP Site Does Not Introduce Significant Distortions into the DNA Structure in the Nucleosomes in vitro

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Mikhail M. Kutuzov^1#, Ekaterina A. Belousova^1#, Valeria M. Dreiman¹, and Olga I. Lavrik^1,a*

¹Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia

^* To whom correspondence should be addressed.

^# These authors contributed equally to the work.

Received: February 28, 2025; Revised: July 17, 2025; Accepted: August 4, 2025

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DNA damage results in distortion of the B-form structure of the DNA double helix. Recognition of such distortion by DNA repair proteins is an important stage in the process initiation. Nucleosome structure imposes restrictions on mobility and plasticity of DNA geometry. Under interaction of repair proteins with nucleosomal DNA, the main issue is the implementation of the DNA structure that characterizes the damage itself in a specific context. In addition, the DNA duplex in a nucleosome has a regular profile of contacts with histones corresponding to the pitch of DNA helix. Changes in the DNA structure could be assessed through the changes in this profile. This profile correlates with availability of the corresponding nucleotides for interaction with the DNA-binding proteins. In our work, it has been shown using footprinting assay that the presence of an AP site within the second or third turn from the 5′-end of the nucleosomal DNA does not significantly affect the profile of DNA contacts with histones.

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KEY WORDS: nucleosome, apurinic/apyrimidinic site, footprinting

DOI: 10.1134/S000629792560053X

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