Enzymatic bypass of G-quadruplex structures containing oxidative lesions

Podbevšek, Peter (author), Plavec, Janez (author)

The function of many DNA processing enzymes involves sliding along the double helix or individual DNA strands. Stable secondary structures in the form of G-quadruplexes are difficult for such enzymes to bypass. We used a polymerase stop assay to determine which structural features of the human telomeric and the BCL2 promoter G-quadruplexes can stall progression of the Klenow fragment. Primer extension profiles revealed that G-quartets are effective roadblocks for the Klenow fragment, while auxiliary base pairs can be easily bypassed. Furthermore, we utilized 8-oxoguanine to simulate oxidative damage in G-rich regions and determine the effects on enzyme bypass. In rare cases, oxidative lesions reduce the level of G-quadruplex bypass. In general, however, oxidative lesions reduce G-quadruplex stability and facilitate bypassing of such G-rich regions, especially if the lesion persists in unfolding intermediates. Our findings using Klenow fragment can be extrapolated to other G-quadruplex forming sequences and enzymes that utilise a clamp-like structure to slide along DNA and are involved in processes such as gene expression regulation and telomere maintenance.

• Language: English
• Keywords: biochemistry, DNA, G-quadruplexes, NMR
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Publication status: Published
• Publication version: Version of Record
• Year: 2025
• Number of pages: 11 str.
• Numbering: Vol. 53, iss. 1, art. gkae1157
• PID: 20.500.12556/RUL-169767
• UDC: 577
• ISSN on article: 1362-4962
• DOI: 10.1093/nar/gkae1157
• COBISS.SI-ID: 222273283
• Publication date in RUL: 09.06.2025

Record is a part of a journal

• Title: Nucleic acids research online
• Shortened title: Nucleic acids res. online
• Publisher: Oxford University Press
• ISSN: 1362-4962
• COBISS.SI-ID: 2172954

Licences

• License: CC BY-NC 4.0, Creative Commons Attribution-NonCommercial 4.0 International
• Link: http://creativecommons.org/licenses/by-nc/4.0/
• Description: A creative commons license that bans commercial use, but the users don’t have to license their derivative works on the same terms.

Secondary language

• Language: Slovenian
• Keywords: biokemija, DNK, g-kvadrupleksi, NMR

Projects

• Funder: ARIS - Slovenian Research and Innovation Agency
• Project number: P1-0242
• Name: Kemija in struktura bioloških učinkovin