Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity.

Authors

Sharon N Greenwood, Rowan University
Alexis N Dispensa, Rowan University
Matthew Wang, Rowan University
Justin R Bauer, Rowan University
Timothy D Vaden, Rowan University
Zhiwei Liu, Rowan University
Brian P Weiser, Rowan University

Document Type

Article

Version Deposited

Published Version

Publication Date

5-20-2025

Publication Title

Biochemistry

DOI

10.1021/acs.biochem.5c00067

Abstract

Because of their ubiquitous presence, ions interact with numerous macromolecules in the cell and affect critical biological processes. Here, we discuss how cations including Mg²⁺ alter the enzymatic activity of a DNA glycosylase by tuning its affinity for DNA. The response of uracil DNA glycosylase (UNG2) to Mg²⁺ ions in solution is biphasic and paradoxical, where low concentrations of the ion stimulate the enzyme, but high concentrations inhibit the enzyme. We analyzed this phenomenon by modeling experimental data with a statistical framework that we empirically derived to understand molecular systems that display biphasic behaviors. Parameters from our statistical model indicate that DNA substrates are nearly saturated with cations under ideal conditions for UNG2 activity. However, the enzyme slows rather abruptly when the ionic content becomes too low or too high due to changes in the electrostatic environment that alter protein affinity for DNA. We discuss how ion occupancy on DNA is dependent on DNA length; thus, the sensitivity of UNG2 to cations is also dependent on DNA length. Finally, we found that Mg²⁺-induced changes in DNA base stacking and dynamics have minimal effects on UNG2, as these outcomes occur at ion concentrations that are much lower than is required for efficient enzyme activity. Altogether, our work demonstrates how cation–DNA interactions, which are likely common in the nucleus, are a key determinant of uracil base excision repair mediated by UNG2.

Recommended Citation

Greenwood, Sharon N; Dispensa, Alexis N; Wang, Matthew; Bauer, Justin R; Vaden, Timothy D; Liu, Zhiwei; and Weiser, Brian P, "Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity." (2025). Rowan-Virtua School of Osteopathic Medicine Departmental Research. 292.
https://rdw.rowan.edu/som_facpub/292

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.

Published Citation

Greenwood SN, Dispensa AN, Wang M, Bauer JR, Vaden TD, Liu Z, Weiser BP. Ion-DNA Interactions as a Key Determinant of Uracil DNA Glycosylase Activity. Biochemistry. 2025 May 20;64(10):2332-2344. doi: 10.1021/acs.biochem.5c00067. Epub 2025 May 7. PMID: 40331587; PMCID: PMC12096439.