@article{0f2edd3f764e4127bfe608d6894072d7,
title = "Uracil-DNA glycosylase efficiency is modulated by substrate rigidity",
abstract = "Uracil DNA-glycosylase (UNG) is a DNA repair enzyme that removes the highly mutagenic uracil lesion from DNA using a base flipping mechanism. Although this enzyme has evolved to remove uracil from diverse sequence contexts, UNG excision efficiency depends on DNA sequence. To provide the molecular basis for rationalizing UNG substrate preferences, we used time-resolved fluorescence spectroscopy, NMR imino proton exchange measurements, and molecular dynamics simulations to measure UNG specificity constants (kcat/KM) and DNA flexibilities for DNA substrates containing central AUT, TUA, AUA, and TUT motifs. Our study shows that UNG efficiency is dictated by the intrinsic deformability around the lesion, establishes a direct relationship between substrate flexibility modes and UNG efficiency, and shows that bases immediately adjacent to the uracil are allosterically coupled and have the greatest impact on substrate flexibility and UNG activity. The finding that substrate flexibility controls UNG efficiency is likely significant for other repair enzymes and has major implications for the understanding of mutation hotspot genesis, molecular evolution, and base editing.",
author = "Orndorff, {Paul B.} and Souvik Poddar and Owens, {Aerial M.} and Nikita Kumari and Ugaz, {Bryan T.} and Samrat Amin and {Van Horn}, {Wade D.} and {van der Vaart}, Arjan and Marcia Levitus",
note = "Funding Information: M.L. acknowledges use of the Ultrafast Laser Spectroscopy Facility at Arizona State University. W.V.H. acknowledges use of the Magnetic Resonance Research Center at Arizona State University. A.v.d.V. acknowledges use of Research Computing at the University of South Florida. This work was supported by the National Science Foundation [# 1918716 to ML and WVH, # 1919096 to AvdV]. Research reported in this publication was also supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM141933 [WVH]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Funding Information: M.L. acknowledges use of the Ultrafast Laser Spectroscopy Facility at Arizona State University. W.V.H. acknowledges use of the Magnetic Resonance Research Center at Arizona State University. A.v.d.V. acknowledges use of Research Computing at the University of South Florida. This work was supported by the National Science Foundation [# 1918716 to ML and WVH, # 1919096 to AvdV]. Research reported in this publication was also supported by the National Institute of General Medical Sciences of the National Institutes of Health under Award Number R35GM141933 [WVH]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
month = dec,
doi = "10.1038/s41598-023-30620-0",
language = "English (US)",
volume = "13",
journal = "Scientific reports",
issn = "2045-2322",
publisher = "Nature Publishing Group",
number = "1",
}