Oxidative Damage Fine‐Tunes G‐Quadruplex Structures in Human Gene Promoters

ABSTRACT Oxidative damage can convert guanine (G) into 8‐oxoguanine ( O8 G), resulting in altered gene expression and genome instability. However, the underlying molecular mechanisms remain poorly understood. Herein, we show that the NEIL3 gene proximal promoter sequence forms a mixture of parallel and hybrid G‐quadruplex structures ( NEIL3 ‐G4s), exhibiting intrinsic structural polymorphism. Strikingly, site‐specific O8 G modifications significantly reduce this polymorphism, promoting the stabilization of either the parallel or the (3+1) hybrid‐1 G4 topology. A single G‐to‐ O8 G substitution is sufficient to trigger a clear structural transition from the parallel to the (3+1) hybrid‐1 G4, highlighting the profound impact of O8 G on G4‐mediated epigenetic regulation. We have determined the NMR solution structures of both native and O8 G‐modified NEIL3 ‐G4s, providing mechanistic insights into how O8 G induces specific G4 structural rearrangements. Functional analysis demonstrates that both forms of NEIL3 ‐G4s can form in extended DNA contexts and inhibit DNA polymerase activity. Under oxidative stress, the formation of NEIL3 ‐G4s correlates with elevated NEIL3 gene expression, suggesting that they play a role as sensors of oxidative damage and function as molecular switches for gene upregulation. Collectively, these findings underscore the crucial role of O8 G‐induced G4 structural plasticity in the cellular response to oxidative stress and in regulating gene expression.