Effect of the Spiroiminodihydantoin Lesion on Nucleosome Stability and Positioning

Abstract

DNA is constantly under attack by oxidants, generating a variety of potentially mutagenic covalently modified species, including oxidized guanine base products. One such product is spiroiminodihydantoin (Sp), a chiral, propeller-shaped lesion that strongly destabilizes the DNA helix in its vicinity. Despite its unusual shape and thermodynamic effect on double-stranded DNA structure, DNA duplexes containing the Sp lesion form stable nucleosomes upon being incubated with histone octamers. Indeed, among six different combinations of lesion location and stereochemistry, only two duplexes display a diminished ability to form nucleosomes, and these only by ∼25%; the other four are statistically indistinguishable from the control. Nonetheless, kinetic factors also play a role: when the histone proteins have less time during assembly of the core particle to sample both lesion-containing and normal DNA strands, they are more likely to bind the Sp lesion DNA than during slower assembly processes that better approximate thermodynamic equilibrium. Using DNase I footprinting and molecular modeling, we discovered that the Sp lesion causes only a small perturbation (±1-2 bp) on the translational position of the DNA within the nucleosome. Each diastereomeric pair of lesions has the same effect on nucleosome positioning, but lesions placed at different locations behave differently, illustrating that the location of the lesion and not its shape serves as the primary determinant of the most stable DNA orientation.

Occurrence, Biological Consequences, and Human Health Relevance of Oxidative Stress-Induced DNA Damage

“…For example, the presence of dGh and dSp could influence the thermal stability and folding of the G-quadruplex, 291 and dSp lesions could disturb the structure of duplex DNA and affect nucleosome positioning. 292 dGh and dSp lesions have been detected in E. coli 197 and in mice, 131 though further studies are needed for systematically assessing their formation and repair in mammals.…”

“…In the viewpoint that 8-oxo-dG is produced at high frequencies and that it is more readily oxidized than dG, the major oxidation products of 8-oxo-dG, i.e., dGh and dSp, may bear a significant impact on cellular functions. For example, the presence of dGh and dSp could influence the thermal stability and folding of the G-quadruplex, and dSp lesions could disturb the structure of duplex DNA and affect nucleosome positioning . dGh and dSp lesions have been detected in E. coli and in mice, though further studies are needed for systematically assessing their formation and repair in mammals.…”

Interrogation of Base Pairing of the Spiroiminodihydantoin Diastereomers Using the α-Hemolysin Latch

“…Recently, the Núñez and Jamieson groups found that the Sp lesion would have minor effects on the stability and positioning of nucleosomal DNA. 22 …”

“…Recently, the groups of Nuńẽz and Jamieson found that the Sp lesion would have minor effects on the stability and positioning of nucleosomal DNA. 22 Interestingly, Sp exists as two stable diastereomers, (+)-(S)-Sp and (−)-(R)-Sp, that originate from the stereocenter formed by the junction of the two heterocyclic rings of Sp (Figure 1A). For the sake of brevity, (+)-(S)-Sp and (−)-(R)-Sp are herein abbreviated as (S)-Sp and (R)-Sp, respectively.…”

“…Therefore, further biochemical experiments with Sp are warranted to improve our understanding of this lesion and how it impacts genomic structures possibly leading to mutations. Recently, the groups of Núñez and Jamieson found that the Sp lesion would have minor effects on the stability and positioning of nucleosomal DNA …”