Modulation of cyclobutane thymine photodimer formation in T11-tracts in rotationally phased nucleosome core particles and DNA minicircles

Abstract

Cyclobutane pyrimidine dimers (CPDs) are DNA photoproducts linked to skin cancer, whose mutagenicity depends in part on their frequency of formation and deamination. Nucleosomes modulate CPD formation, favoring outside facing sites and disfavoring inward facing sites. A similar pattern of CPD formation in protein-free DNA loops suggests that DNA bending causes the modulation in nucleosomes. To systematically study the cause and effect of nucleosome structure on CPD formation and deamination, we have developed a circular permutation synthesis strategy for positioning a target sequence at different superhelix locations (SHLs) across a nucleosome in which the DNA has been rotationally phased with respect to the histone octamer by TG motifs. We have used this system to show that the nucleosome dramatically modulates CPD formation in a T11-tract that covers one full turn of the nucleosome helix at seven different SHLs, and that the position of maximum CPD formation at all locations is shifted to the 5΄-side of that found in mixed-sequence nucleosomes. We also show that an 80-mer minicircle DNA using the same TG-motifs faithfully reproduces the CPD pattern in the nucleosome, indicating that it is a good model for protein-free rotationally phased bent DNA of the same curvature as in a nucleosome, and that bending is modulating CPD formation.

5-Formylcytosine Yields DNA–Protein Cross-Links in Nucleosome Core Particles

“…The variable reactivity of 5fCs in NCPs probably owe to their different exposure and proximity to the histone tails. This is consistent with previous observations that demonstrated that even slight changes in rotational positioning can affect the DNA damage reactivity in NCPs. − …”

Oxidation of 8-Oxo-7,8-dihydro-2′-deoxyguanosine Leads to Substantial DNA-Histone Cross-Links within Nucleosome Core Particles

“…It is known that superhelical location and rotational orientation significantly impact damaged DNA reactivity in NCPs. ,− Herein, NCP-8-oxodGuo 73 /C and NCP-8-oxodGuo 137 /C were employed for addressing the effect of 8-oxodGuo location and orientation on DPC formation. The yield (48%) of 8-oxodGuo oxidation in NCP-8-oxodGuo 73 /C was higher than that of NCP-8-oxodGuo 89 /C (31%).…”

Formation of UV-induced DNA damage contributing to skin cancer development

“…It is well known that the yield of CPDs is lower in the nucleosome than in the linker region 156,157 . A recent work provided accurate information on the favored locations of CPDs within a rotationally phased nucleosome 158 . The ratio between 64PPs and CPDs is also affected by the nucleosome structure 159 .…”