title: Proton-coupled hole hopping in nucleosomal and free DNA initiated by site-specific hole injection.
abstract: Nucleosomes were reconstituted from recombinant histones and a 147-mer DNA sequence containing the damage reporter sequence 5'-…d([2AP]T[GGG](1)TT[GGG](2)TTT[GGG](3)TAT)… with 2-aminopurine (2AP) at position 27 from the dyad axis. Footprinting studies with ˙OH radicals reflect the usual effects of "in" and "out" rotational settings, while, interestingly, the guanine oxidizing one-electron oxidant CO(3)(˙-) radical does not. Site-specific hole injection was achieved by 308 nm excimer laser pulses to produce 2AP(˙+) cations, and superoxide via the trapping of hydrated electrons. Rapid deprotonation (~100 ns) and proton coupled electron transfer generates neutral guanine radicals, G(-H)˙ and hole hopping between the three groups of [GGG] on micro- to millisecond time scales. Hole transfer competes with hole trapping that involves the combination of O(2)(˙-) with G(-H)˙ radicals to yield predominantly 2,5-diamino-4H-imidazolone (Iz) and minor 8-oxo-7,8-dihydroguanine (8-oxoG) end-products in free DNA (Misiaszek et al., J. Biol. Chem. 2004, 279, 32106). Hole migration is less efficient in nucleosomal than in the identical protein-free DNA by a factor of 1.2-1.5. The Fpg/piperidine strand cleavage ratio is ~1.0 in free DNA at all three GGG sequences and at the "in" rotational settings [GGG](1,3) facing the histone core, and ~2.3 at the "out" setting at [GGG](2) facing away from the histone core. These results are interpreted in terms of competitive reaction pathways of O(2)(˙-) with G(-H)˙ radicals at the C5 (yielding Iz) and C8 (yielding 8-oxoG) positions. These differences in product distributions are attributed to variations in the local nucleosomal B-DNA base pair structural parameters that are a function of surrounding sequence context and rotational setting.
authors.affiliation: Beijing Institute of Genomics, Chinese Academy of Science, Beijing 100029, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.forename: Zhi
authors.initials: Z
authors.lastname: Liu
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Geacintov
authors.forename: Vladimir
authors.initials: V
authors.lastname: Shafirovich
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004249:DNA Damage; D006147:Guanine / Q000737:chemistry; D006657:Histones / Q000737:chemistry*; D017665:Hydroxyl Radical / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009707:Nucleosomes / Q000737:chemistry*; D010084:Oxidation-Reduction; D055503:Protein Multimerization; D058849:Protein Refolding; D011522:Protons; D011994:Recombinant Proteins / Q000737:chemistry
chemical_list: D006657:Histones; D009707:Nucleosomes; D011522:Protons; D011994:Recombinant Proteins; D017665:Hydroxyl Radical; D015075:2-Aminopurine; D006147:Guanine; D004247:DNA