Proton-coupled hole hopping in nucleosomal and free DNA initiated by site-specific hole injection

Yang Liu, Zhi Liu, Nicholas E. Geacintov, Vladimir Shafirovich

Research output: Contribution to journalArticlepeer-review


Nucleosomes were reconstituted from recombinant histones and a 147-mer DNA sequence containing the damage reporter sequence 5′-...d([2AP]T[GGG] 1TT[GGG] 2TTT[GGG] 3TAT)... 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.

Original languageEnglish (US)
Pages (from-to)7400-7410
Number of pages11
JournalPhysical Chemistry Chemical Physics
Issue number20
StatePublished - May 28 2012

ASJC Scopus subject areas

  • General Physics and Astronomy
  • Physical and Theoretical Chemistry


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