Oxygen
Dependent Purine Lesions in Double-Stranded
Oligodeoxynucleotides: Kinetic and Computational Studies Highlight
the Mechanism for 5′,8-Cyclopurine Formation
posted on 2020-03-13, 15:22authored byChryssostomos Chatgilialoglu, Leif A. Eriksson, Marios G. Krokidis, Annalisa Masi, Shudong Wang, Rubo Zhang
The reaction of HO• radical with DNA is intensively
studied both mechanistically and analytically for lesions formation.
Several aspects related to the reaction paths of purine moieties with
the formation of 5′,8-cyclopurines (cPu), 8-oxopurines (8-oxo-Pu),
and their relationship are not well understood. In this study, we
investigated the reaction of HO• radical with a
21-mer double-stranded oligodeoxynucleotide (ds-ODNs) in γ-irradiated
aqueous solutions under various oxygen concentrations and accurately
quantified the six purine lesions (i.e., four cPu and two 8-oxo-Pu)
by LC-MS/MS analysis using isotopomeric internal standards. In the
absence of oxygen, 8-oxo-Pu lesions are only ∼4 times more
than cPu lesions. By increasing oxygen concentration, the 8-oxo-Pu
and the cPu gradually increase and decrease, respectively, reaching
a gap of ∼130 times at 2.01 × 10–4 M
of O2. Kinetic treatment of the data allows to estimate
the C5′ radical competition between cyclization and oxygen
trapping in ds-ODNs, and lastly the rate constants of the four cyclization
steps. Tailored computational studies by means of dispersion-corrected
DFT calculations were performed on the CGC and TAT in their double-strand
models for each cPu diastereoisomer along with the complete reaction
pathways of the cyclization steps. Our findings reveal unheralded
reaction mechanisms that resolve the long-standing issues with C5′
radical cyclization in purine moieties of DNA sequences.