Electron hole (radical cation) migration in DNA, where the quantum transport of an injected charge is gated in a correlated manner by the thermal motions of the hydrated counterions, is described here. Classical molecular dynamics simulations in conjunction with large-scale first-principles electronic structure calculations reveal that different counterion configurations lead to formation of states characterized by varying spatial distributions and degrees of charge localization. Stochastic dynamic fluctuations between such ionic configurations can induce correlated changes in the spatial distribution of the hole, with concomitant transport along the DNA double helix. Comparative ultraviolet light-induced cleavage experiments on native B DNA oligomers and on ones modified to contain counterion (Na(+))-starved bridges between damage-susceptible hole-trapping sites called GG steps show in the latter a reduction in damage at the distal step. This reduction indicates a reduced mobility of the hole across the modified bridge as predicted theoretically.

The synthesis and properties of a new class of photoresponsive coumarin polyesters are described. Incorporation of the coumarin chromophore in the polymer chain provides interesting properties such as polymer chain crosslinking upon irradiation at 350 nm and chain un-cross-linking when irradiated at 254 nm. In addition, irradiation at 254 nm also results in polymer chain scission. The cross-linking, uncross-linking, and chain scission properties were studied by ssNMR, ATR-IR, and GPC measurements. These properties enable the fabrication of 2D surfaces having complementary micropatterned features. Also, initial biocompatibility profiles of the polymers and their irradiation products were demonstrated using MTT assays.

Abstract— We describe the synthesis and photophysical studies, including measurements of quantum yields of triplet excited states and singlet oxygen generation of bis(3,5‐dibromo‐2,4,6‐trihydroxyphenyl)squaraine (2) and bis(3,5‐diiodo‐2,4,6‐trihydroxyphenyl)squaraine (3). These dyes exist in solution in the protonated, neutral, single and double depro‐tonated forms, depending on pH. The pKa values of these dyes were found to be relatively lower than those of the parent bis(2,4,6‐trihydroxyphenyl)squaraine (1). Only the single deprotonated forms (Sq) of 2 and 3 showed measurable fluorescence. In microheterogeneous media such as in the presence of β‐cyclodextrin, cetyltrunethylammonium bromide and polyvinylpyrrolidone), bathochromic shifts in the absorption and emission spectra of Sq were observed with a substantial enhancement in their fluorescence yields. Triplet excited states are the main transient intermediates obtained upon 532 nm laser excitation of the various forms of 2 and 3 in methanol. These triplets have lifetimes in the range from 0.061 to 132 μs. The triplet quantum yields of double deprotonated forms are low (φT = <0.01), whereas the neutral and Sq−forms of 2 (φr = 0.12 and 0.22) and 3 (φT= 0.24 and 0.5), respectively, exhibited significant triplet yields. Quantum yields of singlet oxygen generation by Sq−forms of 2 and 3 were determined in methanol and were found to be 0.13 and 0.47, respectively, which are in good agreement with the triplet yields obtained in these systems.

Oxidative damage to DNA, implicated in mutagenesis, aging, and cancer, follows electron loss that generates a radical cation that migrates to a guanine, where it may react with water to form 8-oxo-7,8-dihydroguanine (8-OxoG). Molecular dynamics and ab initio quantum simulations on a B-DNA tetradecamer reveal activated reaction pathways that depend on the local counterion arrangement. The lowest activation barrier, 0.73 eV, is found for a reaction that starts from a configuration where a Na(+) resides in the major groove near the N7 atoms of adjacent guanines, and evolves through a transition state where a bond between a water oxygen atom and a carbon atom forms concurrently with displacement of a proton toward a neighboring water molecule. Subsequently, a bonded complex of a hydronium ion and the nearest backbone phosphate group forms. This counterion-assisted proton shuttle mechanism is supported by experiments exploiting selective substitution of backbone phosphates by methylphosphonates.