Direct Chemical Evidence for Charge Transfer between Photoexcited 2-Aminopurine and Guanine in Duplex DNA

Photoexcited 2-aminopurine (Ap*) is extensively exploited as a fluorescent base analogue in the study of DNA structure and dynamics. Quenching of Ap* in DNA is often attributed to stacking interactions between Ap* and DNA bases, despite compelling evidence indicating that charge transfer (CT) between Ap* and DNA bases contributes to quenching. Here we present direct chemical evidence that Ap* undergoes CT with guanine residues in duplex DNA, generating oxidative damage at a distance. Irradiation of Ap in DNA containing the modified guanine, cyclopropylguanosine (CPG), initiates hole transfer from Ap* followed by rapid ring opening of the CPG radical cation. Ring opening accelerates hole trapping to a much shorter time regime than for guanine radicals in DNA; consequently, trapping effectively competes with back electron transfer (BET) leading to permanent CT chemistry. Significantly, BET remains competitive, even with this much faster trapping reaction, consistent with measured kinetics of DNA-mediated CT. The distance dependence of BET is sharper than that of forward CT, leading to an inverted dependence of product yield on distance; at short distances product yield is inhibited by BET, while at longer distances trapping dominates, leading to permanent products. The distance dependence of product yield is distinct from forward CT, or charge injection. As with photoinduced charge transfer in other chemical and biological systems, rapid kinetics for charge injection into DNA need not be associated with a high yield of DNA damage products

Photogeneration and Migration of Electrons and Holes in Zeolite NaY

Electron transfer and charge migration between electron donors and acceptors encapsulated within dry NaY zeolites are explored using nanosecond laser flash photolysis. The role of the zeolite in these redox processes is examined in order to characterize the intrazeolite mobility of electrons and holes. Electron migration is initiated by photoexciting trans-anethole in NaY containing coadsorbed 1,4-dicyanobenzene as an electron acceptor, while hole migration is initiated by photoexciting chloranil in NaY containing coadsorbed 4,4‘-dimethoxybicumene as an electron donor. The experimental results demonstrate that ultrafast redox reactions (>108 s-1) take place, leading to long-lived charge separated species within the zeolite cavities. The efficiency of these redox processes is examined as a function of donor−acceptor concentration and the presence of nitrous oxide as an electron trap. Interpretation of the experimental data with two independent models provides evidence that the redox chemistry occurring within NaY cannot be completely accounted for by contact interactions between the incorporated molecules. From these models, it is estimated that the zeolite can mediate electron and hole migration over vacant, through-space distances of 11 and 18 Å, respectively

Absolute Reactivity of the 4-Methoxycumyl Cation in Non-Acid Zeolites

The reactivity of the 4-methoxycumyl cation in a series of alkali metal cation-exchanged zeolites (LiY, NaY, KY, RbY CsY, NaX, NaMor, and Naβ) in the absence and presence of coadsorbed alcohols and water is examined using nanosecond laser flash photolysis. In dry zeolites, the absolute reactivity of the carbocation is found to be strongly dependent on the nature of the alkali counterion, the Si/Al ratio, and the framework morphology, with the lifetime of the carbocation in Naβ being almost 10000-fold longer than in CsY. The results suggest a mechanism for carbocation decay involving direct participation of the zeolite framework as a nucleophile, leading to the generation of a framework-bound alkoxy species. Intrazeolite addition reactions of alcohols and water to the 4-methoxycumyl cation can be described in terms of both dynamic and static quenching involving molecular diffusion through the heterogeneous topology and rapid coupling between the alcohol and the carbocation encapsulated within the same cavity. The dynamics of the quenching reactions are different from similar reactions in homogeneous solution due to both the passive and active influences of the zeolite environment. In a passive sense, the zeolite decreases the reactivity of the nucleophilic quencher by hindering molecular diffusion. However, the zeolite actively promotes the efficiency of intracavity coupling by enhancing the deprotonation of the oxonium ion intermediate, allowing the reaction to go to completion

Ligand-Directed Dynamics of Adenine Riboswitch Conformers

Riboswitches harness the structural and dynamic sophistication of RNA to coordinate specific ligand recognition with changes in gene expression. Design of molecules to manipulate riboswitch responses relies on our understanding of their RNA−ligand interactions. Here we demonstrate that for the adenine (A) riboswitch (ARNA) these interactions are highly dynamic. Given that 2-aminopurine (Ap) mimics A in its interactions with ARNA, we use the fluorescence lifetime of Ap to interrogate individual Ap-ARNA conformers (dynamic exchange times > ∼10 ns). Counter to predictions of two state and induced fit models, the ligand-bound A riboswitch is not a single, highly ordered structure:  We detect at least three distinct Ap-ARNA conformers in ensemble solution. Their distribution indicates that they are not high-energy RNA folding intermediates but are instead energetically similar (ΔG -1) conformers whose thermal stability, ligand, and Mg2+ binding affinity differ substantially. Our experimental characterization suggests that these conformers are structurally distinct locally at the ligand binding site and globally in the arrangement of the P2−P3 stems. These results correlate well with recent single molecule characterization of P2−P3 end-to-end distances and exchange rates, but contrast with recent NMR results which suggest that the highly homologous G riboswitch exhibits a static global structure both with and without ligand. These distinct dynamics may well be the root of the divergent specificity and function of the A and G riboswitches. We predict that conformational dynamics within the bound A riboswitch underlie its regulatory responses and that these dynamics are directed by ligand structure