The peroxyl radical exhibits a much stronger reactivity towards C1′–H1′ in duplex DNA with respect to single-stranded DNA.

The static and dynamic structures of DNA duplexes affected by 5S-Tg (Tg, Thymine glycol) epimers were studied using MD simulations and Markov State Models (MSMs) analysis. The results show that the 5S,6S-Tg base caused little perturbation to the helix, and the base-flipping barrier was determined to be 4.4 kcal mol−1 through the use of enhanced sampling meta-eABF calculations, comparable to 5.4 kcal mol−1 of the corresponding thymine flipping. Two conformations with the different hydrogen bond structures between 5S,6R-Tg and A19 were identified in several independent MD trajectories. The 5S,6R-Tg:O6HO6•••N1:A19 hydrogen bond is present in the high-energy conformation displaying a clear helical distortion, and near barrier-free Tg base flipping. The low-energy conformation always maintains Watson–Crick base pairing between 5S,6R-Tg and A19, and 5S-Tg base flipping is accompanied by a small barrier of ca. 2.0 KBT (T = 298 K). The same conformations are observed in the MSMs analysis. Moreover, the transition path and metastable structures of the damaged base flipping are for the first time verified through MSMs analysis. The data clearly show that the epimers have completely different influence on the stability of the DNA duplex, thus implying different enzymatic mechanisms for DNA repair.

SQLE (squalene epoxidase) is a cell membranebound enzyme. It is a target of fungicides and may become a new target for cancer therapy. Therefore, monitoring the content and distribution of the key enzyme in living cells is very challenging. To achieve this goal, tetraphenyl ethylene-Ter (TPE-Ter) was first designed as a new fluorescent probe to SQLE based on its active cavity. Spectral experiments discovered that SQLE/TPE-Ter shows stronger emission with fast response time and low interference from other analytes. Molecular dynamics simulation clearly confirmed the complex structure of SQLE/TPE-Ter, and the key residues contribute to restriction of TPE-Ter single-molecular motion in the cavity. TPE-Ter-specific response to SQLE is successfully demonstrated in living cells such as LO2, HepG2, and fungi. Imaging of TPE-Ter-treated fungi indicates that it can be used to rapidly assess antifungal drug susceptibility (30 min at least). The present work provides a powerful tool to detect content and distribution of SQLE in living cells.

Damaged or mismatched DNA bases are normally thought to be able to flip out of the helical stack, providing enzymes with access to the faulty genetic information otherwise hidden inside the helix. Thymine glycol (Tg) is one of the most common products of nucleic acid damage. However, the static and dynamic structures of DNA duplexes affected by 5R-Tg epimers are still not clearly understood, including the ability of these to undergo spontaneous base flipping. Structural effects of the 5R-Tg epimers on the duplex DNA are herein studied using molecular dynamics together with reliable DFT based calculations. In comparison with the corresponding intact DNA, the cis -5R,6S-Tg epimer base causes little perturbation to the duplex DNA, and a barrier of 4.9 kcal mol –1 is obtained by meta-eABF for cis -5R,6S-Tg base flipping out of the duplex DNA, comparable to the 5.4 kcal mol –1 obtained for the corresponding thymine flipping in intact DNA. For the trans -5R,6R-Tg epimer, three stable local structures were identified, of which the most stable disrupts the Watson–Crick hydrogen-bonded G5/C20 base pair, leading to conformational distortion of the duplex. Interestingly, the relative barrier height of the 5R-Tg flipping is only 1.0 kcal mol –1 for one of these trans -5R,6R-Tg epimers. Water bridge interactions were identified to be essential for 5R-Tg flipping. The study clearly demonstrates the occurrence of partial trans -5R,6R-Tg epimer flipping in solution.

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