The pH-Dependence of the Hydration of 5-Formylcytosine: an Experimental and Theoretical Study

Computational Prediction of One-Electron Oxidation Potentials for Cytosine and Uracil Epigenetic Derivatives

Knowledge of the redox properties of cytosine (C), uracil (U), and their natural derivatives is essential for a deeper understanding of DNA damage, repair, and epigenetic regulation. This study investigates the one-electron oxidation potential (Eox, V) using DFT (B3LYP-D3) and DLPNO-CCSD(T) methods with explicit/implicit (SMD) solvation model. Calculations in the gas phase and aprotic solvents such as acetonitrile showed a high correlation with experimental data (0.96-0.98). In aqueous solutions at pH 7, oxidation potentials are significantly influenced by deprotonation equilibria, as acidic molecules like 5caC become easier to oxidize upon deprotonation. The resulting oxidation potentials reflect a complex interplay of substituent effects, acidity, and protonation states. A pH-dependent model based on the Nernst equation for aqueous solutions demonstrated a correlation coefficient of 0.93. The calculated Eox values for cytosine epigenetic derivatives in water, accounting for deprotonation effects, follow the trend: d_5caC < 5mC < 5caC < 5hmC < C < 5dhmC < 5fC, where "d_" deprotonated, "5ca" 5-carboxy, "5m" 5-methyl, "5hm" 5-hydroxymethyl, "5dhm" 5-dihydroxymethyl, "5f" 5-formyl.

All-polysaccharide, self-healing, pH-sensitive, in situ-forming hydrogel of carboxymethyl chitosan and aldehyde-functionalized hydroxyethyl cellulose

In situ forming hydrogels are promising for biomedical applications, especially in drug delivery. The precursor solution can be injected at the target site, where it undergoes a sol-gel transition to afford a hydrogel. In this sense, the most significant characteristic of these hydrogels is fast gelation behavior after injection. This study describes an all-polysaccharide, rapidly in situ-forming hydrogel composed of carboxymethyl chitosan (CMCHT) and hydroxyethyl cellulose functionalized with aldehyde groups (HEC-Ald). The HEC-Ald was synthesized through acetal functionalization, followed by acid deprotection. This innovative approach avoids cleavage of pyran rings, as is inherent in the periodate oxidation approach, which is the most common method currently employed for adding aldehyde groups to polysaccharides. The resulting hydrogel exhibited fast stress relaxation, self-healing properties, and pH sensitivity, which allowed it to control the release of an encapsulated model drug in response to the medium pH. Based on the collected data, the HEC-Ald/CMCHT hydrogels show promise as pH-sensitive drug carriers.

Unprecedented reactivity of polyamines with aldehydic DNA modifications: structural determinants of reactivity, characterization and enzymatic stability of adducts

Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3'-tetrahydrofuro[2,3,4-ef]-1,4-diazepane ('ribodiazepane') scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3'-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3' end-blocking DNA lesions.

Intramolecular Proton-Coupled Hydride Transfers with Relatively Low Activation Barriers

We report that bifunctional molecules containing hydroxyl and carbonyl functional groups can undergo an effective transfer hydrogenation via an intramolecular proton-coupled hydride transfer (PCHT) mechanism. In this reaction mechanism, a hydride transfer between two carbon atoms is coupled with a proton transfer between two oxygen atoms via a cyclic bond rearrangement transition structure. The coupled transfer of the two hydrogens as H^δ+ and H^δ- is supported by atomic polar tensor charges. The activation energy for the PCHT reaction is strongly dependent on the length of the alkyl chain between the hydroxyl and carbonyl functional groups but relatively weakly dependent on the functional groups attached to the hydroxyl and carbonyl carbons. We investigate the PCHT reaction mechanism using the Gaussian-4 thermochemical protocol and obtain high activation energy barriers (ΔH^‡₂₉₈) of 210.5-228.3 kJ mol^-1 for chain lengths of one carbon atom and 160.2-163.9 kJ mol^-1 for chain lengths of two carbon atoms. However, for longer chain lengths containing 3-4 carbon atoms, we obtain ΔH^‡₂₉₈ values as low as 101.9 kJ mol^-1. Importantly, the hydride transfer between two carbon atoms proceeds without the need for a catalyst or hydride transfer activating agent. These results indicate that the intramolecular PCHT reaction provides an effective avenue for uncatalyzed, metal-free hydride transfers at ambient temperatures.