Conformation-dependent lesion bypass of bulky arylamine-dG adducts generated from 2-nitrofluorene in epigenetic sequence contexts.

Sequence context influences structural characteristics and repair of DNA adducts, but there is limited information on how epigenetic modulation affects conformational heterogeneity and bypass of DNA lesions. Lesions derived from the environmental pollutant 2-nitrofluorene have been extensively studied as chemical carcinogenesis models; they adopt a sequence-dependent mix of two significant conformers: major groove binding (B) and base-displaced stacked (S). We report a conformation-dependent bypass of the N-(2'-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene (dG-FAF) lesion in epigenetic sequence contexts (d[5'-CTTCTC#G*NCCTCATTC-3'], where C# is C or 5-methylcytosine (5mC), G* is G or G-FAF, and N is A, T, C or G). FAF-modified sequences with a 3' flanking pyrimidine were better bypassed when the 5' base was 5mC, whereas sequences with a 3' purine exhibited the opposite effect. The conformational basis behind these variations differed; for -CG*C- and -CG*T-, bypass appeared to be inversely correlated with population of the duplex-destabilizing S conformer. On the other hand, the connection between conformation and a decrease in bypass for flanking purines in the 5mC sequences relative to C was more complex. It could be related to the emergence of a disruptive non-S/B conformation. The present work provides novel conformational insight into how 5mC influences the bypass efficiency of bulky DNA damage.

Probing the Interactions of Perfluorocarboxylic Acids of Various Chain Lengths with Human Serum Albumin: Calorimetric and Spectroscopic Investigations.

Despite an exponential increase in PFAS research over the past two decades, the mechanisms behind how PFAS cause adverse health effects are still poorly understood. Protein interactions are considered a significant driver of bioaccumulation and subsequent toxicity from re-exposure; however, most of the available literature is limited to legacy PFAS. We utilized microcalorimetric and spectroscopic methods to systematically investigate the binding between human serum albumin (HSA) and perfluorocarboxylic acids (PFCAs) of varying chain lengths and their nonfluorinated fatty acid (FA) counterparts. The results reveal the optimal chain length for significant PFCA-HSA binding and some fundamental interactions, i.e., the polar carboxylic head of PFCA is countered by ionizable amino acids such as arginine, and the fluorocarbon tails stabilized by hydrophobic residues like leucine and valine. Additionally, fluorine's unique polarizability contributes to PFCA's stronger binding affinities relative to the corresponding fatty acids. Based on these observations, we posit that PFCAs likely bind to HSA in a "cavity-filling" manner, provided they have an appropriate size and shape to accommodate the electrostatic interactions. The results reported herein widen the pool of structural information to explain PFAS bioaccumulation patterns and toxicity and support the development of more accurate computational modeling of protein-PFAS interactions. TOC graphic created with Biorender.com.

Alginate Encapsulation Stabilizes Xylanase Toward the Laccase Mediator System.

Xylanase, a hydrolytic enzyme, is susceptible to inactivation by the oxidative conditions generated by the laccase mediator system (LMS). Given the impetus to develop a mixed enzyme system for application in biomass processing industries, xylanase was encapsulated with either Cu2+- or Ca2+-alginate and then exposed to the LMS with variations such as mediator type, mediator concentration, and treatment pH. Results demonstrate that alginate-encapsulated xylanase retains substantial activity (> 80%) when exposed to the LMS relative to non-encapsulated xylanase. Cu2+-alginate generally provided better protection than Ca2+-alginate for all mediators, and protection was observed even at a low pH, where the LMS is most potent. Despite encapsulation, xylanase was still capable of hydrolyzing its polymeric substrate xylan, given kcat/Km values within an order of magnitude of that for non-encapsulated xylanase. The alginate matrix does not impede the function of the oxidized mediator, since comparable Vmax values were observed for the conversion of veratryl alcohol to veratraldehyde by free and Cu2+-alginate encapsulated laccase. Overall, these results support development of a mixed enzyme system for biomass delignification and, more broadly, show potential for protecting protein function in an oxidative environment.