Aqueous Wittig reaction-mediated fast fluorogenic identification and single-base resolution analysis of 5-formylcytosine in DNA

A disposable electrochemical magnetic immunosensor for the rapid and sensitive detection of 5-formylcytosine and 5-carboxylcytosine in DNA

5-formylcytosine (5 fC) and 5-carboxylcytosine (5caC) serve as key intermediates in DNA demethylation process with significant implications for gene regulation and disease progression. In this study, we introduce a novel electrochemical sensing platform specifically designed for the sensitive and selective detection of 5 fC and 5caC in DNA. Protein A-modified magnetic beads (ProtA-MBs) coupled with specific antibodies facilitate the immunorecognition and enrichment of these modified bases. Signal amplification is achieved through several chemical reactions involving the interaction between N3-kethonaxl and guanine, copper-free click chemistry for the attachment of dibenzocyclooctyne (DBCO)-Biotin, and the subsequent recognition by streptavidin-conjugated horseradish peroxidase (SA-HRP). The assay's readout is performed on a disposable laser-induced graphene (LIG) electrode, modified with the bead-antibody-DNA complex in a magnetic field, and analyzed using differential pulse voltammetry in a system employing hydroquinone (HQ) as the redox mediator and H2O2 as the substrate. This immunosensor displayed excellent sensitivity, with detection limits of 14.8 fM for 5 fC across a 0.1-1000 pM linear range and 87.4 fM for 5caC across a 0.5-5000 pM linear range, and maintained high selectivity even in the presence of interferences from other DNA modifications. Successful application in quantifying 5 fC and 5caC in genomic DNA from cell extracts, with recovery rates between 97.7% to 102.9%, underscores its potential for clinical diagnostics. N3-kethoxal was used for the first time in an electrochemical sensor. This work not only broadens the toolkit for detecting DNA modifications but also provides a fresh impetus for the development of point-of-care testing (POCT) technologies.

Selective Methylation of Nucleosides via an In Situ Generated Methyl Oxonium

A very mild and efficient procedure has been developed for the preparation of N-methylated uridine, pseudouridine, guanosine and inosine derivatives. This process was compatible with free hydroxyls within the ribose and did not require precautions on the protection or deprotection of other functionalities. The key to this extremely mild methylation without protection relied on the in situ generated methyl oxonium from the Wittig reagent and methanol. A putative mechanism for the selective methylation was also proposed.

Investigation of the effect of antibiotics on 5-formylcytosine content in mazie seedling tissues based on photoelectrochemical biosensor

Given the improved photoactivity of Bi₂S₃ by MXene, an article photoelectrochemical biosensor was designed for 5-formyl-2'-deoxycytidine (5fdCTP) detection, where Bi₂S₃: MXene was selected as photoactive material, polydopamine was used as solid electron donor and 5fdCTP capture reagent, calcined ZIF-8(C-ZIF-8) was chosen as the artificial enzyme. With the catalyzed by C-ZIF-8, 4-chloro-1-naphthol was allegro oxidized by H₂O₂ to form the insoluble benzo-4-chlorohexadienone, and then deposited on the surface of the electrode, Resulting in a decrease of the PEC response. Under the optimum conditions, the sensor has a linear range of 0.001-200 nM and a detection limit of 0.51 pM (3σ). The suitability of the developed method was appraised by investigating the effect of antibiotics on 5fdCTP content in the genomic DNA of the roots of maize seedlings. As a new detection platform, the application of this approach can be expanded to investigative the impact of other pollutants on the content of 5fdCTP in plant or animal tissues, explore the feasibility of 5fdCTP as a new indicator for the ecotoxicological effect of pollutants, and the photoelectrochemical method as a new assessment technique for the ecotoxicological effects of pollutants.

Synthesis of Nucleobase-Modified Oligonucleotides by Post-Synthetic Modification in Solution

Oligonucleotides containing modified nucleobases have applications in various technologies. In general, to synthesize oligonucleotides with different nucleobase structures, each modified phosphoramidite monomer needs to be prepared over multiple steps and then introduced onto the oligonucleotides, which is time-consuming and inefficient. Post-synthetic modification is a powerful strategy for preparing many types of modified oligonucleotides, especially nucleobase-modified ones. Depending on the stage of modification, post-synthetic modification can be divided into two stages: "solid-phase modification," wherein an oligonucleotide attaches to the resin, and "solution-phase modification," wherein an oligonucleotide detaches itself from the resin. In this review, we focus on post-synthetic modification in solution for the synthesis of nucleobase-modified oligonucleotides, except the modifications to linkers for conjugation. Moreover, the reactions are summarized for each modified position of the nucleobases.