Selective Chemical Labeling and Sequencing of 5-Carboxylcytosine in DNA at Single-Base Resolution

Probe-labeled electrochemical approach for highly selective detection of 5-carboxycytosine in DNA

5-carboxycytosine (5caC) plays a critical role as an intermediate form in DNA methylation and demethylation processes. Its distribution and quantity significantly influence the dynamic equilibrium of these processes, thereby impacting the normal physiological activities of organisms. However, the analysis of 5caC presents a significant challenge due to its low abundance in the genome, making it almost undetectable in most tissues. In response to this challenge, we propose a selective method for 5caC detection using differential pulse voltammetry (DPV) at glassy carbon electrode (GCE), hinging on probe labeling. The probe molecule Biotin LC-Hydrazide was introduced into the target base and the labeled DNA was immobilized onto the electrode surface with the help of T4 polynucleotide kinase (T4 PNK). Leveraging the precise and efficient recognition of streptavidin and biotin, streptavidin-horseradish peroxidase (SA-HRP) on the surface of the electrode catalyzed a redox reaction involving hydroquinone and hydrogen peroxide, resulting in an amplified current signal. This procedure allowed us to quantitatively detect 5caC based on variations in current signals. This method demonstrated good linearity ranging from 0.01 to 100 nM with a detection limit as low as 7.9 pM. We have successfully applied it to evaluate the 5caC levels in complex biological samples. The probe labeling contributes to a high selectivity for 5caC detection, while the sulfhydryl modification via T4 PNK efficiently circumvents the limitation of specific sequences. Encouragingly, no reports have been made about electrochemical methods for detecting 5caC in DNA, suggesting that our method offers a promising alternative for 5caC detection in clinical samples.

Base Modifications of Nucleosides via the Use of Peptide-Coupling Agents, and Beyond

Several naturally occurring purine and pyrimidine nucleosides contain an amide linkage as part of the heterocyclic aglycone. Enolization of the amide and conversion to leaving groups at the amide carbon atom permits base modification by addition-elimination types of processes. Although a number of methods have been developed over the years for accomplishing such conversions, the present Personal Account describes efforts from the Lakshman laboratories. Facile activation of the amido groups in nucleobases can be achieved with peptide-coupling agents. Subsequent reaction with nucleophiles then accomplishes the base modifications. In many cases, the activation and displacement steps can be done as two-step, one-pot processes, whereas in other cases, discrete storable activated nucleosides can be isolated for subsequent displacement reactions. Using such an approach a wide range of nucleoside base modifications is readily achievable. In many instances, mechanistic investigations have been conducted so as to understand the activation process.

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.