Universal Enrichment and Sequencing of DNA Modifications Using a Click-Coupled IgG-Protein A/G System

Efficient nucleic acid enrichment is pivotal for deciphering epigenetic modifications and disease biomarkers, yet current methods are constrained by insufficient specificity, poor versatility, and high costs. We developed a universal strategy named "Click-IP-Seq" by leveraging the high-affinity binding between Protein A/G and Fc region of DBCO-modified IgG. This enabled the directional conjugation of DBCO-IgG with any azide-modified nucleic acids via copper-free strain-promoted azide-alkyne cycloaddition (SPAAC) click chemistry, achieving specific capture and enrichment of modified nucleic acids. This method effectively enriches two major DNA modifications, 8-oxo-7,8-dihydroguanine (8-oxo-dG) and 5-hydroxymethylcytosine (5hmC), in model DNA systems. We successfully extended its application to map the genome-wide distribution of 8-oxo-dG in both cultured cells and human tissues. Furthermore, leveraging Click-IP-Seq, we conducted the first comprehensive profiling of 8-oxo-dG distribution and its associated biological functions in human colorectal carcinoma tissues. By repurposing IgG-Protein A/G interactions for DNA modification capture, this work circumvents the conventional reliance on biotin-streptavidin systems for DNA enrichment. Its cost-efficiency and modular design establish it as a viable alternative to biotin-streptavidin methods, offering utility for both fundamental epigenetic research and next-generation molecular diagnostics.