In protein engineering, researchers have extensively explored the incorporation of nonprotein entities into proteins to extend their functionalities to various applications; however, achieving precise modifications of proteins is still challenging. This study demonstrates epitope- and moiety-selective conjugation of nonengineered proteins by integrating "slow-reactive and hydrolysis-resistant" deoxyoxanosine (dOxa) into a "target- and epitope-selective" aptamer. The amine-reactive dOxa-containing aptamers are dominantly single-lysine-selective at recognition sites, achieving significantly high conjugation yields with remarkably low off-target reactions in complex environments under near-physiological conditions through a catalyst-free, one-pot reaction. When stoichiometrically controlled protein-DNA conjugates are efficiently produced for various proteins, high conjugation selectivity enables semipermanent regulation of enzymatic functions, targeted labeling in a protein mixture, and even heterofunctionalization of a single protein. As our dOxa-containing aptamers selectively react with the recognition sites of target proteins among nontargets, we demonstrate bioorthogonal labeling of live-cell surface nucleolin and PTK7 in amine-rich cell media, displaying their distinct distributions. Aptamer-guided dOxa positioning offers a promising strategy for site-specific modification of native proteins in complex environments, opening new avenues for the synergistic collaboration between nucleic acids and proteins.