Conjugation of DNAs to defined locations on a protein surface will offer powerful tools for positioning functional groups and molecules in biological and biomedical studies. However, tagging protein with DNA is challenging in physiological environments, which requires a bioorthogonal approach. Here we report a chemical solution to selectively conjugate DNA aptamer with a protein by protein-aptamer template (PAT)-directed reactions. Since protein-aptamer interactions are bioorthogonal, we exploit PAT as a unique platform for specific DNA-protein cross-linking. We develop a series of modified oligonucleotides for PAT-directed reactions and screen out F-carboxyl as a suitable functionality for selective and site-specific conjugation. The functionality is incorporated into aptamers by our F-carboxyl phosphoramidite with easy synthesis. We also demonstrate the necessity of a linker between the reactive functionality and the aptamer sequences.