Identification and quantification of small organic molecules capable of binding to a protein of interest with reasonable affinity and specificity is a central problem. Via developing DNA-encoded recognizing probe, we validate a proof-of-principle for constructing of small target-to-DNA conversion that screens the small molecule-protein interaction. Successful identification of β-indole acetic acid, abscisic acid, or 2,4-dichlorophenoxyacetic acid/corresponding antibody binding implies its fascinating potential for interrogating small molecule/protein interaction.