A fragment‐based approach for the synthesis of ligands of tRNALys3, the HIV reverse‐transcription primer, is described. The use of NMR spectroscopy has proved to be very useful in this approach, not only to detect low‐affinity complexes between small compounds and RNA, but also to provide information on their binding mode and on the way they can be connected. This NMR‐spectroscopy‐guided analysis enabled