A nucleobase-conjugated peptide, derived from HIV-1 Rev, was designed and synthesized. The peptide which contained the cytosine moiety at the L-α-amino acid side chain bound RRE IIB RNA with high affinity. This study demonstrates the potential of nucleobase-conjugated peptides as RNA-binding molecules. The results of this study provide new insights into the design of RNA-binding peptides and their potential applications in biotechnology and medicine.