Besides generating novel binding peptides or small molecules to their RNA target, successful design of chemically modified RNA constructs capable of tighter binding with their binding peptides is also of significant importance. Herein, the synthesis and binding studies of a series of both wt and mutant bovine immunodeficiency virus (BIV) TAR RNA constructs against its Tat peptide are reported. Understanding the requirements that enable RNA construct binding properties, especially at the hairpin loop or internal bulge, would afford potential therapeutic approaches to control the BIV life cycle.