Retroviral integrase is one of the key enzymes needed to integrate viral DNA into a host cell’s genome for many retroviruses including HIV. Integrase’s role is three-fold. It prepares the ends of the DNA so that they can successfully bind to the target genomic DNA via 3’-processing, it creates a complex with the viral DNA that is capable of transporting it into the nucleus, and it facilitates the insertion of the viral DNA into the host genome. The goal of this research is to help determine what sequence and structural characteristics of the viral DNA terminus are responsible for successful integrase binding and 3’-processing. Through the use of polyacrylamide gel electrophoresis (PAGE) and ³²P end labeling, different substrates are introduced to integrase and the effectiveness of the enzyme in binding to the DNA and carrying out 3’-processing is observed. The importance of terminal structural characteristics as well as individual nucleotides are then determined through a combination of PAGE results, modeling, and NMR-based structural comparisons.