Base pairing is a fundamental structural and functional property that allows the storage and propagation of genetic information by the exploitation of two types of pairing rules: A pairs with T, and G pairs with C. Although nature has confined itself to a four-letter code, synthetic base pairs that pair with each other and not with naturally occurring building blocks (i.e., A, G, C, and T) can expand our genetic repertoire. This is important because such designs can be used in a variety of applications ranging from the development of new synthetic biological systems to new diagnostic agents. Contingent on their wider application is the inherent need to understand not only how synthetic genetic systems pair with each other but also how they mispair with naturally occurring nucleotides. This article describes how an established synthetic genetic system can mispair with a naturally occurring nucleotide.