Recent development of solution-phase molecular-scale Boolean calculations using deoxyribozymes is potentially an important step toward the development of autonomous therapeutic and diagnostic devices. Here, the construction of basic YES, AND, ANDNOT, and ANDANDNOT deoxyribozyme-based logic gates is described. Proto-cols for testing gate activity using fluorescent oligonucleotide probes have been pro-vided, and pointers for gate optimization are included.