Fig. 1.

DNA toolbox uses DNA templates to shape reaction networks performed by a set of three enzymes. (A) Templates (bottom strands) have an input site (3′) and an output site (5′) and receive signal molecules (upper strands). When an input (α) hybridizes to a template, it is elongated by a DNA polymerase (pol.). Inputs bear the recognition site (gray) of a nicking enzyme (nick.) that cuts the elongated upper strand between input and output. Input α and output x then dissociate and are free to start another reaction or to be degraded by a single-strand specific exonuclease (exo.). Following this scheme, three types of modules can be obtained depending on the output sites of the template. (B) Nucleobase quenching on the dye-labeled templates allows sequence-specific monitoring of the reactions.