Research at the interface between chemistry and cybernetics has led to reports of ‘programmable molecules’, but what does it mean to say ‘we programmed a set of solution-phase molecules to do X’? A survey of recently implemented solution-phase circuitry indicates that this statement could be replaced with ‘we pre-mixed a set of molecules to do X and functional subsets of X’. These hard-wired mixtures are then exposed to a set of molecular inputs, which can be interpreted as being keyed to human moves in a game, or as assertions of logical propositions. In nucleic acids-based systems, stemming from DNA computation, these inputs can be seen as generic oligonucleotides. Here, we report using reconfigurable nucleic acid catalyst-based units to build a multipurpose reprogrammable molecular automaton that goes beyond single-purpose ‘hard-wired’ molecular automata. The automaton covers all possible responses to two consecutive sets of four inputs (such as four first and four second moves for a generic set of trivial two-player two-move games). This is a model system for more general molecular field programmable gate array (FPGA)-like devices that can be programmed by example, which means that the operator need not have any knowledge of molecular computing methods.