To solve problems with DNA in microreactors, static systems are not favourable due to programmability. It will be shown that solving Boolean logic with a programmable microfluidic system is a step forward in molecular computing. Not only the use of DNA as information carrier is important but also the integration of electronic computing to control the system and readouts. This paper will show that the optimal configuration of computing in microfluidics is a system containing components analogue with electronic elementary building blocks components, such as switches, logic gates and memory, making it programmable for any type of Boolean problem.