A Geometrical Allosteric DNA Switch

Abstract

AbstractUsing the programmable interactions of DNA, it is possible to design small circuits capable of processing information [1, 2, 3]. Such DNA circuits may be constituted of logic gates [4,5] connected by signal restoration modules [6]. In most DNA logic gates, the sequences of the output and input strands are not independent. Sequence modification of a gate input must be passed on to the output. As this output is usually the input of another downstream gate, this interdependence of input and output greatly limits the scalability of circuits. In order to implement higher-order programming language [7], uncoupling inputs and outputs will be essential. Here we show how geometry can be leveraged to uncouple inputs and outputs in DNA gates. Building on a mechanism recently introduced, the remote toehold [8], we have constructed and tested a robust YES gate whose input and output are unrelated in sequence.KeywordsLogic GateSequence ModificationProgrammable InteractionGate InputNature BiotechnologyThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.