In vitro implementation of a stack data structure based on DNA strand displacement

DNA computing represents an excellent way to organise at a scalable level the design of molecular devices made of nucleic acids. Our work is an example of computation at the molecular scale using a core mechanism known as nucleic-acid "strand displacement cascades" to engineer an in vitro signal recorder based on DNA. The signal recorder implements a stack data structure in which both data as well as operators are represented by single stranded DNA "bricks". The stack grows by adding push and write bricks and shrinks in last-in-first-out manner by adding pop and read bricks. The design of the signal recorder has been optimised using an evolutionary algorithm tailored to optimising nucleic acid sequences that predictively fold into our desired target structures. The device mode of operations have been experimentally tested and imaged via a transmission electron microscopy that demonstrate the capability of the device to store and later release several successive signals.