Using RNA to Control the PX-JX2 Sequence-Dependent DNA Device

This PX-JX2 device entails the unusual PX state of DNA.  We found that it was not possible to bind RNA strands to this state, so we were unable to control this device.  To overcome this problem, we developed a 'cover strand' strategy, wherein we made a single strand of DNA to contain the control regions that produce both states of the device.  We then used RNA strands to cover up the one we did not want.  The machine cycle of the device then looks as follows:

This system works perfectly well to produce the states needed for this device.  The device should now be available to respond to RNA produced by transcriptional circuitry.

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