The switch consists of a medium-strength constitutive promoter (BBa_J23118) flanked by PhiC31 attP and attB sites. PhiC31 integrase (BBa_K1039012) recombines PhiC31 attP and attB to form PhiC31 attR and attL, flipping the orientation of the promoter and the promoter’s direction of transcription. “Flipping” of the switch by PhiC31 integrase (BBa_K1039012) forms the “RL” state of the switch (BBa_K1039011).
Recombination of att sites affords the switch two potential states, with the promoter driving transcription of different genes depending on the state. The two states are described as “PB state” and “RL state”, in reference to the PhiC31 att sites flanking the promoter in each state.
There is a terminator (BBa_J61048) upstream of the promoter to prevent transcription of genes that correspond to the opposite state of the switch.
In this state (PB state), genes on the prefix side of the switch are expressed. Note that these genes must be inverted relative to the BioBrick convention, i.e. they are transcribed from suffix to prefix, rather than prefix to suffix.
In the RL state (BBa_K1039011), genes on the suffix side of the switch are expressed. These genes are oriented in accordance with the BioBrick convention, i.e. they are transcribed from prefix to suffix.
This state (PB state) is recovered from RL state (BBa_K1039011) in the presence of PhiC31 integrase and PhiC31 recombination directionality factor (RDF) (BBa_K1039012 and BBa_K1039013) through recombination of PhiC31 attR and attL, which forms PhiC31 attP and attB.
In summary, PB state is flipped to RL state in the presence of PhiC31 integrase, and RL state is flipped to PB state in the presence of PhiC31 integrase and RDF.
In the absence of integrase or integrase and RDF, the switch will hold its state. In this way, it is a passive digital memory device.
All aspects of this switch are directly inspired by the switch developed by Groth et al., 2004. Spacer sequences between genetic elements are also taken directly from the work of Groth et al.
Note that there is an NheI site on the prefix side of the switch before the attP site. This was placed there as part of an early design of our switch, but does not contribute to functionality.