Fig. 1: Schematic representation of interception systems.
From: Next generation synthetic memory via intercepting recombinase function
a The decision-making rule is shown as bidirectional between STATE 1 and STATE 2. The representative logical operations in decision-making are BUFFER and NOT logical operations. When the INPUT is absent, the OUTPUT is OFF in BUFFER and ON in NOT operation (STATE 1). When the INPUT is present, the OUTPUT is ON in BUFFER and OFF in NOT operation (STATE 2). Once the INPUT is removed, the OUTPUT state reverts to STATE 1. b The synthetic memory rule is shown as unidirectional between STATE 1 and STATE 2. The representative synthetic memory operations are Gain of Function (GOF) and Loss of Function (LOF). The INPUT and OUTPUT state in synthetic memories are the same as decision-making, however, when the INPUT is removed, the OUTPUT state does not revert back to STATE 1. c, d Two types of recombination events are shown. When attB and attP are aligned, recombination results in deletion of the DNA element between attB and attP (c). When attB and attP are anti-aligned, recombination results in inversion of the DNA element between attB and attP (d). Note: The icon for the recombinase is given as a monomer. e Two types of transcription factors used for interception are shown. The blue box shows the repressor mechanism, and the purple box shows the anti-repressor mechanism. The right panel illustrates the regulatory protein template. This system consists of three parts: a dimeric regulatory core domain (RCD or anti-RCD), alternate DNA recognition (ADR), and DNA operator (ONNN). The RCD can be abbreviated as I, G, S, R, E, or F and the superscript + or A represents the repressor or anti-repressor phenotype, respectively. Each RCD has a cognate inducer shown as a colored hexagon. The ADRs are named via the mutation of amino acid positions 17, 18, and 22. DNA operators are named via nucleotide substitutions at positions 6, 5, and 4 relative to the left half-site of the operator (abbreviated as ON6, N5, N4). Each ADR binds a cognate DNA operator shown color-coded in the bottom-right box. f A schematic showing the seven steps that must be completed following a type-I memory circuit’s induction for recombination to occur. g A schematic showing the four steps that must be completed following a type-II memory circuit’s induction for recombination to occur.
