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Table 3 Processes included in the LacI-TetR (LITR) genetic circuit

From: Hypothetical biomolecular probe based on a genetic switch with tunable symmetry and stability

Type of reaction lacI (with Ptet) tetR (with Plac)
Repressor binding \(\text {TetR}_{2} + \mathrm {D}_{l} \underset {q_{t3}}{\overset {k_{t3}}{\rightleftharpoons }} \mathrm {d}_{1}\text {TetR}_{2}\) \(\text {LacI}_{4} + \mathrm {D}_{t} \underset {q_{l3}}{\overset {k_{l3}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}_{4}\)
  \(\mathrm {d}_{1}\text {TetR}_{2} + \mathrm {D}_{l} \underset {q_{t3}}{\overset {k_{t3}}{\rightleftharpoons }} \mathrm {d}_{2}\text {TetR}_{2}\) \(\text {LacI}_{4i} + \mathrm {D}_{t} \underset {q_{l3}}{\overset {0.5k_{l3}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}_{4i}\)
  \(\mathrm {d}_{1}\text {TetR}_{2} + \mathrm {I}_{t} {\overset {k_{t2}}{\rightarrow }} \text {TetR}_{2i} + \mathrm {D}_{l}\) \(\mathrm {d}_{1}\text {LacI}_{4} \underset {q_{l4}}{\overset {200k_{l3}}{\rightleftharpoons }} \mathrm {d}_{2}\text {LacI}_{4}\)
  \(\mathrm {d}_{2}\text {TetR}_{2} + \mathrm {I}_{t} {\overset {k_{t2}}{\rightarrow }} \text {TetR}_{2i} + \mathrm {d}_{1}\text {TetR}_{2}\) \(\mathrm {d}_{1}\text {LacI}_{4i} + \mathrm {I}_{l} {\overset {k_{l5}}{\rightarrow }} \text {LacI}_{4ii} + \mathrm {D}_{t}\)
   \(\mathrm {d}_{1}\text {LacI}_{4} + \mathrm {I}_{l}{\overset {0.5k_{l5}}{\rightarrow }} \text {LacI}_{4i} + \mathrm {D}_{t}\)
   \(\mathrm {d}_{1}\text {LacI}_{4} + \mathrm {I}_{l}\underset {q_{l5}}{\overset {0.5k_{l5}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}_{4i}\)
   \(\mathrm {d}_{2}\text {LacI}_{4} + \mathrm {I}_{l}\underset {q_{l5}}{\overset {k_{l5}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}_{4i}\)
RNAp binding \(\mathrm {D}_{l} + \mathrm {R} \underset {q_{b}}{\overset {k_{b1}}{\rightleftharpoons }} \mathrm {D}^{\mathrm {R}}_{l}\) \(\mathrm {D}_{t} + \mathrm {R} \underset {q_{b}}{\overset {k_{b1}}{\rightleftharpoons }} \mathrm {D}^{\mathrm {R}}_{t}\)
  \(\mathrm {d}_{1}\text {LacI}_{4} + \mathrm {R} \underset {q_{b}}{\overset {k_{lb2}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}^{\mathrm {R}}_{4}\) \(\mathrm {d}_{1}\text {TetR}_{2} + \mathrm {R} \underset {q_{b}}{\overset {k_{tb2}}{\rightleftharpoons }} \mathrm {d}_{2}\text {TetR}^{\mathrm {R}}_{2}\)
  \(\mathrm {d}_{2}\text {LacI}_{4} + \mathrm {R} \underset {q_{b}}{\overset {k_{lb3}}{\rightleftharpoons }} \mathrm {d}_{2}\text {LacI}^{\mathrm {R}}_{4}\) \(\mathrm {d}_{2}\text {TetR}_{2} + \mathrm {R} \underset {q_{b}}{\overset {k_{tb3}}{\rightleftharpoons }} \mathrm {d}_{2}\text {TetR}^{\mathrm {R}}_{2}\)
  \(\mathrm {d}_{1}\text {LacI}_{4i} + \mathrm {R} \underset {q_{b}}{\overset {k_{lb2}}{\rightleftharpoons }} \mathrm {d}_{1}\text {LacI}^{\mathrm {R}}_{4i}\)  
Transcription initiation \(\mathrm {D}^{\mathrm {R}}_{l} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}_{l}\) \(\mathrm {D}^{\mathrm {R}}_{t} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{2} + \mathrm {E}_{t}\)
  \(\mathrm {d}_{1}\text {LacI}^{\mathrm {R}}_{4} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{1} + \mathrm {d}_{1}\text {LacI}_{4}\) \(\mathrm {d}_{2}\text {TetR}^{\mathrm {R}}_{2} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{2} + \mathrm {d}_{2}\text {TetR}_{2}\)
  \(\mathrm {d}_{2}\text {LacI}^{\mathrm {R}}_{4} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{1} + \mathrm {d}_{2}\text {LacI}_{4}\) \(\mathrm {d}_{2}\text {TetR}^{\mathrm {R}}_{2} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{2} + \mathrm {d}_{2}\text {TetR}_{2}\)
  \(\mathrm {d}_{1}\text {LacI}^{\mathrm {R}}_{4i} \overset {\alpha _{i}}{\rightarrow } \mathrm {E}^{1} + \mathrm {d}_{1}\text {LacI}_{4i}\)  
Elongation \(\mathrm {E}_{l} \overset {\alpha _{le}}{\rightarrow } \mathrm {M}_{l} + \mathrm {R} \) \(\mathrm {E}_{t} \overset {\alpha _{te}}{\rightarrow } \mathrm {M}_{t} + \mathrm {R} \)
Translation \(\mathrm {M}_{l} \overset {\alpha _{lt}}{\rightarrow } \text {LacI} + \mathrm {M}_{l} \) \(\mathrm {M}_{t} \overset {\alpha _{tt}}{\rightarrow } \text {TetR} + \mathrm {M}_{t} \)
Dimerization \(\text {LacI} + \text {LacI} \underset {q_{1}}{\overset {k_{1}}{\rightleftharpoons }} \text {LacI}_{2}\) \(\text {TetR} + \text {TetR} \underset {q_{1}}{\overset {k_{1}}{\rightleftharpoons }} \text {TetR}_{2}\)
  \(\text {LacI}_{2} + \text {LacI}_{2} \underset {q_{l2}}{\overset {k_{1}}{\rightleftharpoons }} \text {LacI}_{4}\)  
Repressor Binding \(\text {LacI}_{4} + \mathrm {I}_{l} \underset {q_{l5}}{\overset {k_{l5}}{\rightleftharpoons }} \text {LacI}_{4i}\) \(\text {TetR}_{2} + \mathrm {I}_{t} \underset {q_{t2}}{\overset {k_{t2}}{\rightleftharpoons }} \text {TetR}_{2i}\)
  \(\text {LacI}_{4i} + \mathrm {I}_{l} \underset {q_{l5}}{\overset {k_{l5}}{\rightleftharpoons }} \text {LacI}_{4ii}\) \(\text {TetR}_{2i} + \mathrm {I}_{t} \underset {q_{t2}}{\overset {k_{t2}}{\rightleftharpoons }} \text {TetR}_{2ii}\)
Degradation \(\mathrm {M}_{l} \overset {\gamma _{ml}}{\rightarrow } \oslash \) \(\mathrm {M}_{t} \overset {\gamma _{mt}}{\rightarrow } \oslash \)
  \(\text {LacI} \overset {\gamma _{p}}{\rightarrow } \oslash \) \(\text {TetR} \overset {\gamma _{p}}{\rightarrow } \oslash \)
  \(\text {LacI}_{2} \overset {\gamma _{p}}{\rightarrow } \oslash \) \(\text {TetR}_{2} \overset {\gamma _{p}}{\rightarrow } \oslash \)
  \(\text {LacI}_{4} \overset {\gamma _{p}}{\rightarrow } \oslash \) \(\text {TetR}_{2i} \overset {\gamma _{p}}{\rightarrow } \oslash \)
  \(\text {LacI}_{4i} \overset {\gamma _{p}}{\rightarrow } \oslash \) \(\text {TetR}_{2ii} \overset {\gamma _{p}}{\rightarrow } \oslash \)
  \(\text {LacI}_{4ii} \overset {\gamma _{p}}{\rightarrow } \oslash \)  
  1. The rate constants are written above and below the arrows describing the forward and reverse rate respectively