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Table 1 Processes included in the HOM2 genetic circuit description

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

Type of reaction Gene 1 Gene 2
Repressor binding \(\mathrm {D}^{1}_{00} + \mathrm {P}^{2}_{2} \underset {q_{12}}{\overset {k_{12}}{\rightleftharpoons }} \mathrm {D}^{1}_{10}\) \(\mathrm {D}^{2}_{00} + \mathrm {P}^{1}_{2} \underset {q_{22}}{\overset {k_{22}}{\rightleftharpoons }} \mathrm {D}^{2}_{10}\)
  \(\mathrm {D}^{1}_{10} + \mathrm {P}^{2}_{2} \underset {q_{14}}{\overset {k_{14}}{\rightleftharpoons }} \mathrm {D}^{1}_{20}\) \(\mathrm {D}^{2}_{10} + {P^{1}_{2}} \underset {q_{24}}{\overset {k_{24}}{\rightleftharpoons }} \mathrm {D}^{2}_{20}\)
RNAp binding \(\mathrm {D}^{1}_{00} + \mathrm {R} \underset {q_{13}}{\overset {k_{13}}{\rightleftharpoons }} \mathrm {D}^{1}_{01}\) \(\mathrm {D}^{2}_{00} + \mathrm {R} \underset {q_{23}}{\overset {k_{23}}{\rightleftharpoons }} \mathrm {D}^{2}_{01}\)
  \(\mathrm {D}^{1}_{10} + \mathrm {R} \underset {q_{15}}{\overset {k_{15}}{\rightleftharpoons }} \mathrm {D}^{1}_{11}\) \(\mathrm {D}^{2}_{10} + \mathrm {R} \underset {q_{25}}{\overset {k_{25}}{\rightleftharpoons }} \mathrm {D}^{2}_{11}\)
  \(\mathrm {D}^{1}_{20} + \mathrm {R} \underset {q_{17}}{\overset {k_{17}}{\rightleftharpoons }} \mathrm {D}^{1}_{21}\) \(\mathrm {D}^{2}_{20} + \mathrm {R} \underset {q_{27}}{\overset {k_{27}}{\rightleftharpoons }} \mathrm {D}^{2}_{21}\)
Transcription initiation \(\mathrm {D}^{1}_{01} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{00}\) \(\mathrm {D}^{2}_{01} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{00}\)
  \(\mathrm {D}^{1}_{11} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{10}\) \(\mathrm {D}^{2}_{11} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{10}\)
  \(\mathrm {D}^{1}_{21} \overset {\alpha _{1m}}{\rightarrow } \mathrm {E}^{1} + \mathrm {D}^{1}_{20}\) \(\mathrm {D}^{2}_{21} \overset {\alpha _{2m}}{\rightarrow } \mathrm {E}^{2} + \mathrm {D}^{2}_{20}\)
Elongation \(\mathrm {E}^{1} \overset {\alpha _{1m}^{\prime }}{\rightarrow } \mathrm {M}^{1} + \mathrm {R} \) \(\mathrm {E}^{2} \overset {\alpha _{2m}^{\prime }}{\rightarrow } \mathrm {M}^{2} + \mathrm {R} \)
Translation \(\mathrm {M}^{1} \overset {\alpha _{1p}}{\rightarrow } \mathrm {P}^{1} + \mathrm {M}^{1} \) \(\mathrm {M}^{2} \overset {\alpha _{2p}}{\rightarrow } \mathrm {P}^{2} + \mathrm {M}^{2} \)
Dimerization \(\mathrm {P}^{1} + \mathrm {P}^{1} \underset {q_{11}}{\overset {k_{11}}{\rightleftharpoons }} \mathrm {P}^{1}_{2}\) \(\mathrm {P}^{2} + \mathrm {P}^{2} \underset {q_{21}}{\overset {k_{21}}{\rightleftharpoons }} \mathrm {P}^{2}_{2}\)
Degradation \(\mathrm {M}^{1} \overset {\gamma _{1m}}{\rightarrow } \oslash \) \(\mathrm {M}^{2} \overset {\gamma _{2m}}{\rightarrow } \oslash \)
  \(\mathrm {P}^{1} \overset {\gamma _{1p}}{\rightarrow } \oslash \) \(\mathrm {P}^{2} \overset {\gamma _{2p}}{\rightarrow } \oslash \)
  \(\mathrm {P}^{1}_{2} \overset {\gamma _{1p}/\sigma _{1}}{\rightarrow } \oslash \) \(\mathrm {P}^{2}_{2} \overset {\gamma _{2p}/\sigma _{2}}{\rightarrow } \oslash \)
  1. In the first column, the reaction class is described in words. The reaction rates are written above or below the arrows describing the forward and reverse rate respectively