Team:Kyoto/Hunger/modeling

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Hunger Modeling

We get this new equation for measuring RPU.

Kyoto kiga eqn2.png

derivation

RPU is defined as follows.

Kyoto kiga eqn1.png
(1)

PoPS (Polymerase Per Second) is the unit of absolute “promoter activity”. It is defined as the number of RNA polymerase molecules that pass by the final base pair of the promoter and continue along DNA as an elongation complex.

Kyoto kiga eqn3.png
(2)

Where:

  • [mRNA] is the concentration of mRNA,
  • γ is the mRNA degradation rate,
  • n is the copy number of the plasmid containing the promoter

Following equations related to promoterφ and J23101 are derived because d[mRNA]/dt = 0.

Kyoto kiga eqn4.png
(3)
Kyoto kiga eqn5.png
(4)

If the test promoter φ and the reference standard promoter are measured under the same culture conditions and both promoters are carried on the same backbone plasmid, following equations are approved.

Kyoto kiga eqn6.png
(5)
Kyoto kiga eqn7.png
(6)

Equation(3) divided by (4) is (7) .

Kyoto kiga eqn8.png
(7)

We can reduce (7) because of (5) and (6) and use (1). Then we get this equation.

Kyoto kiga eqn2.png
(8)

So, we can calculate RPU with this equation.


Reference

[1] J. R. Kelly et al., “Measuring the activity of BioBrick promoters using an in vivo reference standard.,” Journal of biological engineering, vol. 3, p. 4, Jan. 2009.