Figure 5
From: Quantitative polymerase chain reaction analysis by deconvolution of internal standard
Geometric model explanation for the differing values of Ψ and E. If two sample amplifications are exponential with the same constant efficiency, then Ψ = E because the dilution factor (segment DA) and cycle spacing Δc q (segment EC) predict the slopes in the trapezoidal figure. However, if the efficiencies drop steadily with cycle number (solid lines) then dilution can result in an increase in geometric mean efficiency (AC has a greater slope than DE). Note that Ψ = 1.87 is established and preserved after 7 cycles, as the spacing DB = EC, and overestimates both E DE = 1.70 and E AC = 1.74. The modelled synthesis of product is determined by a recursive function A n = A n-1 (1 + α n X n ) where A n represents the concentration of two complementary strands at the end of cycle n, α n = K A (P n-1 )2/(1 + K A (P n-1 )2) is the primer-annealed fraction and X n = log10(A n-1 )/(log10(A n-1 ) + I1/2) is the fraction extended by polymerase. P n is the concentration of each primer at the end of cycle n (assumed to be consumed at the same rate, and initiated with P 0 = 2.5 pmoles), K A = 50 pmole-2 is an annealing constant, I1/2 = -1 is an inhibition constant, and the reaction volume unit arbitrarily set to 1. A and D on the ordinate axis represent log10(A 0 ) = -7.778 (104 copies) and log10(A 0 ) = -5.778 (106 copies), respectively, and the threshold line EC has log10(A n ) = -0.5 (1.9 × 1011 copies).