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Table 1 Chemical Reactions for IκBα/NFκB regulatory circuit with NFκB synthetic decoy ODNs. The parameters of the feedback cycle originate from the work of Hoffmann et al. [20] while the ranges of values for specific binding/unbinding rates come from binding microarray data [26] and in vitro kinetic measurements [24, 51]

From: Modeling the therapeutic efficacy of NFκB synthetic decoy oligodeoxynucleotides (ODNs)

Reactions Rate coeff Values
D U +N n D B k don 10 μM−1min−1
D B D U +N n k doff \(\sim LogNormal (\Delta \hat {G}, \sigma ^{2})\)
AD U +N n AD B k son 10 μM−1min−1
AD B AD U +N n k soff [0.02−1] min−1
AD U λ s [0−0.02] min−1
AD B λ s [0−0.02] min−1
OFF+N n ON k on 10 μM−1min−1
ONOFF+N n k off 1 min−1
D B +I n D U +NI n k s [0−10] μM−1min−1
ON+I n OFF+NI n k s [0−10] μM−1min−1
AD B +I n AD U +NI n k s [0−10] μM−1min−1
ONON+mRNA k tr 1.03 μMmin−1
mRNAmRNA+I c k tl 0.2448 min−1
mRNA k d 0.017 min−1
I c I n k in 0.018 min−1
I n I c k out 0.012 min−1
N c N n k Nin 5.4 min−1
N c +I c NI c k f 30 μM−1min−1
NI c N c +I c k b 0.03 min−1
N n +I n NI n k fn 30 μM−1min−1
NI n N n +I n k bn 0.03 min−1
NI c N c α [0.10−0.55] min−1
NI n NI c k NIout 0.83 min−1