A simple thermodynamic model, which is capable of quantitatively describing the kinetics of strand displacement reactions in the presence of base-pair mismatches, using a minimal set of parameters.
solves first passage model for:
- single invader mismatches
- double invader mismatches
- single incumbent mismatches
- mismatch position
- toehold length
- displacement length
- energy parameters dGBP,dGp,dGBM,dGassoc,dGMM
- branch migration rate
- concentration
- mismatch mode (single/double invader, single incumbent)
- optional second mismatch
- optional second toehold (handle with care)
- output option
if output = 1 (preset)
- inverse of mean first passage time
if output = 2:
- inverse of mean first passage time
- first order rate constant
- second order rate constant
- threshold concentration
if output = 3:
- k1 forward (second order rate constant for toehold binding)
- k1 backward (first order rate constant for toehold unbinding)
- k2 (first order rate constant for full displacement)
calculates mean-first-passage-time and plots mismatch position dependence for:
- single invader-target mismatches
- double invader-target mismatches
- single incumbent-target mismatches
uses measured data to perform a fit for:
- energy parameters
- branch migration rate constant
compares measured data to a prediction using the parameters obtained in 02 for:
- incumbent-target mismatches
- double invader-target mismatches
The overall rate constant is seprated into a second- and a first-order contribution:
- concentration dependence
The overall rate constant is seprated into three rate constants to set up a system of ordinary differential equations:
- pulse generation using a DNA network
Irmisch, P.; Ouldridge, T. E.; Seidel, R. Modeling DNA-Strand Displacement Reactions in the Presence of Base-Pair Mismatches. J. Am. Chem. Soc. 2020, 142, 11451−11463. https://doi.org/10.1021/jacs.0c03105