The supporting materials provide detailed derivations and calculations for the quasi-steady state (QSS) analysis of the branch migration (BM) rate constant in toehold exchange reactions. The QSS assumption is valid when the timescale of intermediate equilibration is much shorter than the overall reaction timescale, which is ensured by fitting parameters to experimental conditions. The BM rate constant is derived using a three-step model, considering the production and consumption of intermediates I and J. The critical concentration for the accuracy of the BM rate constant is calculated, showing that the rate constant overestimates the kinetics when intermediate concentrations are high. The binding energies of the toeholds are calculated using default methods and alternative models, including those from Pyshnyi, NUPACK, and Owczarzy. Matlab scripts are provided for fitting rate constants and generating BM rate constants based on toehold energies. The approximations for the BM rate constant and critical concentration are justified, and a simplified flowchart is presented for estimating these values.The supporting materials provide detailed derivations and calculations for the quasi-steady state (QSS) analysis of the branch migration (BM) rate constant in toehold exchange reactions. The QSS assumption is valid when the timescale of intermediate equilibration is much shorter than the overall reaction timescale, which is ensured by fitting parameters to experimental conditions. The BM rate constant is derived using a three-step model, considering the production and consumption of intermediates I and J. The critical concentration for the accuracy of the BM rate constant is calculated, showing that the rate constant overestimates the kinetics when intermediate concentrations are high. The binding energies of the toeholds are calculated using default methods and alternative models, including those from Pyshnyi, NUPACK, and Owczarzy. Matlab scripts are provided for fitting rate constants and generating BM rate constants based on toehold energies. The approximations for the BM rate constant and critical concentration are justified, and a simplified flowchart is presented for estimating these values.