Theoretical investigation of enzymatic hydrolysis of polypeptides in nanofluidic channels

Label-free detection of enzymes using nanofluidic channels requires enzymes to diffuse into a nanochannel and react with substrates already immobilized on the nanochannel surfaces. A theoretical model is necessary to predict the reaction progress in the confined space and translate it to the electrical readouts of the nanochannel. In this paper, enzymatic hydrolysis of polypeptides in nanofluidic channels is considered and a 1-D model is developed that accounts for various reaction kinetics, enzyme diffusion and non-specific adsorption. The polypeptides have multiple cleavage sites which can be cleaved in different orders depending on the type of enzyme. Here it is shown that this process creates two types of reaction fronts inside the nanochannel which advance linearly with time once they are fully developed. Such constant reaction rates can be predicted by an analytical model. The numerical simulations are validated against the experimental results of trypsin–polylysine reaction in nanochannels, and a good agreement between the two is observed. This study deepens our understandings of enzymatic reactions in nanoscale-confined spaces and can guide the development of a fast-response, label-free enzyme sensor based on nanochannels.