Enhancing the sensitivity of nanopipette biosensors for protein analysis

Abstract

Background: This paper compares experimental findings and simulation outcomes of single and multiple protein models moving through a nanopipette biosensor. It provides insights into the factors influencing the process and explores their relevance to proteomics. Methods: Nanopipette biosensors were produced by pulling borosilicate glass tubes and treating them with an electron beam. A scanning electron microscope was used to characterize the nanopipettes. The study measured and modeled ionic currents for the elastase-specific inhibitor protein. Simulation models were developed using the finite element method and Poisson–Boltzmann formalism, considering different protein configurations and translocation scenarios. Results: The results showed that the pore current of a nanopipette decreases as the protein approaches the nanopipette. The minimum pore current occurs at the widest part of the protein, and the current increases as the protein progresses through the nanopipette. For multiple protein translocations, the pore current decreases between the widest parts of the first and second proteins, and the lowest current is observed at the broadest part of the second protein. After the third protein, the pore current remains constant. It is also found that the fractional blockade difference, translocation speed, fluctuation in pore current, and dwell time are all affected by the number of proteins translocating through the nanopipette. The fractional blockade difference, the decrease in pore current caused by the protein, increases with the number of proteins while the translocation speed decreases. The fluctuation in pore current and dwell time is also longer for three-protein translocations than for single-protein translocations. Conclusion: This study offers valuable insights into biomolecule transport through nanopipettes, enhances our understanding of protein dynamics in restricted environments, and significantly contributes to single-protein sequencing studies, drug screening, and proteomics.