pH-mediated regulation of polymer transport through SiN pores

¹ Department of Physics, Bilkent University - Ankara 06800, Turkey
² QTF Centre of Excellence, Department of Applied Physics, Aalto University - FI-00076 Aalto, Finland
³ Department of Applied Physics and QTF Center of Excellence, Aalto University School of Science P.O. Box 11000, FI-00076 Aalto, Espoo, Finland
⁴ Interdisciplinary Centre for Mathematical Modelling and Department of Mathematical Sciences, Loughborough University - Loughborough, Leicestershire LE11 3TU, UK

^(a) buyukdagli@fen.bilkent.edu.tr
^(b) Tapio.Ala-Nissila@aalto.fi

Received: 9 June 2018
Accepted: 11 August 2018

Abstract

We characterize the pH-controlled polymer capture and transport through silicon nitride (SiN) pores subject to protonation. A charge regulation model able to reproduce the experimental zeta potential of SiN pores is coupled with electrohydrodynamic polymer transport equations. The formalism can quantitatively explain the experimentally observed non-monotonic pH dependence of avidin conductivity in terms of the interplay between the electroosmotic and electrophoretic drag forces on the protein. We also scrutinize the DNA conductivity of SiN pores. We show that in the low-pH regime where the amphoteric pore is cationic, DNA-pore attraction acts as an electrostatic trap. This provides a favorable condition for fast polymer capture and extended translocation required for accurate polymer sequencing.