Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit

• Published in: ACS sensors 2017-08, Vol.2 (8), p.1184-1190
• Main Authors: Bodrenko, Igor V, Wang, Jiajun, Salis, Samuele, Winterhalter, Mathias, Ceccarelli, Matteo
• Format: Article
• Language: English
• ISSN: 2379-3694; 2379-3694
• DOI: 10.1021/acssensors.7b00311

To quantify small molecule penetration into and eventually permeation through nanopores, we applied an improved excess-noise analysis of the ion current fluctuation caused by entering molecules. The kinetic parameters of substrate entry and exit are derived from a two-state Markov model, analyzing the substrate concentration dependence of the average ion current and its variance. Including filter corrections allows one to detect the transition rates beyond the cutoff frequency, f c, of the instrumental ion-current filter. As an application of the method, we performed an analysis of the single-channel ion current of Meropenem, an antibiotic of the carbapenem family, interacting with OmpF, the major general outer membrane channel of Escherichia coli bacteria. At 40 °C we detected the residence time of Meropenem inside OmpF of about 500 nsmore than 2 orders of magnitude smaller than f c –1 and close to the diffusion limit of few hundred nanoseconds. We also have established theoretical limit conditions under which the substrate-induced channel blockages can be detected and suggest that submicrosecond-scale gating kinetic parameters are accessible with existing experimental equipment.