Quantitative Description of Polyethylene Glycol in an Alpha-Hemolysin Pore

Abstract

We present a theoretical framework that guides the interpretation of experimental nanopore data with broad applications in single molecule sensing. Poly-ethylene glycol (PEG) in particular, is important since it can be used as a surrogate for detecting nucleotides when sequencing DNA (2012, Nature Scientific Reports, 2:684). Here, all atom molecular dynamics (MD) simulations are used to refine the model of Reiner et al. (2010, PNAS 107(27):12080) to characterize the interactions of PEG with an alpha hemolysin (αHL) nanopore. The model, in which PEG is represented as a uniformly charged cylinder, yields two key quantities that are compared with experiment: the ratio of ionic current across the pore due to the presence of PEG over the open channel value (blockade depth), and the residence time. The model assumes that these quantities cannot be described by the volume occupied by PEG inside the pore alone, but must also include complexes formed by PEG with cations. MD simulations are used to test this assumption and refine parameters in the model that are otherwise difficult to measure directly, such as the volume occupied by PEG inside the pore and the local concentration of electrolyte, found to be approximately half the bulk value. MD simulations are also used to test a central hypothesis in the theoretical model that PEG complexes cations to acquire a net positive charge. We confirm that this is indeed the case and that five PEG subunits participate in forming crown-ether like sub-structures with a single cation. The refined theoretical model is then fit to blockade depth and residence time values measured experimentally as a function of PEG size (varying from 1000 g/mol to 2000 g/mol). We find that the theoretical predictions of the model agree quantitatively with experiment thereby validating its assumptions.