Biophysics of Polynucleotide Interactions with OmpF Nanopore Forming Protein, Possible Tool for DNA Sequencing

Abstract

OmpF ion channel porin is a water filled trimer found in the outer membrane of Escherichia coli. The crystal structure of channel shows constriction zone with a diameter of about 0.6 nm halfway down the nanopore barrel. In this study, single molecule OmpF protein was reconstituted into artificial bilayer and it's channel activity was investigated by means of voltage clamp technique. The results showed that the presence of polynucleotides caused different pattern of ion current and gating in the channel at different potential differences and polarities. It seams due to the effect of the applied pd on the amino acids side chain in the channel lumen, the potential gradient and it's direction play vital role in producing unique signature for certain polynucleotides. The current pattern could not directly be related to each strand by single factor analysis and different approaches and variants should be applied simultaneously to distinguish polynucleotides from each other. Although we restricted our studies to 10 nucleotide strands, results indicate that it can well be applied to longer ones. Furthermore, it was found that introduced polyT, polyG, polyC to the cis side at micro molar range have more effect than lower ones. Further to the investigation of polynucleotide effect with nano channel, we hope to use the result of the current study to address gene trans-location into bacteria.