Detection of RNAP-DNA complexes using solid state nanopores

Transcription is the first step in gene expression where DNA is copied into RNA. It is extensively studied at the bulk level especially the regulation mechanism, which in cancerous cells is impaired. We were interested in studying E. coli RNAP enzyme at the single-molecule level for its functional as well as molecular motor properties. With nanopore sensing, we were able to observe RNA polymerase-DNA complexes translocate through nanopores and able to distinguish between individual complexes and bare RNA polymerase. We were also able to observe orientation of RNA polymerase in the nanopore whether flow or electric field predominates. The complexity of the signals from the protein-DNA complexes experiment motivated us to develop level detection software. This software is based on a change detection method called the CUSUM algorithm. OpenNanpore software was designed to analyze in details current blockages in nanopore signals with very little prior knowledge on the signal. With this work one can separate events according to their number of levels and study those sub-populations separately. © 2013 IEEE.