Solid-state nanopore detection of partially denatured dsDNA with single-strand binding protein: a preliminary analysis

Abstract

In this work we investigate the use of a nanopore sensor to detect single-strand binding protein (SSB) attached to AT-rich denaturation bubbles in genomic double-stranded (ds) DNA. DNA from the{lambda} bacteriophage was heated in the presence of E. coli SSB at temperatures predicted to open denaturation bubbles near the center of the molecule. A solid state nanopore sensor measured the ionic current as the DNA-SSB solution flowed through the pore, detecting blockades due to the translocation of biomolecules. Large current spikes were observed in the translocating DNA molecules, consistent with SSB binding. However, spikes were largely localized at either end of the DNA molecule, rather than at the predicted sites. We discuss the physico-chemical effects behind this disagreement and prospects for the future use of this technique for genomic mapping.