Oligonucleotide structures analysis using a single alpha hemolysin nanopore

The use of nanopores as a micromanipulation technique is a promissing approach to handle untethered single oligonucleotides. In our lab we try to use theses alpha-hemolysins nanopores as a way to sequentially open stem loop structures of ssDNA or ssRNA in order to understand the principles of the unzipping processes in confined geometry or shearing modes.

In combination with fluorescence detection we use the nanopore as a way to detect the cotranscriptional folding of RNA structure as they emerge from the pore lumen. The RNA structure unzips on one side and rezips on the other side of the nanopore. FRET pairs could be used to study the interchange between theses structures.