Determining Molecular Structure Using Nanopores

Abstract

RNA molecules contain sequence-dependent secondary structures that yield specific biological functions.One approach to study RNA structure employs optical tweezers in which individual RNA molecules, tethered between micrometer-sized particles, are progressively pulled apart.Since folded regions unzip in order of increasing stability, the shortcoming of this approach is that the readout does not yield the location of the unfolding regions, rendering reconstruction of the secondary structure cumbersome if not impossible. Another approach is pulling RNA molecules through nanopores, which reports on molecular structure through parameters as current blockade and translocation time.We propose to integrate these two approaches to measure the secondary structure of RNA. This integrated approach allows one to sequentially unfold the molecule and simultaneously measure the position and stability of the unfolding regions. As a proof of concept, we will measure the unfolding of a single RNA hairpin as shown in the adjacent figure. This new approach fills the gap in currently available techniques and provides a more straightforward determination of molecular secondary (and potentially tertiary) structure. Results of such measurements will be an important step forward in solving the outstanding RNA folding problem and understanding the shape-dependent function of RNA molecules.View Large Image | View Hi-Res Image | Download PowerPoint Slide