Ionic Permeability and Mechanical Properties of DNA Origami Nanoplates on Solid-State Nanopores

Abstract

While DNA origami is a popular and versatile platform, its structural properties are still poorly understood. In this study we use solid-state nanopores to investigate the ionic permeability and mechanical properties of DNA origami nanoplates. DNA origami nanoplates of various designs are docked onto solid-state nanopores where we subsequently measure their ionic conductance. The ionic permeability is found to be high for all origami nanoplates. We observe the conductance of docked nanoplates, relative to the bare nanopore conductance, to increase as a function of pore diameter, as well as to increase upon lowering the ionic strength. The honeycomb lattice nanoplate is found to have slightly better overall performance over other plate designs. After docking, we often observe spontaneous discrete jumps in the current, a process which can be attributed to mechanical buckling. All nanoplates show a non-linear current-voltage dependence with a lower conductance at higher applied voltages, which we attribute to a physical bending deformation of the nanoplates under the applied force. At sufficiently high voltage (force), the nanoplates are strongly deformed and can be pulled through the nanopore. These data show that DNA origami nanoplates are typically very permeable to ions and exhibit a number of unexpected mechanical properties which are interesting in their own right, but also need to be considered in the future design of DNA origami nanostructures. KeywordsDNA origami; nanopore; ionic permeability; mechanical properties Solid-state-nanopore research 1, 2 is an area which has been gaining much attention due to its potential applications in sequencing, biosensing, and as a tool for biophysics. In this technique an electric field is applied across a membrane containing a single pore. Charged molecules such as DNA experience an electrophoretic force which pulls them through the pore. Molecules are detected by the temporary reduction (or increase at low salt) in the ionic current which they cause as they pass through the pore. Despite recent advances 1, 2 in solid-* Corresponding author.c.dekker@tudelft.nl.

Graphene nanodevices for DNA sequencing

“…Such protein-graphene hybrids or DNA origami-graphene structures [122][123][124] could provide means to control the motion of DNA molecules. Yet another alternative is to use plasmonics to control a DNA molecule in a nanopore [125,126].…”

Transport mechanisms in nanopores and nanochannels: can we mimic nature?

“…Recent work by the Keyser [75] and Dekker [76] groups shows interesting voltage-dependent conductivity changes in nanopores modified by DNA-origamis (a DNA-origami is a nanostructure created by directed folding of DNA). For example, DNA-origami caps bearing a central aperture and dangling tails were trapped at the entrance of a glass nanopore under a positive applied potential bias.…”

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami‐induced local destruction of silicon dioxide

“…The exact positioning of DNA origamis further enables a nanoscale platform, e.g., for examining single--molecule level reactions [21] or translocations of molecules [19,20]. In addition, studying mechanical [22] and electrical [22,23] properties of single DNA origamis becomes possible when the structures are precisely integrated into the measurement setup.…”

“…We used two straight brick--like shapes stacked either in square--(SQL) [33] or honeycomb lattice (HCL) [3] of DNA helices, and two other structures having either a curved 'C'--shape or an angular 'L'--shape in honeycomb lattice (HCL). Previous work has revealed that 2D and 3D origamis can be substantially deformed under high electric fields [18,22]. For this reason, we examined the influence of the trapping force (electric field gradient) on the structural deformation of the origamis and tuned the trapping parameters accordingly.…”