Large-Conductance Transmembrane Porin Made from DNA Origami

Kerstin Göpfrich*, Chen-Yu Li*, Maria Ricci, Satya Prathyusha Bhamidimarri, Jejoong Yoo, Bertalan Gyenes, Alexander Ohmann, Mathias Winterhalter, Aleksei Aksimentiev, and Ulrich F. Keyser
ACS Nano 10(9) 8207-8214 (2016)
DOI:10.1021/acsnano.6b03759  BibTex

DNA nanotechnology allows for the creation of three-dimensional structures at nanometer scale. Here, we use DNA to build the largest synthetic pore in a lipid membrane to date, approaching the dimensions of the nuclear pore complex and increasing the pore-area and the conductance tenfold compared to previous man-made channels. In our design, nineteen cholesterol-tags anchor a megadalton funnel-shaped DNA origami porin in a lipid bilayer membrane (see equilibration trajectory, require login to nanoHUB). Confocal imaging and ionic current recordings reveal spontaneous insertion of the DNA porin into the lipid membrane, creating a transmembrane pore of tens of nanosiemens conductance (see ionic current trajectory). All-atom molecular dynamics simulations characterize the conductance mechanism at the atomic level and independently confirm the DNA porins' large ionic conductance.

Molecular dynamics simulation of DNA origami porin in a lipid bilayer membrane. The DNA strands are shown in blue and yellow; the cholesterol groups are shown in gray. The lipid bilayer membrane is drawn as a green molecular surface. The slide bar at the lower right corner indicates the progression of the trajectory in nanoseconds (ns). The first 32 ns illustrate the equilibration trajectory, which is followed by a simulation at a +100 mV bias. At the beginning of the movie, a static rendering of the system is rotated to show the overall structure. The second stage of the movie illustrates the structural fluctuations during the equilibration; lipid molecules facing the viewer are hidden for clarity. In the last stage of the movie, the half of the DNA origami porin facing the viewer is removed and the transmembrane region of the channel is enlarged to illustrate the ion transport. Red spheres show instantaneous locations of potassium ions. For clarity, only those potassium ions that contribute significantly to the transmembrane ionic current (about 10% of all ions) are shown.