Gating-like Motions and Wall Porosity in a DNA Nanopore Scaffold Revealed by Molecular Simulations

Abstract

Recently developed synthetic membrane pores composed of folded DNA enrich the current range of natural and engineered protein pores and of nonbiogenic channels. Here we report all-atom molecular dynamics simulations of a DNA nanotube (DNT) pore scaffold to gain fundamental insight into its atomic structure, dynamics, and interactions with ions and water. Our multiple simulations of models of DNTs that are composed of a six-duplex bundle lead to a coherent description. The central tube lumen adopts a cylindrical shape while the mouth regions at the two DNT openings undergo gating-like motions which provide a possible molecular explanation of a lower conductance state observed in our previous experimental study on a membrane-spanning version of the DNT (ACS Nano 2015, 9, 1117-26). Similarly, the central nanotube lumen is filled with water and ions characterized by bulk diffusion coefficients while the gating regions exhibit temporal fluctuations in their aqueous volume. We furthermore observe that the porous nature of the walls allows lateral leakage of ions and water. This study will benefit rational design of DNA nanopores of enhanced stability of relevance for sensing applications, of nanodevices with tunable gating properties that mimic gated ion channels, or of nanopores featuring defined permeation behavior.

Stability and dynamics of membrane-spanning DNA nanopores

“…The thickness profile reveals that membrane thinning occurs around the DNT and persists for up to ∼ 2 nm away from its surface. As in our previous (AT) simulations of a DNT in aqueous solution27, water is present both within the lumen of the nanotube and also (to a lesser extent) within the walls of the nanotube itself. Lipid density can be seen to overlap radially with DNA density, confirming the close interactions of lipid molecules and DNA of the nanopore noted above.…”

“…1) embedded in a simple model (phosphatidylcholine; PC) lipid bilayer. The starting model for most of the simulations was obtained by coarse-graining a representative structure (obtained by clustering) from a previous simulation of a DNT scaffold in aqueous solution27, which was then modified to add a hydrophobic surface band20, and inserted in a PC bilayer (see Methods for details). The resultant DNT-bilayer system, with water and ions (1 M NaCl) on either face of the membrane, was simulated for 1 μs (six repeats; see Table 1).…”

“…A number of DNT designs have been explored1819222324 and have been characterized functionally, both when reconstituted into artificial lipid bilayers22025 and when inserted into the membranes of cells26. Computational studies have been used to explore, for example, their conformational dynamics in relation to ion permeation2728. Electroporation has also been used to introduce DNA nanostructures into cells29.…”

“…MD simulations have also been employed to examine the conformational dynamics and permeation properties of nanopores (for example, refs 33, 34, 35, 36, 37, 38, 39, 40, 41), including those formed by non-membrane-spanning DNTs2742 and a single bilayer-spanning DNA duplex43. Recently, MD simulations have provided an estimate of the free energy substantive barrier to insertion of unmodified DNA into a lipid bilayer, while suggesting that the presence of divalent cations may lower the energetic barrier44.…”

Charge Neutralization Drives the Shape Reconfiguration of DNA Nanotubes

“…Molecular dynamics (MD) simulations have also revealed interesting properties, [5] including ion flow and gating-like behaviors in these DNA-based nanochannels. [6] …”