Structure and Electrical Properties of DNA Nanotubes Embedded in Lipid Bilayer Membranes

TL;DR

This study uses molecular dynamics simulations to analyze the stability, lipid interactions, and ionic conductance of DNA nanotubes embedded in lipid bilayers, revealing gating effects and ionic conductance variations with salt concentration.

Contribution

It provides detailed insights into the structural stability, lipid interactions, and ionic transport properties of DNA nanotube nanopores in lipid membranes, including gating mechanisms.

Findings

Lipid head groups form a toroidal structure around the DNA nanotube.

Ionic conductance varies from 4.3 nS to 20.6 nS with salt concentration.

Gating effects observed with ssDNA and dsDNA overhangs.

Abstract

Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 microsecond long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane. Further, we explore the effect of ionic concentrations to the in-solution structure and stability of the lipid-DNT complex. Transmembrane ionic current measurements for the constant electric field MD simulation provide the I-V characteristics of the water filled DNT lumen in lipid membrane. With increasing salt concentrations, the measured values of transmembrane ionic conductance of the porous DNT lumen vary from 4.3 nS to 20.6 nS. Simulations of the DNTs with ssDNA and dsDNA overhangs at the mouth of the pore show gating effect with remarkable difference in the transmembrane ionic conductivities for open and close state nanopores.