2017/10/16 by Himanshu Joshi, Prabal K. Maiti, Joshi, Himanshu +1
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Advanced biosensing and bioanalysis techniques #Biological Physics (physics.bio-ph) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #Nanopore and Nanochannel Transport Studies #Soft Condensed Matter (cond-mat.soft) #Subcellular Processes (q-bio.SC) #cond-mat.soft #physics.bio-ph #q-bio.SC
paper · pdf · doi:10.48550/arxiv.1710.06001
Accepted for publication in Nucleic Acid Research, 11 Figures and 3 Tables
arxiv created 2017/10/16 · openalex publication_date 2017/10/16 · arxiv updated 2017/10/18 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.