Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes

Joshi, Himanshu and Maiti, Prabal K (2018) Structure and electrical properties of DNA nanotubes embedded in lipid bilayer membranes. In: NUCLEIC ACIDS RESEARCH, 46 (5). pp. 2234-2242.

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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 mu s 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 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.

Item Type:	Journal Article
Publication:	NUCLEIC ACIDS RESEARCH
Publisher:	OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
Additional Information:	Copy right for the article belong to OXFORD UNIV PRESS, GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND
Department/Centre:	Division of Mechanical Sciences > Aerospace Engineering(Formerly Aeronautical Engineering)
Date Deposited:	11 Apr 2018 19:57
Last Modified:	11 Apr 2018 19:57
URI:	http://eprints.iisc.ac.in/id/eprint/59516

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