Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures

Diana Morzy, Roger Rubio-Sánchez, Himanshu Joshi, Aleksei Aksimentiev, Lorenzo Di Michele, and Ulrich F. Keyser
Journal of the American Chemical Society 143(19) 7358-7367 (2021)
DOI:10.1021/jacs.1c00166  BibTex

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The interplay between nucleic acids and lipids underpins several key processes in molecular biology, synthetic biotechnology, vaccine technology, and nanomedicine. These interactions are often electrostatic in nature, and much of their rich phenomenology remains unexplored in view of the chemical diversity of lipids, the heterogeneity of their phases, and the broad range of relevant solvent conditions. Here we unravel the electrostatic interactions between zwitterionic lipid membranes and DNA nanostructures in the presence of physiologically relevant cations, with the purpose of identifying new routes to program DNA−lipid complexation and membrane-active nanodevices. We demonstrate that this interplay is influenced by both the phase of the lipid membranes and the valency of the ions and observe divalent cation bridging between nucleic acids and gel-phase bilayers. Furthermore, even in the presence of hydrophobic modifications on the DNA, we find that cations are still required to enable DNA adhesion to liquid-phase membranes. We show that the latter mechanism can be exploited to control the degree of attachment of cholesterol-modified DNA nanostructures by modifying their overall hydrophobicity and charge. Besides their biological relevance, the interaction mechanisms we explored hold great practical potential in the design of biomimetic nanodevices, as we show by constructing an ion-regulated DNA-based synthetic enzyme.

Abstract

The interplay between nucleic acids and lipids underpins several key processes in molecular biology, synthetic biotechnology, vaccine technology, and nanomedicine. These interactions are often electrostatic in nature, and much of their rich phenomenology remains unexplored in view of the chemical diversity of lipids, the heterogeneity of their phases, and the broad range of relevant solvent conditions. Here we unravel the electrostatic interactions between zwitterionic lipid membranes and DNA nanostructures in the presence of physiologically relevant cations, with the purpose of identifying new routes to program DNA−lipid complexation and membrane-active nanodevices. We demonstrate that this interplay is influenced by both the phase of the lipid membranes and the valency of the ions and observe divalent cation bridging between nucleic acids and gel-phase bilayers. Furthermore, even in the presence of hydrophobic modifications on the DNA, we find that cations are still required to enable DNA adhesion to liquid-phase membranes. We show that the latter mechanism can be exploited to control the degree of attachment of cholesterol-modified DNA nanostructures by modifying their overall hydrophobicity and charge. Besides their biological relevance, the interaction mechanisms we explored hold great practical potential in the design of biomimetic nanodevices, as we show by constructing an ion-regulated DNA-based synthetic enzyme.

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A video illustrating a 1.1 μs MD simulation of a dsDNA molecule interacting with a gel-phase (DPPE) lipid bilayer membrane. Periodic images of the system along both y-axis (left to right) and z-axis (up and down) are shown to illustrate the binding of DNA across the periodic boundary of the simulation system. The periodic boundary along y-axis is appriximately shown by solid blue lines, whereas the dahed blue line shows the periodic boundary of the simulation cell along z-axis. The backbone of the DNA is shown in green. The nucleotide bases of the 21-base pair DNA fragment in one simulation unit cell are shown in light blue whereas those from the periodic images are shown in white. Non-hydrogen atoms of the lipid membrane are shown as blue (N), tan (P), red (O), and cyan (C) spheres. Water and ions are not shown for clarity. 

A video illustrating a 1.2 μs MD simulation of a dsDNA molecule interacting with a fluid-phase (DPhPE) lipid bilayer membrane. Periodic images of the system along both y-axis (left to right) and z-axis (up and down) are shown to illustrate the binding of DNA across the periodic boundary of the simulation system. The periodic boundary along y-axis is appriximately shown by solid blue lines, whereas the dahed blue line shows the periodic boundary of the simulation cell along z-axis. The backbone of the DNA is shown in green. The nucleotide bases of the 21- base pair DNA fragment in one simulation unit cell are shown in light blue whereas those from the periodic images are shown in white. Non-hydrogen atoms of the lipid membrane are shown as blue (N), tan (P), red (O), and cyan (C) spheres. Water and ions are not shown for clarity.

A video illustrating the strong binding of dsDNA molecule to a gel-phase (DPPE) lipid bilayer membrane. The video covers the last 90 ns of the equilibrium MD run (same as Movie 1) but explicitly shows the magnesium ions and their first solvation shell, Mg[H2O]62+, depicted as red and white spheres.  The periodic boundary along y-axis is appriximately shown by solid blue lines, whereas the dahed blue line shows the periodic boundary of the simulation cell along z-axis.