A synthetic enzyme built from DNA flips 107 lipids per second in biological membranes

Alexander Ohmann,Chen-Yu Li,Kevin N Baumann,Jejoong Yoo,Ulrich F Keyser,Aleksei Aksimentiev,Christopher Maffeo,Kareem Al Nahas,Kerstin Göpfrich

doi:10.1038/s41467-018-04821-5

Alexander Ohmann, Chen-Yu Li + Show 7 more

Open Access

https://doi.org/10.1038/s41467-018-04821-5

Copy DOI

Abstract

Mimicking enzyme function and increasing performance of naturally evolved proteins is one of the most challenging and intriguing aims of nanoscience. Here, we employ DNA nanotechnology to design a synthetic enzyme that substantially outperforms its biological archetypes. Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal pore that connects the membrane’s inner and outer leaflets. The membrane insertion catalyzes spontaneous transport of lipid molecules between the bilayer leaflets, rapidly equilibrating the lipid composition. Through a combination of microscopic simulations and fluorescence microscopy we find the lipid transport rate catalyzed by the DNA nanostructure exceeds 107 molecules per second, which is three orders of magnitude higher than the rate of lipid transport catalyzed by biological enzymes. Furthermore, we show that our DNA-based enzyme can control the composition of human cell membranes, which opens new avenues for applications of membrane-interacting DNA systems in medicine.

Highlights

Mimicking enzyme function and increasing performance of naturally evolved proteins is one of the most challenging and intriguing aims of nanoscience
In contrast to flippases and floppases that require energy input for maintaining the asymmetric lipid composition, scramblases are activated to rapidly and passively dismantle the asymmetric partitioning of the lipids, which typically occurs during critical events such as cell activation, blood coagulation, and apoptosis[6,7,8,9]
The observed shifts are consistent with the increased molecular weight and cross-sections of the modified DNA nanostructures, which confirms their successful assembly and incorporation of the cholesterol tags

Summary

Introduction

Mimicking enzyme function and increasing performance of naturally evolved proteins is one of the most challenging and intriguing aims of nanoscience. Consisting of only eight strands, our DNA nanostructure spontaneously inserts into biological membranes by forming a toroidal pore that connects the membrane’s inner and outer leaflets. We utilize the DNA-induced toroidal pore to design a fully functional synthetic scramblase that facilitates rapid mixing of lipids between membrane leaflets. The scrambling activity of our de novo designed DNA-made enzyme outperforms any known biological scramblase by several orders of magnitude. This is remarkable given that the catalytic rates of previous enzymatically active DNA nanostructures fall orders of magnitude behind natural benchmarks[22,23]

Methods

Results

Conclusion