Membrane Scaffolds Enhance the Responsiveness and Stability of DNA-Based Sensing Circuits

Abstract

Target-induced DNA strand displacement is an excellent candidate for developing analyteresponsive DNA circuitry to be used in clinical diagnostics and synthetic biology. While most available technologies rely on DNA circuitry free to diffuse in bulk, here we explore the use of liposomes as scaffolds for DNA-based sensing nanodevices. Our proof-of-concept sensing circuit responds to the presence of a model target analyte by releasing a DNA strand, which in turn activates a fluorescent reporter. Through a combination of experiments and coarse-grained Monte Carlo simulations, we demonstrate that the presence of the membrane scaffold accelerates the process of oligonucleotide release and suppresses undesired leakage reactions, making the sensor both more responsive and robust.

A modular, dynamic, DNA-based platform for regulating cargo distribution and transport between lipid domains

“…33,34 In many cases, biomimetic DNA nanostructures, rendered amphiphilic by hydrophobic tags, have been interfaced to synthetic lipid membranes to replicate the response of cell-membrane machinery. Examples include DNA architectures mediating artificial cell-adhesion and tissue formation, 35–41 regulating transport, 42,43 enabling signal transduction, 44 and tailoring membrane curvature. 45,46…”

“…33,34 In many cases, biomimetic DNA nanostructures, rendered amphiphilic by hydrophobic tags, have been interfaced to synthetic lipid membranes to replicate the response of cell-membrane machinery. Examples include DNA architectures mediating artificial celladhesion and tissue formation, [35][36][37][38][39][40][41] regulating transport, 42,43 enabling signal transduction, 44 and tailoring membrane curvature. 45,46 Importantly, amphiphilic DNA nanostructures have been demonstrated to undergo preferential partitioning when anchored to phaseseparated synthetic bilayers, an effect which is reminiscent of membrane-protein partitioning in rafts.…”

“…For instance, the stimuli-triggered reshuffling of membrane-bound objects between lipid phases can enable highly sought behaviors such as signal transduction, communication and local membrane sculpting. 45 Examples include stimuli-induced co-localization of synthetic receptors initiating artificial signalling cascades 44 and herding of objects capable of influencing local membrane curvature, thus directing morphological re-structuring such as tubular growth 76 and exosome/endosome budding. 46,77,78 (…”

A Modular, Dynamic, DNA-Based Platform for Regulating Cargo Distribution and Transport between Lipid Domains

“… 33 , 34 In many cases, biomimetic DNA nanostructures, rendered amphiphilic by hydrophobic tags, have been interfaced to synthetic lipid membranes to replicate the response of cell-membrane machinery. Examples include DNA architectures mediating artificial cell adhesion and tissue formation, 35 − 41 regulating transport, 42 , 43 enabling signal transduction, 44 and tailoring membrane curvature. 45 , 46 …”

Membrane activity of a DNA-based ion channel depends on the stability of its double-stranded structure

“…Due to the unparalleled ease of controlling nucleic acids' structure at the molecular scale, DNA nanoengineering is widely investigated for variety of applications, amongst them mimicking membrane remodelling proteins 1,2 , biological sensing 3,4 , building nanopores [5][6][7] , designing plasmonic architectures 8 . Alongside these implementations, synthetic biology aims to create DNA-based transmembrane structures working as artificial enzymes and ion channels [9][10][11][12][13][14] .…”