DNA-Based Mimics of Membrane Proteins Lipid-DNA Interactions Determine Function

Nucleic acids, particularly DNA, are used as a nanoscale building material, due to their unique controllability via complementarity of base pairing. One of the potential applications of DNA nanotechnology is creating synthetic constructs mimicking function of membrane proteins. These natural molecular machines function embedded in the lipid bilayer. Similar membrane attachment of DNA-based structures is achieved by modifying the nucleic acid with hydrophobic anchors, most commonly cholesterol. Aiming at developing a fully functional and controllable synthetic membrane construct, the first step I undertook was to understand and utilize fundamental interactions between molecules: DNA, cholesterol and lipids. Instead of starting with a complicated DNA-based model mimicking protein architecture, here I have created a set of simple systems that allowed me to examine the major interactions between involved molecules. This work describes four aspects of the DNA-lipid systems that I have built and studied experimentally. Firstly, I have analysed the effects of membrane-spanning DNA duplex on the lipids’ arrangement in the pore and presented how this arrangement can be remodelled depending on the hydrophilicity of the DNA design. Secondly, I have looked at the same system from the opposite perspective - studied and prevented the distortion of the transmembrane DNA construct induced by the surrounding lipids. Thirdly, I have evaluated the importance of ions in mediating DNA-lipid interactions, reporting analysis of two electrostatic phenomena: screening and bridging. Finally, utilizing a nanoengineered four-helix structure, I discussed surfactant’s influence on DNA membrane insertion efficiency, showing that aggregation of the nanostructures is one of the major factors determining their spontaneous membrane-spanning. While the understanding of phenomena in minimalistic systems is crucial for further development of complex pore-forming constructs, here I showed that even simple DNA nanostructures, when rationally designed, can mimic functionality of natural membrane proteins.EPSRC; Winton Programme for the Physics of Sustainabilit

A Surfactant Enables Efficient Membrane Spanning by Non-Aggregating DNA-Based Ion Channels.

Funder: Friedrich Naumann FoundationFunder: Cambridge Philosophical SocietyFunder: Winton Programme for the Physics of SustainabilityFunder: Jane Bourque-Driscoll FundDNA nanotechnology makes use of hydrophobically modified constructs to create synthetic membrane protein mimics. However, nucleic acid structures exhibit poor insertion efficiency, leading to a low activity of membrane-spanning DNA protein mimics. It is suggested that non-ionic surfactants improve insertion efficiency, partly by disrupting hydrophobicity-mediated clusters. Here, we employed confocal microscopy and single-molecule transmembrane current measurements to assess the effects of the non-ionic surfactant octylpolyoxyethylene (oPOE) on the clustering behavior and membrane activity of cholesterol-modified DNA nanostructures. Our findings uncover the role of aggregation in preventing bilayer interactions of hydrophobically decorated constructs, and we highlight that premixing DNA structures with the surfactant does not disrupt the cholesterol-mediated aggregates. However, we observed the surfactant's strong insertion-facilitating effect, particularly when introduced to the sample separately from DNA. Critically, we report a highly efficient membrane-spanning DNA construct from combining a non-aggregating design with the addition of the oPOE surfactant.DM acknowledges funding from the Winton Programme for the Physics of Sustainability and the Engineering and Physical Sciences Research Council (EPSRC, project ref. 1948702). MS acknowledges funding from the Friedrich Naumann Foundation, the Jane Bourque-Driscoll Fund and the Cambridge Philosophical Society. UFK acknowledges the ERC Consolidator Grant (De-signer-Pores 647144)

Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures.

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

Cations Regulate Membrane Attachment and Functionality of DNA Nanostructures.

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

Membrane Activity of a DNA-Based Ion Channel Depends on the Stability of Its Double-Stranded Structure.

DNA nanotechnology has emerged as a promising method for designing spontaneously inserting and fully controllable synthetic ion channels. However, both insertion efficiency and stability of existing DNA-based membrane channels leave much room for improvement. Here, we demonstrate an approach to overcoming the unfavorable DNA-lipid interactions that hinder the formation of a stable transmembrane pore. Our all-atom MD simulations and experiments show that the insertion-driving cholesterol modifications can cause fraying of terminal base pairs of nicked DNA constructs, distorting them when embedded in a lipid bilayer. Importantly, we show that DNA nanostructures with no backbone discontinuities form more stable conductive pores and insert into membranes with a higher efficiency than the equivalent nicked constructs. Moreover, lack of nicks allows design and maintenance of membrane-spanning helices in a tilted orientation within the lipid bilayer. Thus, reducing the conformational degrees of freedom of the DNA nanostructures enables better control over their function as synthetic ion channels.Winton Programme for the Physics of Sustainability EPSRC Scholarship (1948702). EPSRC Cambridge NanoDTC (EP/S022953/1) ERC consolidator grant (DesignerPores 647144) National Science Foundation USA (DMR-1827346) XSEDE allocation grant (MCA05S028) Leadership Resource Allocation (MCB20012

Interplay of the mechanical and structural properties of DNA nanostructures determines their electrostatic interactions with lipid membranes.

Acknowledgements: D. M. and M. M. C. B. acknowledge the support from the Volkswagen Stiftung “Life?” (Grant No. 98200). V. C. and M. M. C. B. acknowledge the support from the Swiss National Science Foundation (Eccellenza Grant PCEGP2_181137). R. R. S. acknowledges support from the EPSRC CDT in Nanoscience and Nanotechnology (NanoDTC, Grant No. EP/L015978/1), the Mexican National Council for Science and Technology and the Cambridge Trust. R. R. S. and L. D. M. acknowledge funding from the Royal Society Research Fellows Enhanced Research Expenses (RF/ERE/210029). L. D. M. acknowledges support from a Royal Society University Research Fellowship (UF160152) and from the European Research Council (ERC) under the Horizon 2020 Research and Innovation Programme (ERC-STG No. 851667 NANOCELL). The authors thank Dr Jorieke Weiden and Dr Eva Kursinkal for their help with DNA origami protocols.Nucleic acids and lipids function in close proximity in biological processes, as well as in nanoengineered constructs for therapeutic applications. As both molecules carry a rich charge profile, and frequently coexist in complex ionic solutions, the electrostatics surely play a pivotal role in interactions between them. Here we discuss how each component of a DNA/ion/lipid system determines its electrostatic attachment. We examine membrane binding of a library of DNA molecules varying from nanoengineered DNA origami through plasmids to short DNA domains, demonstrating the interplay between the molecular structure of the nucleic acid and the phase of lipid bilayers. Furthermore, the magnitude of DNA/lipid interactions is tuned by varying the concentration of magnesium ions in the physiologically relevant range. Notably, we observe that the structural and mechanical properties of DNA are critical in determining its attachment to lipid bilayers and demonstrate that binding is correlated positively with the size, and negatively with the flexibility of the nucleic acid. The findings are utilized in a proof-of-concept comparison of membrane interactions of two DNA origami designs - potential nanotherapeutic platforms - showing how the results can have a direct impact on the choice of DNA geometry for biotechnological applications

Selective Integrin α₅β₁ Targeting through Spatially Constrained Multivalent DNA-Based Nanoparticles

Targeting cells specifically based on receptor expression levels remains an area of active research to date. Selective binding of receptors cannot be achieved by increasing the individual binding strength, as this does not account for differing distributions of receptor density across healthy and diseased cells. Engaging receptors above a threshold concentration would be desirable in devising selective diagnostics. Integrins are prime target candidates as they are readily available on the cell surface and have been reported to be overexpressed in diseases. Insights into their spatial organization would therefore be advantageous to design selective targeting agents. Here, we investigated the effect of activation method on integrin α5β1 clustering by immunofluorescence and modeled the global neighbor distances with input from an immuno-staining assay and image processing of microscopy images. This data was used to engineer spatially-controlled DNA-scaffolded bivalent ligands, which we used to compare trends in spatial-selective binding observed across HUVEC, CHO and HeLa in resting versus activated conditions in confocal microscopy images. For HUVEC and CHO, the data demonstrated an improved selectivity and localisation of binding for smaller spacings ~7 nm and ~24 nm, in good agreement with the model. A deviation from the mode predictions for HeLa was observed, indicative of a clustered, instead of homogeneous, integrin organization. Our findings demonstrate how low-technology imaging methods can guide the design of spatially controlled ligands to selectively differentiate between cell type and integrin activation state

DNA-liposome hybrid carriers for triggered cargo release

The design of simple and versatile synthetic routes to accomplish triggered-release properties in carriers is of particular interest for drug delivery purposes. In this context, the programmability and adaptability of DNA nanoarchitectures in combination with liposomes have great potential to render biocompatible hybrid carriers for triggered cargo release. We present an approach to form a DNA mesh on large unilamellar liposomes incorporating a stimuli-responsive DNA building block. Upon incubation with a single-stranded DNA trigger sequence, a hairpin closes, and the DNA building block is allowed to self-contract. We demonstrate the actuation of this building block by single-molecule Förster resonance energy transfer (FRET), fluorescence recovery after photobleaching, and fluorescence quenching measurements. By triggering this process, we demonstrate the elevated release of the dye calcein from the DNA–liposome hybrid carriers. Interestingly, the incubation of the doxorubicin-laden active hybrid carrier with HEK293T cells suggests increased cytotoxicity relative to a control carrier without the triggered-release mechanism. In the future, the trigger could be provided by peritumoral nucleic acid sequences and lead to site-selective release of encapsulated chemotherapeutics.The research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (Agreement No. 337969). K.N.B., P.S.C., and T.P.J.K. are grateful for financial support from the Biotechnology and Biological Sciences Research Council (BBSRC), the Newman Foundation, the Wellcome Trust, and the Cambridge Centre for Misfolding Diseases. D.M. is supported by the Winton Programme for the Physics of Sustainability, as well as the Engineering and Physical Sciences Research Council (EPSRC). P.T. gratefully acknowledges funding by the Bavarian Ministry of Science and the Arts through the ONE MUNICH Project “Munich Multiscale Biofabrication” and by the LMU-Cambridge strategic partnership. S.H.A. acknowledges funding by the Gobierno de Aragón-FSE (Research Group E47_20R).Peer reviewe

DNA-Liposome Hybrid Carriers for Triggered Cargo Release

The encapsulation of chemotherapeutics by biocompatible carrier structures holds great promise to preserve their therapeutic activity and favor their delivery to tumor sites. To enhance the bioavailability of a drug at the targeted tissue, triggered release mechanisms have received increasing research interest. Many approaches rely on exogeneous triggers such as the irradiation of ultrasound, visible or even ionizing electromagnetic waves. However, such exogenous triggers can be challenging to implement in a specific manner. Therefore, designing carriers responsive to endogenous moieties, such as nucleic acid biomarkers, is a desirable step in the search of personalized drug delivery nanoplatforms. This study presents an approach to building a biocompatible DNA-liposome hybrid nanocarrier for potential triggered release purposes. We form a DNA mesh on large unilamellar liposomes incorporating a trigger-responsive DNA building block. Upon incubation with a single-stranded DNA trigger sequence a hairpin closes and the building block is allowed to self-contract. By this process, we demonstrate elevated release of the dye calcein and the drug doxorubicin. The incubation of the doxorubicin-laden active hybrid carrier with HEK293T cells suggests increased cytotoxicity relative to a control carrier without the triggered release mechanism. In the future, the trigger could be provided by peritumoral nucleic acid sequences and lead to site-selective release of encapsulated chemotherapeutics