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Instruments / Technical Area	Publication Details	Published
I22-Small angle scattering & Diffraction	Sculpting DNA-based synthetic cells through phase separation and phase-targeted activity Layla Malouf , Diana A. Tanase , Giacomo Fabrini , Ryan A. Brady , Miguel Paez-Perez , Adrian Leathers , Michael J. Booth , Lorenzo Di Michele Chem 210 DOI: 10.1016/j.chempr.2023.10.004 Diamond Proposal Number(s): [29072] Open Access Show Abstract ▼ Abstract: Synthetic cells, like their biological counterparts, require internal compartments with distinct chemical and physical properties where different functionalities can be localized. Inspired by membrane-less compartmentalization in biological cells, here, we demonstrate how microphase separation can be used to engineer heterogeneous cell-like architectures with programmable morphology and compartment-targeted activity. The synthetic cells self-assemble from amphiphilic DNA nanostructures, producing core-shell condensates due to size-induced de-mixing. Lipid deposition and phase-selective etching are then used to generate a porous pseudo-membrane, a cytoplasm analog, and membrane-less organelles. The synthetic cells can sustain RNA synthesis via in vitro transcription, leading to cytoplasm and pseudo-membrane expansion caused by an accumulation of the transcript. Our approach exemplifies how architectural and functional complexity can emerge from a limited number of distinct building blocks, if molecular-scale programmability, emergent biophysical phenomena, and biochemical activity are coupled to mimic those observed in live cells.	Nov 2023
I22-Small angle scattering & Diffraction	Influence of hydrophobic moieties on the crystallization of amphiphilic DNA nanostructures Michal Walczak , Ryan A. Brady , Adrian Leathers , Jurij Kotar , Lorenzo Di Michele The Journal Of Chemical Physics 158 DOI: 10.1063/5.0132484 Diamond Proposal Number(s): [24537, 29072] Open Access Show Abstract ▼ Abstract: Three-dimensional crystalline frameworks with nanoscale periodicity are valuable for many emerging technologies, from nanophotonics to nanomedicine. DNA nanotechnology has emerged as a prime route for constructing these materials, with most approaches taking advantage of the structural rigidity and bond directionality programmable for DNA building blocks. Recently, we have introduced an alternative strategy reliant on flexible, amphiphilic DNA junctions dubbed C-stars, whose ability to crystallize is modulated by design parameters, such as nanostructure topology, conformation, rigidity, and size. While C-stars have been shown to form ordered phases with controllable lattice parameter, response to stimuli, and embedded functionalities, much of their vast design space remains unexplored. Here, we investigate the effect of changing the chemical nature of the hydrophobic modifications and the structure of the DNA motifs in the vicinity of these moieties. While similar design variations should strongly alter key properties of the hydrophobic interactions between C-stars, such as strength and valency, only limited differences in self-assembly behavior are observed. This finding suggests that long-range order in C-star crystals is likely imposed by structural features of the building block itself rather than the specific characteristics of the hydrophobic tags. Nonetheless, we find that altering the hydrophobic regions influences the ability of C-star crystals to uptake hydrophobic molecular cargoes, which we exemplify by studying the encapsulation of antibiotic penicillin V. Besides advancing our understanding of the principles governing the self-assembly of amphiphilic DNA building blocks, our observations thus open up new routes to chemically program the materials without affecting their structure.	Feb 2023
I22-Small angle scattering & Diffraction	Reaction-diffusion patterning of DNA-based artificial cells Adrian Leathers , Michal Walczak , Ryan A. Brady , Assala Al Samad , Jurij Kotar , Michael J. Booth , Pietro Cicuta , Lorenzo Di Michele Journal Of The American Chemical Society 13 DOI: 10.1021/jacs.2c06140 Diamond Proposal Number(s): [28071] Open Access Show Abstract ▼ Abstract: Biological cells display complex internal architectures with distinct micro environments that establish the chemical heterogeneity needed to sustain cellular functions. The continued efforts to create advanced cell mimics, namely, artificial cells, demands strategies for constructing similarly heterogeneous structures with localized functionalities. Here, we introduce a platform for constructing membraneless artificial cells from the self-assembly of synthetic DNA nanostructures in which internal domains can be established thanks to prescribed reaction–diffusion waves. The method, rationalized through numerical modeling, enables the formation of up to five distinct concentric environments in which functional moieties can be localized. As a proof-of-concept, we apply this platform to build DNA-based artificial cells in which a prototypical nucleus synthesizes fluorescent RNA aptamers that then accumulate in a surrounding storage shell, thus demonstrating the spatial segregation of functionalities reminiscent of that observed in biological cells.	Sep 2022
I22-Small angle scattering & Diffraction	Modulating membrane fusion through the design of fusogenic DNA circuits and bilayer composition Miguel Paez-Perez , I. Alasdair Russell , Pietro Cicuta , Lorenzo Di Michele Soft Matter 112 DOI: 10.1039/D2SM00863G Diamond Proposal Number(s): [28071] Open Access Show Abstract ▼ Abstract: Membrane fusion is a ubiquitous phenomenon linked to many biological processes, and represents a crucial step in liposome-based drug delivery strategies. The ability to control, ever more precisely, membrane fusion pathways would thus be highly valuable for next generation nano-medical solutions and, more generally, the design of advanced biomimetic systems such as synthetic cells. In this article, we present fusogenic nanostructures constructed from synthetic DNA which, different from previous solutions, unlock routes for modulating the rate of fusion and making it conditional to the presence of soluble DNA molecules, thus demonstrating how membrane fusion can be controlled through simple DNA-based molecular circuits. We then systematically explore the relationship between lipid-membrane composition, its biophysical properties, and measured fusion efficiency, linking our observations to the stability of transition states in the fusion pathway. Finally, we observe that specific lipid compositions lead to the emergence of complex bilayer architectures in the fusion products, such as nested morphologies, which are accompanied by alterations in biophysical behaviour. Our findings provide multiple, orthogonal strategies to program lipid-membrane fusion, which leverage the design of either the fusogenic DNA constructs or the physico/chemical properties of the membranes, and could thus be valuable in applications where some design parameters are constrained by other factors such as material cost and biocompatibility, as it is often the case in biotechnological applications.	Aug 2022
B21-High Throughput SAXS I22-Small angle scattering & Diffraction	Flexibility defines structure in crystals of amphiphilic DNA nanostars Ryan Brady , Will T. Kaufhold , Nicholas J. Brooks , Vito Foderà , Lorenzo Di Michele Journal Of Physics: Condensed Matter 31 DOI: 10.1088/1361-648X/aaf4a1 Diamond Proposal Number(s): [17271, 16970] Show Abstract ▼ Abstract: DNA nanostructures with programmable shape and interactions can be used as building blocks for the self-assembly of crystalline materials with prescribed nanoscale features, holding a vast technological potential. Structural rigidity and bond directionality have been recognised as key design features for DNA motifs to sustain long-range order in 3D, but the practical challenges associated with prescribing building-block geometry with sufficient accuracy have limited the variety of available designs. We have recently introduced a novel platform for the one-pot preparation of crystalline DNA frameworks supported by a combination of Watson–Crick base pairing and hydrophobic forces (Brady et al 2017 Nano Lett. 17 3276–81). Here we use small angle x-ray scattering and coarse-grained molecular simulations to demonstrate that, as opposed to available all-DNA approaches, amphiphilic motifs do not rely on structural rigidity to support long-range order. Instead, the flexibility of amphiphilic DNA building-blocks is a crucial feature for successful crystallisation.	Feb 2019
I22-Small angle scattering & Diffraction	An amphiphilic-DNA platform for the design of crystalline frameworks with programmable structure and functionality Ryan A. Brady , Nicholas J. Brooks , Vito Foderà , Pietro Cicuta , Lorenzo Di Michele Journal Of The American Chemical Society DOI: 10.1021/jacs.8b09143 Diamond Proposal Number(s): [17271, 19371] Show Abstract ▼ Abstract: The reliable preparation of functional, ordered, nanostructured frameworks would be a game changer for many emerging technologies, from energy storage to nanomedicine. Underpinned by the excellent molecular recognition of nucleic acids, along with their facile synthesis and breadth of available functionalizations, DNA Nanotechnology is widely acknowledged as a prime route for the rational design of nanostructured materials. Yet, the preparation of crystalline DNA frameworks with programmable structure and functionality remains a challenge. Here we demonstrate the potential of simple amphiphilic DNA motifs, dubbed C-stars, as a versatile platform for the design of programmable DNA crystals. In contrast to all-DNA materials, in which structure depends on the precise molecular details of individual build-ing blocks, the self-assembly of C-stars is controlled uniquely by their topology and symmetry. Exploiting this robust self-assembly principle we design a range of topologically identical, but structurally and chemically distinct C-stars that following a one-pot reaction self- assemble into highly porous, functional, crystalline frameworks. Simple design variations allow us to fine-tune the lattice parameter and thus control the partitioning of macromolecules within the frameworks, embed responsive motifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.	Oct 2018
I22-Small angle scattering & Diffraction	Crystallization of amphiphilic DNA C-Stars Ryan A. Brady , Nicholas J. Brooks , Pietro Cicuta , Lorenzo Di Michele Nano Letters DOI: 10.1021/acs.nanolett.7b00980 Diamond Proposal Number(s): [14217, 15030, 15530] Open Access Show Abstract ▼ Abstract: Many emerging technologies require materials with well-defined 3D nanoscale architectures. Production of these structures is currently underpinned by self-assembling amphiphilic macromolecules or engineered all-DNA building blocks. Both these approaches produce restricted ranges of crystal geometries due to synthetic amphiphiles’ simple shape and limited specificity, or the technical difficulties in designing space-filling DNA motifs with targeted shapes. We have overcome these limitations with amphiphilic DNA-nanostructures, or “C-Stars”, that combine the design freedom and facile functionalization of DNA-based materials with robust hydrophobic interactions. C-Stars self-assemble into single crystals exceeding 40 μm in size with lattice parameters exceeding 20 nm.	Apr 2017

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