Publications
64 results found
Brady RA, Kaufhold WT, Brooks NJ, et al., 2019, Flexibility defines structure in crystals of amphiphilic DNA nanostars, JOURNAL OF PHYSICS-CONDENSED MATTER, Vol: 31, ISSN: 0953-8984
Lutz T, Clowsley AH, Lin R, et al., 2018, Versatile multiplexed super-resolution imaging of nanostructures by Quencher-Exchange-PAINT, Nano Research, Vol: 11, Pages: 6141-6154, ISSN: 1998-0124
The optical super-resolution technique DNA-PAINT (Point Accumulation Imaging in Nanoscale Topography) provides a flexible way to achieve imaging of nanoscale structures at ∼10-nanometer resolution. In DNA-PAINT, fluorescently labeled DNA “imager” strands bind transiently and with high specificity to complementary target “docking” strands anchored to the structure of interest. The localization of single binding events enables the assembly of a super-resolution image, and this approach effectively circumvents photobleaching. The solution exchange of imager strands is the basis of Exchange-PAINT, which enables multiplexed imaging that avoids chromatic aberrations. Fluid exchange during imaging typically requires specialized chambers or washes, which can disturb the sample. Additionally, diffusional washout of imager strands is slow in thick samples such as biological tissue slices. Here, we introduce Quencher-Exchange-PAINT—a new approach to Exchange-PAINT in regular open-top imaging chambers—which overcomes the comparatively slow imager strand switching via diffusional imager washout. Quencher-Exchange-PAINT uses “quencher” strands, i.e., oligonucleotides that prevent the imager from binding to the targets, to rapidly reduce unwanted single-stranded imager concentrations to negligible levels, decoupled from the absolute imager concentration. The quencher strands contain an effective dye quencher that reduces the fluorescence of quenched imager strands to negligible levels. We characterized Quencher-Exchange-PAINT when applied to synthetic, cellular, and thick tissue samples. Quencher-Exchange-PAINT opens the way for efficient multiplexed imaging of complex nanostructures, e.g., in thick tissues, without the need for washing steps. [Figure not available: see fulltext.].
Brady RA, Brooks NJ, Foderà V, et al., 2018, Amphiphilic-DNA platform for the design of crystalline frameworks with programmable structure and functionality, Journal of the American Chemical Society, Vol: 140, Pages: 15384-15392, ISSN: 1520-5126
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 building 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.
Brady RA, Brooks NJ, Foderà V, et al., 2018, An Amphiphilic-DNA Platform for the Design of Crystalline Frameworks with Programmable Structure and Functionality
<jats:p>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 building 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 mo- tifs that can induce isothermal disassembly, and include chemical moieties to capture target proteins specifically and reversibly.</jats:p>
Di Michele L, Jana PK, Mognetti BM, 2018, Steric interactions between mobile ligands facilitate complete wrapping in passive endocytosis, PHYSICAL REVIEW E, Vol: 98, ISSN: 2470-0045
Lutz T, Clowsley AH, Lin R, et al., 2018, Versatile Multiplexed Super-Resolution Imaging of Nanostructures by Quencher-Exchange-Paint, 62nd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 349A-349A, ISSN: 0006-3495
Jayasinghe ID, Clowsley AH, Lin R, et al., 2018, Molecular Scale Visualisation of Variable Clustering Properties of the Cardiac Ryanodine Receptor, 62nd Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 118A-118A, ISSN: 0006-3495
Jayasinghe I, Clowsley AH, Lin R, et al., 2018, True Molecular Scale Visualization of Variable Clustering Properties of Ryanodine Receptors, CELL REPORTS, Vol: 22, Pages: 557-567, ISSN: 2211-1247
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- Citations: 70
Borro BC, Parolini L, Cicuta P, et al., 2017, Interaction with prefibrillar species and amyloid-like fibrils changes the stiffness of lipid bilayers, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 19, Pages: 27930-27934, ISSN: 1463-9076
Rautu SA, Orsi D, Di Michele L, et al., 2017, The role of optical projection in the analysis of membrane fluctuations, SOFT MATTER, Vol: 13, Pages: 3480-3483, ISSN: 1744-683X
Talbot EL, Kotar J, Parolini L, et al., 2017, Thermophoretic migration of vesicles depends on mean temperature and head group chemistry, NATURE COMMUNICATIONS, Vol: 8, ISSN: 2041-1723
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- Citations: 35
Brady R, Brooks NJ, Cicuta P, et al., 2017, Crystallization of amphiphilic DNA C-Stars, Nano Letters, Vol: 17, Pages: 3276-3281, ISSN: 1530-6992
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.
Amjad OA, Mognetti BM, Cicuta P, et al., 2017, Membrane Adhesion through Bridging by Multimeric Ligands, LANGMUIR, Vol: 33, Pages: 1139-1146, ISSN: 0743-7463
Talbot EL, Parolini L, Kotar J, et al., 2017, Thermal-driven domain and cargo transport in lipid membranes, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 114, Pages: 846-851, ISSN: 0027-8424
Jayasinghe I, Clowsley A, Lutz T, et al., 2016, TRUE MOLECULAR SCALE ANALYSIS OF THE CALCIUM RELEASE MACHINERY OF THE HEART WITH ENHANCED SUPER-RESOLUTION IMAGING, Autumn Meeting of the British-Society-for-Cardiovascular-Research (BSCR), Publisher: BMJ PUBLISHING GROUP, Pages: A2-A3, ISSN: 1355-6037
Di Michele L, Bachmann SJ, Parolini L, et al., 2016, Communication: Free energy of ligand-receptor systems forming multimeric complexes, Journal of Chemical Physics, Vol: 144, Pages: 1-5, ISSN: 0021-9606
Ligand-receptor interactions are ubiquitous in biology and have become popular in materials in view of their applications to programmable self-assembly. Although complex functionalities often emerge from the simultaneous interaction of more than just two linker molecules, state of the art theoretical frameworks enable the calculation of the free energy only in systems featuring one-to-one ligand/receptor binding. In this Communication, we derive a general formula to calculate the free energy of systems featuring simultaneous direct interaction between an arbitrary number of linkers. To exemplify the potential and generality of our approach, we apply it to the systems recently introduced by Parolini et al. [ACS Nano 10, 2392 (2016)] and Halverson and Tkachenko [J. Chem. Phys. 144, 094903 (2016)], both featuring functionalized Brownian particles interacting via three-linker complexes.
Talbot E, Parolini L, Kotar J, et al., 2016, Migration of Vesicles and their Domains in a Thermal Gradient, 60th Annual Meeting of the Biophysical-Society, Publisher: CELL PRESS, Pages: 70A-70A, ISSN: 0006-3495
Parolini L, Kotar J, Di Michele L, et al., 2016, Controlling Self-Assembly Kinetics of DNA-Functionalized Liposomes Using Toehold Exchange Mechanism, ACS NANO, Vol: 10, Pages: 2392-2398, ISSN: 1936-0851
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- Citations: 63
Bachmann SJ, Kotar J, Parolini L, et al., 2016, Melting transition in lipid vesicles functionalised by mobile DNA linkers, SOFT MATTER, Vol: 12, Pages: 7804-7817, ISSN: 1744-683X
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- Citations: 26
Zaccone A, Terentjev I, Di Michele L, et al., 2015, Fragmentation and depolymerization of non-covalently bonded filaments, JOURNAL OF CHEMICAL PHYSICS, Vol: 142, ISSN: 0021-9606
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- Citations: 7
Parolini L, Mognetti BM, Kotar J, et al., 2015, Volume and porosity thermal regulation in lipid mesophases by coupling mobile ligands to soft membranes, Nature Communications, Vol: 6, Pages: 1-10, ISSN: 2041-1723
Short DNA linkers are increasingly being exploited for driving-specific self-assembly of Brownian objects. DNA-functionalized colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach has been applied to compliant units, including emulsion droplets and lipid vesicles. The liquid structure of these substrates introduces new degrees of freedom: the tethers can diffuse and rearrange, radically changing the physics of the interactions. Unlike droplets, vesicles are extremely deformable and DNA-mediated adhesion causes significant shape adjustments. We investigate experimentally the thermal response of pairs and networks of DNA-tethered liposomes and observe two intriguing and possibly useful collective properties: negative thermal expansion and tuneable porosity of the liposome networks. A model providing a thorough understanding of this unexpected phenomenon is developed, explaining the emergent properties out of the interplay between the temperature-dependent deformability of the vesicles and the DNA-mediated adhesive forces.
Shimobayashi SF, Mognetti BM, Parolini L, et al., 2015, Direct measurement of DNA-mediated adhesion between lipid bilayers, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 17, Pages: 15615-15628, ISSN: 1463-9076
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- Citations: 33
Di Michele L, Mognetti BM, Yanagishima T, et al., 2014, Effect of Inert Tails on the Thermodynamics of DNA Hybridization, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, Vol: 136, Pages: 6538-6541, ISSN: 0002-7863
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- Citations: 38
Di Michele L, Fiocco D, Varrato F, et al., 2014, Aggregation dynamics, structure, and mechanical properties of bigels, SOFT MATTER, Vol: 10, Pages: 3633-3648, ISSN: 1744-683X
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- Citations: 54
Di Michele L, Eiser E, Fodera V, 2013, Minimal Model for Self-Catalysis in the Formation of Amyloid-Like Elongated Fibrils, JOURNAL OF PHYSICAL CHEMISTRY LETTERS, Vol: 4, Pages: 3158-3164, ISSN: 1948-7185
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- Citations: 9
Di Michele L, Varrato F, Kotar J, et al., 2013, Multistep kinetic self-assembly of DNA-coated colloids, NATURE COMMUNICATIONS, Vol: 4, ISSN: 2041-1723
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- Citations: 103
Di Michele L, Eiser E, 2013, Developments in understanding and controlling self assembly of DNA-functionalized colloids, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, Vol: 15, Pages: 3115-3129, ISSN: 1463-9076
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- Citations: 71
Varrato F, Di Michele L, Belushkin M, et al., 2012, Arrested demixing opens route to bigels, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 19155-19160, ISSN: 0027-8424
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- Citations: 81
Di Michele L, Zaccone A, Eiser E, 2012, Analytical theory of polymer-network-mediated interaction between colloidal particles, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 10187-10192, ISSN: 0027-8424
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- Citations: 17
Yanagishima T, Di Michele L, Kotar J, et al., 2012, Diffusive behaviour of PLL-PEG coated colloids on λ-DNA brushes - tuning hydrophobicity, SOFT MATTER, Vol: 8, Pages: 6792-6798, ISSN: 1744-683X
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- Citations: 12
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