OPT-ASSEMBLY · Optimal design of frustrated self assembly building blocks
Horizon 2020 — Marie Skłodowska-Curie Actions
- Duration
- 2022-09-01 → 2024-08-31
- EU contribution
- €141,779
- Participants
- 1
- Scheme
- MSCA-IF
Lines connect the coordinator with its partners.
Results in brief
Optimal design of frustrated self assembly building blocks
Many nanostructures in nature form via the headless self assembly of elements, sometimes orders of magnitudes smaller than the resulting structure. Examples include viral protein capsids, bacterial microcompartments and other shelled organelles. These structures are diverse in shape and functionality, yet, they all form from a few types of building blocks, spontaneously, governed by pure thermodynamics. Nature's remarkable success in economically and robustly assembling such structures of various sizes, shapes and functionalities has long puzzled scientists and was envied by material engineers, and with good reasons: the ability to assemble synthetic nanostructures gives rise to a series of technological applications including drug delivery, virus trapping and photonic applications. A relatively recent method to implement such self assembling building blocks is DNA origami, where DNA strands are carefully designed and folded into triangular blocks which, in turn, can attach to each other and self assemble into the pre-programmed shape. In many cases, however, the assembly process goes off-pathway resulting in off-target structures which are useless from the technological standpoint. Finding the optimal design principles in creating building blocks which assemble into the desired target with high fidelity was the main objective of the project. While collaborating closely with experimentalists, the project itself was purely theoretical and computational and we used a coarse grained Monte Carlo simulation scheme developed by us to explore various design principles and guide the experiments. Inspired by viral capsids, initially we focused on creating small, icosahedral-shaped shells from a single subunit species, then soon transitioned to build higher complexity shells with more technological interest.
Data: CORDIS, © European Union
Project objective
Nature's ability to organize building blocks into large structures of finite size has inspired many researchers to attempt similar constructs with synthetic subunits. DNA origami triangles are such synthetically built subunits capable to self assemble to shells of various shapes. Subunits and their interactions are typically designed so that they match the target shell geometry as much as possible. Such designs, however, require an increasing number of subunit types as the target shell complexity increases. Instead, we propose a computational scheme aimed to reduce the required subunit specificity in such assemblies, by relaxing the exact geometrical constraints on the target surface and exploiting subunit deformability. Two example structures will be considered, in both of which subunits are triangular and the assembly is stress mediated. The first one is an icosahedral structure of either of two sizes, both in a mechanically stressed state. Our aim is to find the appropriate subunit design which assembles both sizes with prescribed yields, from a single type of subunits, by adjusting the subunit's mechanical properties. The second structure is an ellipsoidal shell, which, again, we aim to assemble from a single species of subunits. Finite compliance allows subunits to adapt to the local geometry and coordination, however, the associated frustration raises the problem of controling long range elastic interactions and rules out naive subunit designs. As a solution, we propose an optimization approach to efficiently adjust the subunits' mechanical properties until a target free energy minimum is reached at the required sizes and shapes. We use a coarse grained triangle model with a grand canonical Monte Carlo scheme for equilibrium and dynamical simulations. Progressing from the fastest towards the most accurate estimates of the free energy we intend to provide a full stack methodology for finding the most optimal subunit parameters given a target structure.
Original text from CORDIS.
Participants
- UNIVERSITATEA BABES BOLYAI · Cluj-NapocaCoordinatorRomania
Links
Data: CORDIS, © European Union