Isothermal self-assembly of multicomponent and evolutive DNA nanostructures

16 March 2022, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Self-assembly is both an advantageously spontaneous process to organize molecular or colloidal entities into synthetic functional superstructures and a key-feature of how life builds its components. However, compared to their living counterparts, synthetic materials made by self-assembly usually lack some of the interesting properties of living systems such as multicomponent character or capability to adapt, transform and evolve. Here we describe an isothermal multicomponent DNA self-assembly method that recapitulates all these characteristics and leads to user-defined objects with programmable shape, site-specific function, intrinsic reconfigurability and unprecedented capacity of major transformation and shape evolution. Using a generic magnesium-free buffer containing NaCl, we show that a complex cocktail of hundreds of different DNA strands can spontaneously assemble at room or body temperature to form desired DNA origamis of various shapes with site-specific protein functionalization, extended nanogrids or single-strand tile-assemblies. In situ atomic force microscopy allows us to follow the self-assembly process and demonstrate that DNA origami assembly proceeds through multiple folding pathways, the system escaping kinetic traps until it reaches its equilibrium target structure. We also show that, under thermodynamic control, this method allows a given system to self-select its most stable shape in a large pool of competitive DNA strands. We finally demonstrate the first giant morphological transformation of DNA origamis spontaneously evolving at constant temperature from one shape to a radically different one by the massive exchange of all its constitutive staple strands. This method greatly expands the repertoire of shapes and functions attainable by isothermal self-assembly as well as provides tools to design evolutive DNA assemblies, with applications ranging from directed or self-adaptive morphological changes to nanostructure optimization by evolution.

Keywords

DNA nanotechnology
Self-assembly
DNA origami
nanogrids
smart materials
isothermal assembly
Evolution
Reconfigurable materials
protein
DNA tiles
AFM
Atomic force microscopy

Supplementary materials

Title
Description
Actions
Title
Supporting Information
Description
This file includes: 1. Materials 2. Methods 3. Supplementary figures 4. Supplementary tables 5. Legends of supplementary movies 6. Supplementary references
Actions
Title
Movie S1
Description
Direct observation of the Λ-to Δ-origami transition on a mica-supported lipid bilayer (DOPC) in the TAENa buffer at room-temperature (T = 26 °C). At t = 0 min, addition of the missing A-side staples (Fig. S12), following the protocol given in Methods section, paragraph “Real-time imaging of the Λ→Δ isothermal evolution on a lipid bilayer surface”. Observation by AFM at the same position over 223 min. Scale bar: 300 nm
Actions
Title
Movie S2
Description
Crop (375 nm x 375 nm) of Movie S1 around the origami labelled B in Fig. 3.
Actions
Title
Movie S3
Description
Crop (375 nm x 375 nm) of Movie S1 around the origami labelled C in Fig. 3.
Actions
Title
Movie S4
Description
Crop (375 nm x 375 nm) of Movie S1 around the origami labelled D in Fig. 3.
Actions

Supplementary weblinks

Comments

Comments are not moderated before they are posted, but they can be removed by the site moderators if they are found to be in contravention of our Commenting Policy [opens in a new tab] - please read this policy before you post. Comments should be used for scholarly discussion of the content in question. You can find more information about how to use the commenting feature here [opens in a new tab] .
This site is protected by reCAPTCHA and the Google Privacy Policy [opens in a new tab] and Terms of Service [opens in a new tab] apply.