Dynamic folding and assembly of DNA Origamis: isothermal nanomachines powered by light – DYOR

1) The dynamics of origami self-assembly is characterized by ultra-fast, high resolution and environmental (in liquid phase, whose composition is changeable, and at controlled temperature) atomic force microscopy (HS-AFM)
2) Isothermal assembly is obtained by adjusting the ionic composition such that oligonucleotides can self-assemble at room temperature to form any kind of origami with a user-defined morphology.
3) Photocontrol is achieved through the implementation of light-sensitive DNA intercalators previously developed by the team
4) The formation of 3D structures is obtained thanks to the discovery of a novel phenomenon of super-folding of origami during their adsorption on soft cationic surfaces obtained by layer-by-layer assembly of polymers.

The results of major scientific interest are:
1) the description of a new method for the assembly and isothermal functionalization of DNA nanostructures (origami, nanogrids). This study is completed. An article on the subject is currently under revision
2) the possibility for the first time to control by light the fusion and hybridization properties of origami. This was possible thanks to the implementation of light-sensitive DNA intercalators previously developed by our team.
3) the discovery of a reversible overfolding phenomenon allowing to dynamically convert 2D nanostructures (origami, nanogrids) into 3D structures, and to use the latter as support for guests (chemical functions, proteins). This study has been published as a «hot paper« in the journal Angewandte Chemie International Edition:
K. Nakazawa, F. El Fakih, V. Jallet, C. Rossi-Gendron, M. Mariconti, L. Chocron, M. Hishida, K. Saito, M. Morel, S. Rudiuk, D. Baigl. «Reversible supra-folding of user-programmed functional DNA nanostructures on fuzzy cationic substrates.« Angew. Chem. Int. Ed. 2021, 60, 15214 -15219
4) the possibility of isothermal transformation from one morphology to another. Proof of concept has been established and finalization of this study is expected to result in a high impact paper.

For the rest of this project, we will focus on two main points. First, we will continue our exploration of the isothermal transformation of origami. Indeed, by studying the isothermal formation of origami, and by understanding that the mechanism comes from a massive phenomenon of strand displacements under thermodynamic control, we anticipated and observed that it was possible to induce the formation of an origami of a given morphology (e.g. a rectangle) into another shape (e.g. a triangle), in an isothermal way (at room temperature), by simply exposing the initial origami to a set of competing oligonucleotides potentially leading to a more thermodynamically stable shape. This kind of morphological reconfiguration, much sought after by the community, has never been described and these first results could lead to a major result and allow, what is at the heart of this ANR project, dynamic and reconfigurable origami of a new kind. The other focus will be on the application of all the dynamic actuation methods developed during the first two years on functionalized origami to dynamically control the spatial and temporal distribution of invited entities: proteins on the one hand to control the dynamics of enzymatic activity, and particles on the other hand to control the optical coupling properties that result from them.

1 peer-reviewed article :
1. K. Nakazawa, F. El Fakih, V. Jallet, C. Rossi–Gendron, M. Mariconti, L. Chocron, M. Hishida, K. Saito, M. Morel, S. Rudiuk, D. Baigl. Reversible supra-folding of user-programmed functional DNA nanostructures on fuzzy cationic substrates. Angew. Chem. Int. Ed. 2021, 60, 15214 –15219

3 invited talks in international conferences :
1. D. Baigl. « Reconfigurable self-assembly: from self-foldable DNA nanomachines to photoswitchable dissipative colloidal crystals. » Conférence invitée lors du congrès Applications of Diffusiophoresis in Drying, Freezing and Flowing Colloidal Suspensions. Lausanne (Suisse), 30 octobre-1 novembre 2019
2. D. Baigl. « Reconfigurable self-assembly: from evolutive DNA nanomachines to living 2D and 3D crystals. » Conférence invitée lors du congrès Colloids 2019. Okinawa (Japon), 3-8 novembre 2019.
3. D. Baigl. « Reconfigurable self-assembly: from self-foldable DNA nanomachines to photoswitchable dissipative colloidal crystals. » Conférence invitée lors du congrès Gordon Research Conference Engineered Response in Soft Matter. Ventura (États-Unis), 2-7 février 2020

1 invited talk in a national conference:
1. D. Baigl. « Softening DNA nanotechs at room temperature: optical melting and hybridization, giant shape reconfigurability and photoswitchable hybrid crystals. » Conférence invitée lors du symposium DNA Nanotech, Paris (France), 25 octobre 2019.

1 invited outreach conference :
1. D. Baigl. « Magie molle : Nanomachines ADN, optofluidique et taches de café ». Conférence invitée lors du 9ème Colloque « De la Recherche à l’Enseignement ». Paris, 07 septembre 2019.

DNA origami, a revolutionary technique invented in 2006, allows for programming the folding of a large DNA molecule into virtually any desired geometry with a nanometric resolution. This method leads to exquisite yet highly static structures. Here we propose to make DNA origamis dynamic and controllable by external stimulations and apply them as programmable, stimulus-responsive nanoscaffolds. First, we will achieve reversible photocontrol of origami folding at constant temperature by implementing a new class of molecules able to affect the melting of DNA in a photodependent manner. Second, we will exploit dynamic assembly principles using standard and photosensitive DNA condensation agents to assemble origamis into novel stimulus-responsive 3D superstructures. As origamis are easily functionalized at predefined positions, we will finally exploit the resulting dynamic origamis as stimulus-triggerable 2D and 3D nanoscaffolds to control the spatio-temporal distribution of proteins and nanoparticles as well as their coupling properties. This will allow us to photoregulate the catalytic activity of enzymatic cascades and to control optical properties of a new kind of photoswitchable particle nanoclusters.