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From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies Mathieu Surin, Sébastien Ulrich

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From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies Mathieu Surin, Sébastien Ulrich From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies Mathieu Surin, Sébastien Ulrich To cite this version: Mathieu Surin, Sébastien Ulrich. From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies. ChemistryOpen, Wiley, 2020, 9 (4), pp.480-498. 10.1002/open.202000013. hal- 02989483 HAL Id: hal-02989483 https://hal.archives-ouvertes.fr/hal-02989483 Submitted on 18 Nov 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. REVIEW developing non-covalent methodologies that enable the robust, From interaction to function in precise, and predictable arrangement of molecules into functional supramolecular systems.[4] DNA-templated supramolecular 1.2. Why using nucleic acids as templates? self-assemblies Besides their prominent biological functions as encoding matter, nucleic acids such as DNA and RNA have been recently [a] [b] Mathieu Surin* and Sébastien Ulrich* considered as building blocks for the bottom-up construction of 1D, 2D or even 3D nanomaterials. For instance, the field of DNA Abstract: DNA-templated self-assembly represents a rich and nanotechnology,[5] based in part on DNA origami,[6] where the growing subset of supramolecular chemistry where functional sequence of nucleic acids can be harnessed and computed to self-assemblies are programmed in a versatile manner using program the self-fabrication of complex multi-component nucleic acids as readily-available and readily-tunable templates. nanostructures, is blooming. The interest in nucleic acids as In this review, we summarize the different DNA recognition biomolecular templates originates from their water-solubility, modes and the basic supramolecular interactions at play in this their ease of production through chemical synthesis or molecular context. We discuss the recent results that report the DNA- biology techniques, and the diverse yet highly programmable templated self-assembly of small molecules into complex yet primary structure (sequence), secondary structure (folding, precise nanoarrays, going from 1D to 3D architectures. Finally, shape, chirality) and tertiary structures (e.g. origami, tiles, we show their emerging functions as photonic/electronic cubes) they can adopt.[7] In addition, DNA contains a huge nanowires, sensors, gene delivery vectors, and supramolecular information density that can serve to encode information for catalysts, and their growing applications in a wide range of area storage (up to 2 bits per nucleotide) or, for instance, to program from materials to biological sciences. sequence-controlled polymers that are structurally unrelated to nucleic acids.[8] While the covalent modification and functionalization of nucleic 1. Introduction acids require delicate synthetic methodologies, supramolecular approaches interestingly use non-modified and readily-available [7b, 9] 1.1. Why organizing molecules in precise nanoarrays? nucleic acids. A supramolecular approach also offers room for self-correction during self-assembly, erasing intermediates Supramolecular assemblies can display distinct and unique formed under kinetic control and leading to the formation of the properties compared to the individual molecules they are made thermodynamic product. However, achieving the controlled of. For instance, light-harvesting complexes serve as a beautiful organization of small molecules onto nucleic acid requires a example showing how the organization of chromophores is deep understanding of the binding mechanisms and non- instrumental for directing the cascade of energy and electron covalent interactions at play with nucleic acids. Consequently, transfer processes.[1] Viruses constitute another striking example, this knowledge guides the adequate molecular design of nucleic for which a precise number of proteins forming a capsid are acid ligands. Finally, by characterizing the resulting templated arranged with a high level of organization around the genomic self-assembly one may evidences emerging functions arising nucleic acid, which is essential for its delivery, and from the collective supramolecular organization of the system. assembly/disassembly processes.[2] Recently, researchers have In this review, we aim at providing an overview of this field, reported many examples in the fields of electronics, sensing, which could help in guiding the reader toward the design of delivery, and catalysis that illustrate emerging collective functional DNA-templated supramolecular assemblies. It is properties arising from supramolecular organizations occurring specifically oriented towards organic molecules appropriately at different levels.[3] Such a change in the properties when going engineered to bind DNA and to be organized via a template from molecules to organized supramolecular assemblies is due effect. For reports on DNA recognition by metal complexes and to the intermolecular communication that is made possible by DNA-templated assembly of inorganic nanostructures, the the close proximity of molecules held together through non- reader is referred to as recent accounts (see, for example, [10] [11] covalent interactions. There is therefore a strong interest in references and , respectively). We start this review by providing a short overview of the possible recognition modes between single molecules and DNA [a] Dr. Mathieu Surin (or RNA). Then, we describe the recent advances of nucleic Laboratory for Chemistry of Novel Materials, Center of Innovation acids templating of small organic molecules, partitioned by the and Research in Materials and Polymers (CIRMAP), University of main type of recognition mode at play. Various types of Mons-UMONS, 7000 Mons, Belgium supramolecular organizations driven by the template effect are E-mail: [email protected] [b] Dr. Sébastien Ulrich considered, and we particularly show the main trends towards IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier, sophisticated supramolecular systems. We then shortly review France the recent developments on DNA-templated polymerization, i.e. E-mail: [email protected] the polymerization of (supra)molecular guests pre-assembled REVIEW onto the nucleic acid template, in particular for dynamic DNA features a major and a minor groove – differing in size and polymerization processes. Finally, we focus this account on the hydration – that can accommodate ligands. In summary, DNA unique functions that may be achieved using DNA-templated can offer four handles for supramolecular interactions with supramolecular self-assemblies, with potential applications in ligands: base pairing, recognition of phosphodiesters, photonic wires, conducting nanowires, (bio)sensors, delivery recognition by groove binding, and recognition by intercalation systems, and catalysts. (Figure 1).[14] Mathieu Surin carried out his PhD with Prof. Roberto Lazzaroni (University of Mons) and a post-doc with Prof. Paolo Samorì (ISIS, Université de Strasbourg). In 2009, he was appointed as research associate at the Fund for Scientific Research (FNRS, Belgium) and he developed a research line on DNA-based supramolecular assemblies. In 2015, he was invited professor at the University of Montpellier. Since 2017, he is associate professor within the University of Mons. His main research interests are supramolecular chemistry and bio-inspired (nano)materials. Sébastien Ulrich carried out his PhD with Prof. Jean-Marie Lehn (Université de Strasbourg, France), and post-docs with Prof. Harry L. Anderson (Oxford University, UK) and Prof. Eric T. Kool (Stanford University, CA, USA). In 2011 he joined the group of Prof. Pascal Dumy, first in Grenoble, then in Montpellier, France where he was recruited by the CNRS in 2012 to develop his current research interests in the field of supramolecular bioorganic chemistry. In 2017, he was awarded the CNRS Bronze Medal. Figure 1. Possible recognition modes of organic molecules to single-stranded DNA (top) and double-stranded DNA (bottom). Examples of minor groove- binding and intercalation modes were extracted from the Protein Data Bank. 2. Binding to DNA Nucleic acids are like necklaces of nucleobases (Adenine A, 2.1. Recognition of nucleobases Cytosine C, Guanine G, Thymine T or possibly uracil U) covalently tethered to a ribose sugar, assembled through Base-pairing is a straightforward way to bind DNA in a selective phosphodiester bridges. Nucleic acids are poly-anions in which manner and would make possible the binding of different nucleobases are engaged in π-stacking interactions with one molecules in a precise array based on the DNA sequence. another. Base pairing, through complementary Watson-Crick- Indeed, the Watson-Crick base-pairing approach has been type or Hoogsteen-type hydrogen bonds, results in the folding of undertaken by several researchers, who covalently attached a single-stranded DNA (ssDNA), the formation of helicoidal nucleobase to a non-natural molecule, in view of pairing the double-stranded DNA (dsDNA), or more complex structures like synthetic molecule to complementary nucleobases of a single- triplex, i-motif
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