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Dynamic synthetic molecular duplexes

Periodic Reporting for period 1 - DyNAmics (Dynamic synthetic molecular duplexes)

Reporting period: 2017-03-01 to 2019-02-28

Precise control of macroscopic properties at molecular level is one of the biggest challenges of modern science. Nature accomplishes this by adding information to matter, and organizes chemical system of nonliving components into living, biological systems. Achieving a deep knowledge on the appropriate manipulation of the intermolecular non-covalent interactions, will allow chemistry to be not only the science of the structure and transformation of matter, but also an information science, involving the storage of information at the molecular level. Inspired by the most fascinating nature’s information system, the DNA, “DyNAmics” performs a modular and highly flexible synthesis of novel information carrying monomers, able to self-organize in duplex structure, through both covalent and non-covalent bonds formation. The reliability, robustness and the dynamic formation of H-bond based duplex, together with the template ability in a dynamic combinatorial system, is investigated. By quantitative assessment of multivalent recognition of complementary sequences and imperfections in the duplex formation of non-complementary and defective sequences, valuable information on the structural features and fidelity of supramolecular assembly formation of various sequences can be obtained. Reliable formation of dynamic synthetic duplexes would allow precise control over supramolecular interactions and will lay the foundation for formation of smart advanced materials with unprecedented properties, such as innovative data storage materials and new Constitutional Dynamic Materials. Furthermore, this will be crucial for the development of efficient template directed synthesis for information encoding molecules. The development of these challenging concepts took longer than foreseen and two years of research has been insufficient to implement this system for efficient template synthesis of sequence oligomers. Promising initial results have been obtained which validate the chosen approach.
The work performed in this project has covered several aspects related to the main scope, which is the development of novel information carrying monomers, able to self-organize in duplex structure, through both covalent and non-covalent bonds formation.
Synthesis - The designed monomers resulted to be unstable under the reaction conditions, hence we had to redesign new hydrogen bonding (HB) donor and acceptor monomers. However, thanks to the planned modular synthetic strategy, we were able to synthesise HB monomers that can be assembled as sequence controlled oligomers, via imine formation and subsequent reductive amination. (Article 2)
Duplex formation - An efficient synthetic procedure has been developed and different omosequence oligomers have been synthesized. Studying the assembly properties, we have been able to demonstrate that the synthesized oligomers are able to for HB-driven duplexes with the complementary sequence-oligomers in organic solvents such as toluene and chloroform. In addition we deeply studied the folding properties of the backbone, using mixed oligomers. (Articles 1, 2, 4)
Dynamic Combinatorial Chemistry – We studied and developed optimal conditions for Dynamic combinatorial experiments, using the synthesized HB donor and acceptor monomers. Solubility issues have been solved and we developed HPLC methods that allow the analysis of imine population with no need of reducing to stable amines.
Finally, when we used reduced oligomers as templates in DCC experiments, we surprisingly found that specific oligomers can behave as catalyst for imine formation, but in a recognition, dependent manner. The fact that properties typical of biocatalyst such as enzyme, can already emerge from simple sequence defined oligomers, represent the fundamental for new interesting studies.

[1] F. Szczypiński, L. Gabrielli, C.A. Hunter, Chem. Sci., 2019, accepted, SC-EDG-04-2019-001669.
[2] L. Gabrielli, C.A. Hunter, “Imine based oligomers able to form duplex in organic solvents” in preparation.
[3] L. Gabrielli, C.A. Hunter, “Emergence of fully synthetic oligomers able to perform recognition-dependent catalysis” in preparation.
[4] L. Gabrielli, C.A. Hunter, “Modulation of folding properties and supramolecular assemblies by tuning the backbone properties of hydrogen bonding polyamines” in preparation.

[1] Luca Gabrielli “Multianalyte 19F-NMR detection with a nanoparticle-based displacement assay”. “ISMSC / ISACS 2017, Cambridge (UK) July 02-06, 2017 

Invited seminars:
[1] “Dynamic synthetic molecular duplexes” as seminar at the University of Padova – Chemistry Department, Padova, Italy, October 10, 2017.

Public outreach:
[1] Y-RICH – Design your future (27th May, 2019) Università la Sapienza – Roma, Italy.
1. Development of oligomers able to form duplexes in chloroform
2. Insight in the importance of backbone flexibility for synthetic duplex formation
3. Development of innovative method for HPLC detection of imine based dynamic combinatorial library, without the need of reducing to stable amine.
4. Emergence and studies of sequence defined oligomers able to perform recognition-dependent catalysis toward imine formation.
These results provide new perspectives for the development of innovative fully synthetic sequence defined oligomers, able to perform recognition and catalysis.