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Time-Programmed Self-Assemblies and Dynamic Materials

Periodic Reporting for period 4 - TimePROSAMAT (Time-Programmed Self-Assemblies and Dynamic Materials)

Reporting period: 2020-10-01 to 2021-10-31

Unlike automobiles that run on combustion engines with gasoline and that can drive autonomously using computers, living beings run on chemical fuels and derive their intelligent adaptation capabilities from (bio)chemical and structural networks. Life on the molecular level can be described in its essence as a true far-from-equilibrium self-organization process in which chemical energy is used to create work against gradients and in which (bio)chemical reaction networks provide the local, brain-free computational intelligence to adapt with a tailored response in complex sensory landscape. By keeping the molecular systems outside of equilibrium in energy-rich states, living systems can react much faster and with higher adaptation capabilities, as the energy for the change and adaptation is already present. Such living systems, after being fed with sufficient energy, operate autonomously by keeping the molecular systems powered up using the chemical energy provided through the conversion of food.

In synthetic systems, we have so far mastered controlled structure formation in a process called self-assembly, which is an equilibrium type structure formation into static structures. Autonomous and dynamic and intelligent behavior is largely absent and these systems have at best become switchable through the integration of responsive materials. This has allowed to make passively switchable materials that adapt in an equilibrium scenario to a new energy landscape with a different function. While those static materials have had large success in translation to consumer products, such as in switchable hydrogels or for optical materials, great advances can be envisaged if we can incorporate the dynamics of life into life-like, autonomous materials systems – the topic of this proposal TimeProSAMAT.

TimeProSAMAT aims to go the next step and targets the introduction of concepts to program the time domain of self-assembled systems and materials to reach autonomous behavior in CLOSED systems under non-equilibrium conditions. This involves the following key strategies of controlling the kinetics of assembly and disassembly pathways: (i) Modulation of an energy-consuming surrounding by feedback systems, (ii) dissipative structure formation and (iii) active structural feedback. After reaching a fundamental understanding on a self-assembly level, we want to capitalize on these enabling self-assembly concepts by providing entirely new and original approaches to dynamic soft materials with internally encoded self-regulation features (similar to a self-destruction mechanism), opening doors to active functionalities and adaptive properties beyond what classical responsive equilibrium self-assembly can offer.

Such autonomous materials systems find application in autonomous soft robotics, for self-destroying gels in the biomedical field, or for making tamper-proof optical security features to protect high value and perishable goods.
Read more about such concepts in the 10th year anniversary issue of Soft Matter: " Approaches to program the time domain of self-assemblies" Soft Matter, 2015,11, 7857-7866
1. We have developed new pH feedback mechanisms using different activator/dormant deactivator pairs and have successfully coupled them to the self-assembly and materials level and have shown time-programmed photonic gels, time-programmed conformational switches for the DNA i-motif and time-programmed i-motif-based DNA hydrogels that feature also programmable lag times. (Adv. Mater. 2017, 29, 1521; Chem. Sci. 2017, 8, 4100; Nano Letters 2017, 17, 4989; Angew. Chem. Int. Ed. 60, 22537 (2021); Angew. Chem. Int. Ed. 60, 22537 (2021))
2. We have established the ATP-fueled dynamic covalent bond system for the antagonistic reaction scheme of the T4 Ligase and restriction enzymes. This has allowed us to not only program the lifetimes of the corresponding systems, but also allowed us to manipulate the properties and the dynamics of the dynamic steady state in the fueled non-equilibriums state. Sci. Adv., 5, eaaw0590, (2019).
3. We have identified the nucleobase-dependent phase segregation behavior of ssDNA and coupled this to the formation of unconventional non-equilibrium morphologies, such as protocells. (Nature Nanotechnology, 2018,13, 730).
5. We have established autonmous metabolic adaptation scenarios inside of such protocells using a combination of artificial metalloenzymes and chemical downstream reactions (Nat. Nanotechnol. 1856 (2020)).
4. We have generated mechanosensing DNA hydrogels that can sense forces and open pathways towards actutators, soft robotics and for artificial mechanosensing matrices to study cellular traction forces and control mechanobiology. (Nature Communications, 2019,10, 529).
5. We have been extending the building block scope to 3D DNA Origami to make more complex self-regulating self-assemblies. (Sci. Adv. 7, eabj5827 (2021); Nanoscale 12, 16995 (2020); Small 17, 2005668 (2021); Angew. Chem. Int. Ed. 59, 5515 (2020).)
6. We have been working on metabolic type reaction networks of pH-modulating enzymes to increase the chemical reaction network complexity, implement new feedback mechanisms and orient towards logic gates. (Angew. Chem. Int. Ed. 60, 22537 (2021))
7. We have been developing synthetic schemes for DNA-polymer hybrids (J. Am. Chem. Soc. 142, 16610 (2020).).
8. We have been developing complex ATP-driven DNA systems, including self-sorting systems, as well as transient multivalency to bridge hierarchcial length scales, light-switchable ATP fuels, and several examples of pathway complexity. (Angew. Chem. Int. Ed. 59, 12084 (2020). J. Am. Chem. Soc. 142, 685, (2020).
Angew. Chem. Int. Ed. 59, 18161 (2020), Nat. Commun. 11, 3658 (2020), J. Am. Chem. Soc. 142, 21102 (2020), Chem 6, 3329 (2020), Nat. Commun. 14, 5132 (2021).)
1. versatile pH-Feedback systems in acidic and basic regime that are programmable in their lifecycles. Ability to program the time domain of self-assembling systems, e.g. DNA, peptides, block copolymer structures to make autonomous hydrogels or optical devices.
2. ATP-dissipating system that operates in balance between fusion and cleavage of DNA strands with programmable lifecycles and dynamics.
3. Discovery of an unknown phase seperation phenomenon of ssDNA, which can be used to make functional DNA protocells by pathway complexity
4. Discovery of strain-adaptive hydrogels with controlled sacrficial bonds by implementation of mechanofluorescent DNA folding motifs
5. Strongly refined and advanced synthetic methods for polymer DNA conjugates
6. We have developed several examples of pathway complexity and light switching in driven DNA systems
7. We have discovered how self-sorting in multicomponents systems can be implemented and how it is possible to bridge from the molecular scale to the colloidal self-assembly scale and to a systems scale.
9. We have connect uphill-driven ATP reaction networks with downhill-oriented strand displacement cascades, that allowed to make self-resettable strand displacement systems and transient DNA nanotubes.
10. We have identified how molecular-scale chemical reaction networks can be coupled to the transient organization of functions and structures (colloids, DNA nanotubes, origami self-assemblies, coacervates)
11. We have identified chemo-structural feedback mechanisms in pH landscapes
Time Programmed Autonomous Materials Systems