Pathway Complexity in Fuel-Driven DNA Nanostructures with Autonomous Reconfiguration of Multiple Dynamic Steady States

Abstract

We introduce pathway complexity on a multicomponent systems level in chemically fueled transient DNA polymerization systems, achieving autonomous evolution over multiple structural dynamic steady states from monomers to dimers, oligomers of dimers to randomized polymer structures before being ultimately degraded back to monomers once the fuel is consumed. The enabling key principle is to design monomer species having kinetically selected molecular recognition in the structure-forming step and which are reconfigured in an enzymatic reaction network. This non-equilibrium systems chemistry approach to pathway complexity provides new conceptual insights in fuel-driven automatons and autonomous materials design.Nature relies on non-equilibrium structures and processes to perform work by dissipating energy stored in ATP or GTP. 1-4 Pathway complexity plays a pivotal role to associate those dynamic structures and thus realize a living system. For instance, intracellular signaling networks involve multiple steps of ATP/GTP-powered phosphorylation and enzyme activation for downstream regulations. 5-8 Thus far, synthetic systems with fuel-driven transient properties are developed in the fields of systems chemistry, materials science and synthetic biology. 4,[9][10][11][12] Synthetic systems requiring continuous energy influx have extended the features and functions of present-day functional materials. [13][14] Most presently existing fuel-driven systems show single trajectories of their non-equilibrium states, such as helical structure switching, 15 supramolecular polymerization, 14, 16 nanoreactors, 13, 17 transient hydrogels, [18][19] and photonic materials. 20 On the contrary, in classical supramolecular chemistry, pathway complexity is regularly exploited to transiently pass energetically downhill from metastable structures to equilibrium. 21-22 A relevant example showing multiple states in an autonomous fashion is the case of supramolecular helicity switching coupled to hydrolysis of environmental ATP to ADP, AMP, and to adenosine. 15 In directly chemically driven systems, Boekhoven and coworkers recently showed that small fuel amounts allowed the formation of reversibly assembling transient clusters, while large fuel amounts lead to a trapping of aggregates in a non-transient fashion. 23 Critically, pathway-controlled uphill fuel-driven systems involving multiple building blocks with an autonomous structural reconfiguration of multiple dynamic transient states have not been shown by any previous report. Such a concept would however be very valuable to promote a further integration of systems chemistry concepts with reaction networks and dissipative and transient structure formation.The difficulty in implementing such a concept in synthetic system is related to the need for highest levels of programmability and ability for deterministic autonomous reconfiguration leading to multiple transient dynamic steady-state (DySS) structures, which is a profound challenge in supramolecular chemistry. 24-26 On the contrary, DNA ...

ATP‐Responsive and ATP‐Fueled Self‐Assembling Systems and Materials

“…ATP-fueled systems for autonomous systems design relate to the emerging and very active field of non-equilibrium self-assemblies. [42,81,84,88,200] Even though an elaboration on all differences of the various approaches is not the central part of this review, it is important to point to some major ones. By discriminating how ATP is stored and used in the assembled structures, two major types of ATP fuel-driven self-assemblies have been developed.…”

“…Compared to the standard 4 nt sticky end, 1 nt sticky ends showed a significant lag time for the ATP‐fueled DNA polymerization due to their much weaker ability for hybridization. [ 200 ] This difference allowed to introduce pathway complexity in a multicomponent systems by designing monomer species having kinetically selected molecular recognition in the structure‐forming step. This could be realized for instance by combining two complementary AB/AʹBʹ monomer species (M3, M4) bearing a 1 nt and a 4 nt sticky overhang on each side ( Figure ).…”

“…This could be realized for instance by combining two complementary AB/AʹBʹ monomer species (M3, M4) bearing a 1 nt and a 4 nt sticky overhang on each side ( Figure ). [ 200 ] Upon fueling with ATP, the system evolved first into a dimer state due to preferential ligation of the complementary 4 nt sticky ends (lifetime 1). Later on oligomers of the dimers emerged by the slower ligation of the 1 nt sticky ends (even numbers of monomers, lifetime 2).…”

Transient DNA‐Based Nanostructures Controlled by Redox Inputs

“…Yet, in all these cases adaptability originates from changes in the free energy landscape caused by the external trigger. The transient self‐assembly of DNA‐based nanostructures and the kinetic control of DNA‐based nanodevices has only recently been achieved using synthetic gene circuits or DNA‐recognizing enzymes as the fuel‐consuming units . DNA self‐assembly in these systems is characterized by the instalment of a dynamic kinetic steady state in which an anabolic reaction leads to DNA‐hybridization, whilst a catabolic enzymatic reaction concurrently causes disassembly by hydrolysing hybridized DNA.…”

Polymer Transformers: Interdigitating Reaction Networks of Fueled Monomer Species to Reconfigure Functional Polymer States

“…Previously, for simple, single-species ERNs of this type, we confirmed that i) the degree of ligation in the dynamic steady state (DySS) plateau depends on the ratio of ligase/REase, ii) structural dynamics (constant bond shuffling and subunit exchange) occurs, and iii) the lifetimes depend on the ATP concentration. [16,18,19] The adaptive transformation will operate as follows ( Figure 1 b): First, ligase (black) and ATP polymerize the three monomers into a mixed copolymer, serving as a homogenous initial material state. Afterwards, we add two REases (green, red) as signals with a certain ratio to dynamize the system.…”