Chemically Fueled Self‐Assembly in Biology and Chemistry

Abstract

Life is a non‐equilibrium state of matter maintained at the expense of energy. Nature uses predominantly chemical energy stored in thermodynamically activated, but kinetically stable, molecules. These high‐energy molecules are exploited for the synthesis of other biomolecules, for the activation of biological machinery such as pumps and motors, and for the maintenance of structural order. Knowledge of how chemical energy is transferred to biochemical processes is essential for the development of artificial systems with life‐like processes. Here, we discuss how chemical energy can be used to control the structural organization of organic molecules. Four different strategies have been identified according to a distinguishable physical‐organic basis. For each class, one example from biology and one from chemistry are discussed in detail to illustrate the practical implementation of each concept and the distinct opportunities they offer. Specific attention is paid to the discussion of chemically fueled non‐equilibrium self‐assembly. We discuss the meaning of non‐equilibrium self‐assembly, its kinetic origin, and strategies to develop synthetic non‐equilibrium systems.

Insights from an information thermodynamics analysis of a synthetic molecular motor

“…In the SI (section V B), we show that the condition TΣ mech =0 implies K r = 1, while the condition TΣ mech > 0 implies K r = 1, with forward movement when K r > 1. This shows how the nonequilibrium thermodynamic framework, which focuses on energetic aspects quantified by the dissipation TΣ mech , is consistent with previous analysis [15][16][17]49 focusing on kinetic aspects quantified by K r , which determines the sign of the current J according to equation ( 4). This reiterates the effectiveness of this information-thermodynamics-based approach and, again, demonstrates the usefulness of this minimalist molecular motor as a Rosetta Stone for the translation of meaning and understanding between different frameworks for describing phenomena.…”

The Biotin–Avidin Interaction in Biotinylated Gold Nanoparticles and the Modulation of Their Aggregation

“…This aggregation mode takes advantage of the very slow response to the change of the relative concentration of AuNPs and avidin once the initial interaction has occurred. This means that by careful additions of precise amounts of nanoparticles and avidin in the correct sequence, one may reach the formation of aggregates under kinetic control that are in fact out of equilibrium [42]. The equilibrium is represented by the small clusters (2-3 nanoparticles) present in Figure 6A.…”

Dissipative operation of pH-responsive DNA-based nanodevices

“…The functional state has to be maintained in a dissipative manner, that is until fuel exhaustion. 4 Recently, artificial dissipative systems have been described in the fields of assembly/disassembly of aggregates, 5 host–guest chemistry, 6 and fully abiotic 7 molecular machines. In this context, because of the high predictability, reversibility of the involved interactions, and programmability, synthetic DNA has emerged as a powerful material to engineer non-equilibrium machines, devices, 8 and nanostructures with a transient behavior.…”