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Page 8 of 25 Zhong et al. Chem Synth 2023;3:27 https://dx.doi.org/10.20517/cs.2023.15

Figure 4. (A) Dissipative operation of a nucleic acid-based nanodevice fueled by sulfur-disulfide reactions; (B) Schematic illustration of
the transient DNA system induced by CPA- and NAA-fueled dissipative pH value changes. Figure 4A is quoted with permission from
Grosso et al. [111] Figure 4B is quoted with permission from Mariottini et al. [113] . CPA: cyanopropanoic acid; NAA: nitroacetic acid.

designed to be in two switchable conditions that respond to the pH value changes, a duplex form at a high
pH value and an intramolecular triplex form at a low pH value. The dissipative CPA pH modulator is
employed to induce the transient transformation of the nanoswitch between the duplex form and triplex
form. In the second case, a reconfigurable DNA receptor is designed to include a pH-responsive stem-loop
domain for the structural transformation and a cargo-strand bonding site for the uptake of the DNA cargo
strand. The NAA fuels the release/uptake of the cargo strand. Adding NAA to the system leads to an acidic
condition and the transformation of the DNA duplex structure to the triplex form. This structural
reconfiguration destabilizes the interaction between the cargo strand and the DNA receptor, releasing the
cargo from the nanostructure. With the dissipation of NAA, the pH value returns to the neutral condition,
and the triplex structure is dissociated. As a result, the receptor restores its cargo-uptake ability and reloads
the cargo strand.

Furthermore, by introducing photo-sensitive molecules, light can be an ideal fuel source for constructing
dissipative systems [114-116] . Compared to the above chemical fuels employed in the dissipative operation of
DNA-based systems, light presents a series of advantages, including the diverse options in the intensity and
wavelength, the convenient control in time and space, and no waste molecules accumulated in the system.
For example, Wang et al. utilized an azobenzene-modified DNA strand (F) as a photo-sensitive molecule to
operate the dissipative behavior of the DNA-based system . The trans-azobenzene units can intercalate
[116]
into the DNA duplex structure and stabilize the resulting DNA structure (F/G). Upon UV light irradiation (
t
λ = 440 nm), trans-azobenzene units are photoisomerized to the cis-state, which leads to the dissociation of
the DNA duplex. The strand-displacement reaction between the released strand G and the Y-shaped
structure H/I/J/K leads to the formation of G/J/K and H/I. Under the heat condition, the cis-azobenzene
unit is thermally dissipated back to the trans-azobenzene state. Then, the trans-azobenzene-modified strand
F displaces strand G from the structure G/J/K to recover the duplex structure (F/G) and the Y-shaped
t
structure (H/I/J/K). The repeatable dissipative behavior of the system is presented by the time-dependent
concentration changes of intermediate structure I/H.

Beyond the transformation of the physical and chemical changes to the transient DNA signals, nucleic acid-
based dynamic networks can generate more complex dynamic behaviors driven by enzymes and
DNAzyme [106,116-120] .

Transient signals by DNAzyme-catalyzed reactions
Metal-ion-dependent DNAzymes have been applied to drive nucleic acid-based far-from-equilibrium
networks for years [116,117] . Recently, Wang et al. reported a gated dissipative network operated by the Pb -
2+
ion-dependent DNAzyme, as shown in Figure 5 . Two gates in the network act as thresholds, enabling the
[116]