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Page 18 of 25 Zhong et al. Chem Synth 2023;3:27 https://dx.doi.org/10.20517/cs.2023.15

accumulator records the dynamic signals transmitted from the fluctuation filter through molecular catalysis.
Through the construction of a mixed-cell community, the synthetic molecular system can sense, analyze,
and process meaningful stimuli from the environment or the release of natural cells rather than weak noise.
This study contributes to constructing artificial molecular biological systems with more bionic functions
and even specific living activities and provides a new way to understand and regulate the natural biological
reaction networks.

Beyond intracellular signaling dynamics, the communication between the synthetic cells that represent the
sociability of artificial cells is critical to developing complex living systems [152-156] . Joesaar et al. proposed a
general approach to engineer intercommunication networks between the populations of protocells, as
[155]
shown in Figure 11 . Each of the protocells in the populations is made of two parts, a protein-based
microcapsule mimicking the semi-permeable membrane of the natural cell and a nucleic acid-based
reaction network module acting as the information-processing unit. The protein-based microcapsule,
named proteinosome, is permeable to short (< 100 bases), singlestranded nucleic acids and is highly suitable
for developing a protocellular communication platform. The nucleic acid-based reaction network module is
designed to encode and decode molecular information through enzyme-free DNA strand-displacement
reactions. It is modified with streptavidin for encapsulation in the proteinosome. Individual protocells can
be engineered to perform various tasks, such as signal detection, signal transduction, signal cascading, signal
amplification, feedback operation, and Boolean logic operations. The programmability and orthogonality of
DNA reactions make DNA strands ideal molecular information to minimize unintended cross-interactions
in protocellular communities. Several populations of protocells can exchange information simultaneously
on crisscrossed pathways, and one population can efficiently transfer messages to several other populations.
Therefore, compartmentalized nucleic acid-based network modules allow collective signaling dynamics in
the protocell populations, such as multiplex sensing, cascaded amplification, bidirectional communication,
and distributed logic operations. In addition, transcriptional genelet and CRISPR/Cas-based DNA
machinery were also applied to develop protocellular signaling networks for mimicking cellular features .
[156]

Similarly, the transcriptional genelet module is established and encapsulated in the protocells. The
encapsulation and activation of DNA templates were demonstrated by generating RNA aptamer signals in
the presence of T7 RNAP and external DNA trigger strands. Then, the functional transcription genelet
module encapsulated in the protocell generates diffusive RNA signals, which could be sensed by the
neighboring protocells and trigger the signal cascade or the localization of Cas nucleases in the neighboring
protocells. These findings highlight the opportunities for combining the programmability of DNA
nanotechnology with the capabilities of semi-permeable proteinosome in protocellular signaling networks
and provide a further step towards complex signaling dynamic behaviors in protocells.

The above examples show how the information encoded in the sequence of nucleic acids regulates chemical
reactions and inter-molecular interactions to produce nucleic acid-based dynamic networks for information
processing. Combining the nucleic acid-based dynamic network and compartmentalized systems represents
a new way to construct protocells with living features. These understandings are crucial in laying the
groundwork for building complexity in multi-component systems and highlighting the potential of nucleic
acid-based dynamic networks for signal transduction in artificial cells.

CONCLUSION AND OUTLOOK
Living systems illustrate the importance of the organization of interacting components in complex dynamic
networks [9-10] . DNA, RNA, proteins, and other components organized in the manner of equilibrium, near
equilibrium, far-from-equilibrium, or collaborative patterns form diverse biological networks [57,83] . These