Distributed DNA-based Communication in Populations of Synthetic Protocells

Abstract

Developing distributed communication platforms based on orthogonal molecular communication channels is a crucial step towards engineering artificial multicellular systems. Here, we present a general and scalable platform entitled 'Biomolecular Implementation of Protocellular Communication' (BIO-PC) to engineer distributed multichannel molecular communication between populations of non-lipid semipermeable microcapsules. Our method leverages the modularity and scalability of enzyme-free DNA strand-displacement circuits to develop protocellular consortia that can sense, process and respond to DNA-based messages. We engineer a rich variety of biochemical communication devices capable of cascaded amplification, bidirectional communication and distributed computational operations. Encapsulating DNA strand-displacement circuits further allows their use in concentrated serum where non-compartmentalized DNA circuits cannot operate. BIO-PC enables reliable execution of distributed DNA-based molecular programs in biologically relevant environments and opens new directions in DNA computing and minimal cell technology.Living cells communicate by secreting diffusible signaling molecules that activate key molecular processes in neighboring cells 1,2 . These molecular communication channels facilitate information distribution among cells, enabling collective information processing functions that cannot be achieved by cells in isolation 3,4 . Synthetic biologists have advanced the engineering of synthetic cell-cell communication systems based on living cells resulting in multicellular consortia capable of complex sender-receiving functions 5-9 , bidirectional 10,11 and synchronized 12 communication and distributed computations 13,14 . However, engineering synthetic gene networks in living cells remains challenging due to the large number of context dependent effects arising from, among others, competition between shared resources and loading effects 15 . In contrast, developing molecular communication channels among abiotic synthetic protocell compartments has received much less attention than in living systems 16,17 . Due to their minimalistic design, engineering distributed information processing functions in fully synthetic multicellular communities has several advantages including a high degree of control and reduced design-build-test cycles. Abiotic protocellular consortia, based on lipid or non-lipid compartments and wired by orthogonal information channels, would thus present a versatile technology for the bottom-up construction of complex cell-population behaviors 18,19,20 . Although some elegant strategies to achieve one-way intercellular communication in fully synthetic protocellular systems have been reported 21,22,23,24 , a scalable methodology for implementing distributed functions involving bidirectional communication across populations of protocells is currently lacking.Here, we present Biomolecular Implementation of Protocellular Communication (BIO-PC), a highly programmable protocellular messaging system that ena...

Dynamic and scalable DNA-based information storage

“…Similar capabilities in DNA-based systems would significantly increase their value and competitiveness. ssDNA overhangs have previously been used to execute computations in the context of toehold switches [40][41][42][43] , and we therefore hypothesized they could be used to implement instorage file operations. As a proof-of-principle, we implemented locking, unlocking, renaming, and deleting files and showed these operations could be performed at room temperature (Fig.…”

Dynamic DNA-based information storage

“…Similar capabilities in DNA-based systems would significantly increase their value and competitiveness. DNA has previously been used to execute computations [23][24][25] , and we therefore hypothesized toeholds could be used to implement in-storage file operations. As a proof-of-principle, we implemented locking, unlocking, renaming, and deleting files and showed these operations could be performed at room temperature (Figure 4).…”

Automated Leak Analysis of Nucleic Acid Circuits

“…Circuit-level techniques for reducing leaks include toehold-sized clamps, additional long domains in molecular cascades, translocating a single nucleotide between domains using interdomain bridging , and multiarm junction substrates to make leakage energetically unfavorable . Further techniques include spatial localization of species to DNA origami − or protocells to reduce interference through physical separation, threshold gates to consume leaks on inputs to logic circuits, , and creating a shadow copy of the circuit to cancel out leaks by shadow cancellation . While each of these approaches is able to mitigate leaks in specific contexts, leak mitigation of DSD circuits in general still remains a challenge.…”