Molecular instructions in living cells can be timed rather like the notes or chords in a piece of music. For example, a finite number of genes can be activated and expressed in different orders, for different durations, to permit the assembly (or disassembly) of different polymers. A few genes, then, can give rise to many structures, similar to the way a few notes or chords can give rise to many musical compositions.
Emulating the conductor-like abilities of living cells, researchers from the UCLA Samueli School of Engineering and the University of Rome Tor Vergata in Italy have developed synthetic genes that can be controlled like the genes in living cells. Instead of waving a conductor’s baton, the researchers used a promoter “nicking” and strand displacement strategy to activate their synthetic genes, which would then express RNA molecules to the degree necessary to activate or deactivate the self-assembly function of distinct DNA-based monomers.
Essentially, the researchers showed how a suite of simple building blocks can be programmed to make complex biomolecular materials, in this case, nanoscale tubes from DNA tiles. The researchers also indicated that the same components can also be programmed to break up the design for different materials.
All of this work was orchestrated by Elisa Franco, PhD, a professor of mechanical and aerospace engineering and bioengineering and head of the Dynamic Nucleic Acid Systems Laboratory at UCLA Samueli. Details of the work recently appeared in Nature Communications, in a paper titled, “Developmental assembly of multi-component polymer systems through interconnected synthetic gene networks in vitro.”
“Here we demonstrate how the sequential activation or deactivation of distinct DNA building blocks can be modularly coordinated to form distinct populations of self-assembling polymers using a transcriptional signaling cascade of synthetic genes,” the article’s authors wrote. “Our building blocks are DNA tiles that polymerize into nanotubes, and whose assembly can be controlled by RNA molecules produced by synthetic genes that target the tile interaction domains.”
“[We] can obtain spatially and temporally different outcomes in nanotube assembly, including random DNA polymers, block polymers, and as well as distinct autonomous formation and dissolution of distinct polymer populations,” the authors continued. “Our work demonstrates a way to construct autonomous supramolecular materials whose properties depend on the timing of molecular instructions for self-assembly and can be immediately extended to a variety of other nucleic acid circuits and assemblies.”
“We had the idea of recreating in the laboratory similar gene cascades that, depending on the timing of gene activation, could induce the formation, or the disassembly, of synthetic materials,” said co-author Francesco Ricci, PhD, a professor of chemical science at the University of Rome Tor Vergata.
In their study, the researchers used building blocks of DNA tiles formed by a few synthetic DNA strands. They then created a solution containing millions of these tiles, which interacted with one another to form micron-scale tubular structures. The structures form only in the presence of a specific RNA molecule that triggers the formation. A different RNA trigger molecule can also induce the disassembly of the same structures.
Then, they programmed different synthetic genes that produce the RNA triggers at specific times so that the formation and dissolution of the DNA structures can be timed with precision. By connecting these genes together, they created a synthetic genetic cascade, similar to that of a fruit fly, which can control not only when a certain type of DNA structure forms or dissolves, but also its specific compositional properties at a given time.
“Our approach is not limited to DNA structures, it can be extended to other materials and systems that rely on the timing of biochemical signals,” said Daniela Sorrentino, PhD, a postdoctoral scholar in Franco’s laboratory and the study’s first author. “By coordinating these signals, we can assign different functions to the same components, creating materials that spontaneously evolve from the same parts. This opens up exciting advances in synthetic biology and paves the way for new applications in medicine and biotechnology.”
Franco stated that the scientists’ work “suggests a way toward scaling up the complexity of biomolecular materials by taking advantage of the timing of molecular instructions for self-assembly, rather than by increasing the number of molecules carrying such instructions. This points to the exciting possibility of generating distinct materials that can spontaneously ‘develop’ from the same finite set of parts by simply rewiring the elements that control the temporal order of assembly.”
