Analysis of the Innovation Trend in Cell-Free Synthetic Biology

Cell-free synthetic biology is a maturing field that aims to assemble biomolecular reactions outside cells for compelling applications in drug discovery, metabolic engineering, biomanufacturing, diagnostics, and education. Cell-free systems have several key features. They circumvent mechanisms that have evolved to facilitate species survival, bypass limitations on molecular transport across the cell wall, enable high-yielding and rapid synthesis of proteins without creating recombinant cells, and provide high tolerance towards toxic substrates or products. Here, we analyze ~750 published patents and ~2000 peer-reviewed manuscripts in the field of cell-free systems. Three hallmarks emerged. First, we found that both patent filings and manuscript publications per year are significantly increasing (five-fold and 1.5-fold over the last decade, respectively). Second, we observed that the innovation landscape has changed. Patent applications were dominated by Japan in the early 2000s before shifting to China and the USA in recent years. Finally, we discovered an increasing prevalence of biotechnology companies using cell-free systems. Our analysis has broad implications on the future development of cell-free synthetic biology for commercial and industrial applications.

DNA origami cryptography for secure communication

Biomolecular cryptography exploiting specific biomolecular interactions for data encryption represents a unique approach for information security. However, constructing protocols based on biomolecular reactions to guarantee confidentiality, integrity and availability (CIA) of information remains a challenge. Here we develop DNA origami cryptography (DOC) that exploits folding of a M13 viral scaffold into nanometer-scale self-assembled braille-like patterns for secure communication, which can create a key with a size of over 700 bits. The intrinsic nanoscale addressability of DNA origami additionally allows for protein binding-based steganography, which further protects message confidentiality in DOC. The integrity of a transmitted message can be ensured by establishing specific linkages between several DNA origamis carrying parts of the message. The versatility of DOC is further demonstrated by transmitting various data formats including text, musical notes and images, supporting its great potential for meeting the rapidly increasing CIA demands of next-generation cryptography.

Isotachophoresis applied to biomolecular reactions

This review discusses research developments and applications of isotachophoresis (ITP) to the initiation, control, and acceleration of chemical reactions, emphasizing reactions involving biomolecular reactants such as nucleic acids, proteins, and live cells.

Complete sampling of an enzyme reaction pathway: a lesson from gas phase simulations

With proper sampling strategy, convergence of free energy profiles of biomolecular reactions in the gas phase can be achieved in microseconds of simulation.

Design Tradeoffs

This chapter describes some of the design tradeoffs arising from the interaction between synthetic circuits and the host organism. It first considers the effects of competition for shared cellular resources on circuits' behavior. In particular, circuits (endogenous and exogenous) share a number of cellular resources. The insertion or induction of synthetic circuits in the cellular environment changes for these resources, with possibly undesired repercussions on the functioning of the circuits. Independent circuits may become coupled when they share common resources that are not in overabundance. This fact leads to constraints among the concentrations of proteins in synthetic circuits, which should be accounted for in the design phase. Next, the chapter looks at the effect of biological noise on the design of devices requiring high gains. Specifically, the chapter illustrates possible design tradeoffs between retroactivity attenuation and noise amplification that emerge due to the intrinsic noise of biomolecular reactions.