Synthetic RNA Switches

Today in my searches for the hot new trends in synthetic biology, I found a news article from Science Daily with an intriguing title: "Scientists Achieve First Rewire of Genetic Switches." Rewiring genetic switches sounds pretty neat, but this headline was intriguing to me first of all because it's kind of late to the party--in fact one of the first papers in modern synthetic biology back in 2000 was about engineered genetic switches: "Construction of a genetic toggle switch in Escherichia coli". When I looked more closely, the article wasn't about this kind of transcriptional switch though, but about an RNA-based control mechanism, the riboswitch. Riboswitches are parts of messenger RNA molecules that fold up on themselves in such a way that they can turn the expression of the gene they belong to on and off, depending on whether there is a small molecule bound to the RNA structure, first described by one of my college biochem professors, Ron Breaker. Riboswitches that respond to all sorts of metabolites control the activity of a lot of different genes, and many people have worked on engineering riboswitches and other synthetic RNA aptamers that will bind many different kinds of molecules. I'm curious to read the paper that the news story refers to and to see how their work differs or improves on previous engineering (the paper won't be published until next week, I'll add the link when it goes live), but in the meantime it got me thinking about how cool RNA engineering is and all the cool synthetic biology that people have done with RNA molecules.

Engineered RNA is very versatile for controlling gene expression because RNA is a dual function molecule; RNA can carry a code, like DNA, but unlike DNA, that code can also cause folds and bends in the RNA sequence that create shapes that can perform enzymatic activities like binding chemicals and binding to and/or cleaving RNA or DNA. Engineered RNA sequences can be programmed to bind to an mRNA gene transcript, preventing it from being translated into protein and becoming active. These RNA aptamers can be designed to change shape when they bind a specific small molecule, rapidly falling off the gene and activating expression.

Figure 1--Schematic of synthetic RNA aptamers for control of gene expression from my review article:
More complicated gene expression control switches have also been programmed into the mRNA sequence of synthetic genes, allowing for more complex control of gene expression in response to multiple different input chemicals. These riboswitches have different "arms" that can each bind to different molecules, and depending on how they are designed, will work together to make different logic gates, requiring both, neither, or either one of the input molecules to cause gene expression.

Figure 2--Synthetic RNA Logic Gates from my friend Patrick's review article:

Methods for artificial evolution of synthetic riboswitches that bind to arbitrary small molecules have been improving in the past few years and there are now hundreds of different sequences that can be used in these kinds of synthetic applications. Different combinations of these riboswitches in addition to other control systems, as well as switches that respond to different and crazier molecules can be used to make increasingly complicated synthetic genetic circuits, with all kinds of crazy applications from medicine and gene therapy, biotech and metabolic engineering, to better understanding of the basic science of gene control.