Molecular programming breakthrough could create better molecular assemblers

Over the past couple of months there have been world firsts in the creation of DNA robots and Molecular robots, the latter of which ended up forming a molecular scale production line that was used to build a couple of molecules, and albeit the first prototype of its kind, it's the world's first true Molecular Assembler.

Ever since molecular assemblers, or, more specifically, being able to “manipulate objects at a molecular level,” has been of interest the creation of, in this respect, DNA molecules that follow specific instructions, have also always been of interest. Now a breakthrough by a team of researchers in the US could help give us more precise molecular control of a wide range of “synthetic chemical systems,” and the teams breakthrough, the creation of a synthetic chemical amplifier and oscillator, opens the door for other engineers around the world to create molecular machines with new, complex behaviours.

The team from the University of Texas in Austin, which was led by David Soloveichik and Niranjan Srinivas created their new system using a method that will eventually allow them to embed what they’re calling “sophisticated circuit computation” within molecular systems that one day will have applications in advanced manufacturing, healthcare and nanotech, and during their study they managed to demonstrate that they could program their synthetic chemical oscillators by building DNA molecules that followed specific instructions.

They also said that their discovery suggests that DNA can be much more than simply a passive molecule used solely to carry genetic information.

“DNA can be used in a much more active manner,” Soloveichik said, “we can actually make it dance, with a rhythm, if you will. This suggests that nucleic acids (DNA and RNA) might be doing more than we thought, which can even inform our understanding of the origin of life, since it is commonly thought that early life was based entirely on RNA.”

The team’s new synthetic system could also one day be used in artificial cells, synthetic biology or even in future molecular assemblers to make sure that molecular scale processes happen in the order they’re supposed to. But oscillation is just one example of sophisticated molecular behaviour. Looking beyond oscillators, this work opens the door for engineers to create more sophisticated molecular machines, such as the DNA and molecular robots I mentioned earlier, and depending on how the molecular machines are programmed, it’ll be feasible to engineer different behaviours into them such as communication and signal processing, problem solving and decision making, control of motion, and so on, the kind of circuit computation generally attributed only to electronic circuits.

“As engineers, we are very good at building sophisticated electronics, but biology uses complex chemical reactions inside cells to do many of the same kinds of things, like making decisions,” Soloveichik said, “eventually, we want to be able to interact with the chemical circuits of a cell, or fix malfunctioning circuits or even reprogram them for greater control. But in the near term, our DNA circuits could be used to program the behaviour of cell-free chemical systems that synthesise complex molecules, diagnose complex chemical signatures and respond to their environments.”

The team developed their new oscillator by building DNA molecules that have a specific programming language, producing a repeatable workflow that can generate other complex temporal patterns and respond to input chemical signals, and they compiled their language down to precise interactions, a standard practice in the field of electronics but completely novel in biochemistry.

The team’s research was conducted as part of the National Science Foundation’s (NSF) Molecular Programming Project, which launched in 2008 as a faculty collaboration to turn molecular programming into a sophisticated, user friendly and widely used technology for creating nanoscale devices and systems.

Details of their research was published in the journal Science.