Artificial biochemical clocks control the timing of DNA nanomachines

We have used an artificial biochemical oscillator to drive the motion of a simple biomolecular nanodevice constructed from DNA. The way in which the coupling of the device to the oscillator affects the performance of the combined system sheds light on the general problem of modularity and “back-action” in complex biochemical systems.

HFSP Young Investigator Grant holders Friedrich Simmel and Erik Winfree and colleagues
authored on Mon, 24 October 2011

We have used an artificial biochemical oscillator to drive the motion of a simple biomolecular nanodevice constructed from DNA. The way in which the coupling of the device to the oscillator affects the performance of the combined system sheds light on the general problem of modularity and “back-action” in complex biochemical systems.

One of the goals of bionanotechnology and in vitro synthetic biology is the creation of "autonomous" molecular systems – systems that "run by themselves", without external control. As one step in this direction, we here used an artificial biochemical “clock” to control a variety of bio-molecular processes - the motion of a DNA “nanomachine”, and the production of functional RNA molecules. This is roughly analogous to the situation in biological systems, in which biochemical oscillators control processes such as cell division, structure formation, or metabolic processes.

Our biochemical clock consists of two artificial gene templates (“genelets”), from which regulatory RNA molecules are produced by in vitro transcription. The genelets influence each other by mutual activation and inhibition, resulting in an oscillatory feedback circuit.

We molecularly coupled the oscillator circuit to a variety of load processes. For instance, RNA molecules produced by the oscillator genelets were used to drive the motion of “DNA tweezers”, a simple nanomechanical device made from DNA, or to control the production of RNA aptamers. We systematically varied the amount of load to the circuit to study how the dynamics of the oscillator were affected by the load. We found that for high load concentrations the performance of the oscillator degraded considerably. To overcome the detrimental “back-action” of the load processes, we developed an “insulator” circuit – a molecular amplifier – that effectively decoupled the load from the core oscillator and allowed us to operate the system even under very high load conditions.

Our oscillator system represents one of the first realizations of an in vitro molecular clock that is used to drive other biochemical processes in a modular fashion. Our detailed study of load-circuit interactions contributes to the understanding of two important challenges for synthetic biology: the synchronization of biomolecular processes and the design of modular and scalable biochemical circuits.

 

Figure Top: An oscillator circuit is made from two “genelets” SW21 and SW12 that are coupled to each other via two regulatory RNA molecules rA1 (an activator) and rI2 (an inhibitor). One of the RNA molecules (here: rA1) is also used to drive a DNA nanomechanical device (“DNA tweezers”).  Bottom: Fluorescence traces recorded from the oscillator itself (T21) and the DNA tweezers, demonstrating the successful control of the motion of the DNA tweezers by the oscillator circuit.

 

Reference

Timing molecular production and motion with a synthetic transcriptional clock.Elisa Franco, Eike Friedrichs, Jongmin Kim, Ralf Jungmann, Richard Murray, Erik Winfree, Friedrich C. Simmel. Proc. Natl. Acad. Sci. U.S.A. 108, E784-E793 (2011).DOI: 10.1073/pnas.1100060108.

Pubmed link

PNAS link