Bottom-up construction of in vitro switchable memories

Abstract

Reaction networks displaying bistability provide a chemical mechanism for long-term memory storage in cells, as exemplified by many epigenetic switches. These biological systems are not only bistable but switchable, in the sense that they can be flipped from one state to the other by application of specific molecular stimuli. We have reproduced such functions through the rational assembly of dynamic reaction networks based on basic DNA biochemistry. Rather than rewiring genetic systems as synthetic biology does in vivo, our strategy consists of building simplified dynamic analogs in vitro, in an artificial, well-controlled milieu. We report successively a bistable system, a two-input switchable memory element, and a single-input push-push memory circuit. These results suggest that it is possible to build complex time-responsive molecular circuits by following a modular approach to the design of dynamic in vitro behaviors. Our approach thus provides an unmatched opportunity to study topology/function relationships within dynamic reaction networks.

An analytical approach to bistable biological circuit discrimination using real algebraic geometry

“…The analysis of an equilibrium polynomial with a zero root-for example, that describing a recently developed DNA-based circuit that achieves bistability through a combination of mutual inhibition and autocatalysis [34]-presents challenges, because Sturm's theorem requires that neither of the limits of the region of interest (in our case, 0 and þ1) be roots. Under these circumstances, one could choose an e , 0 for the lower limit; however, in this case, there is no guarantee that the three roots found by Sturm's theorem will all represent physically real, positive quantities (because one or more of the roots could in theory lie between e and 0).…”

Motif analysis for small-number effects in chemical reaction dynamics

“…12,17,[33][34][35] The list of motifs provided herein should be helpful in searching for other candidates of biochemical reactions in which the small-number effect is expected to play an important role within a cell. Furthermore, considering recent advances in synthetic biology, [36][37][38] the list is also expected to be useful for designing a system that shows the small-number effect. Of course, our criterion can also be applied to larger network motifs using the criterion described for a multivariable system given in the supplementary material.…”

Enzyme-free nucleic acid dynamical systems

“…Since the discovery of well-mixed chemical oscillators (1,2), synthetic reaction networks with complex temporal dynamics have been engineered based on small-molecule interactions, such as redox chemistries (3). More recently, the information-based chemistry underlying the central dogma of molecular biology has been used to create a variety of dynamical systems, such as bistable switches and oscillators in living cells (4)(5)(6)(7) and in simplified cell-free systems (8)(9)(10)(11)(12)(13)(14) that involve a limited number of enzymes. However, the range of dynamical behaviors demonstrated by synthetic systems does not yet approach the complexity and sophistication of biological circuits (15,16).…”