Abstract
The field of DNA computing is devoted to the creation of devices capable of processing information signals encoded on biological substrates. These signals are intended to propagate in cascades of biochemical reactions in which they naturally undergo a progressive reduction. Preventing signal reduction becomes crucial considering applications in biological environments where molecular cues are scarce. Although catalytic gates have been developed using the toehold-exchange mechanism for logic gate circuits, the matter remains unaddressed for logic reasoning devices. Inspired by the main work in biomolecular logic programming, we present a new encoding scheme for facts, rules, and queries to implement backward/forward chaining inference paths via catalytic DNA strand displacement cascades. In this context, we take advantage of fueling reactions to recover inputs, which preserve their availability to react with different implication gates. Our molecular design is thermodynamically analyzed by providing suitable sequences for the correct formation of structures. With regard to the kinetic performance, data from simulations suggest that the model operates efficiently even with identified crosstalk reactions.
Highlights
Biomolecular computing is concerned with the engineering of devices made from biomolecules showing some computational behavior
As in the work of Ran et al [30], we focus on the resolution of simple logic programs in both backward and forward reasoning modes, but using instead an enzyme-free strand displacement architecture
Both sugar-phosphate backbones run in opposite directions, bound by complementary bases projected into the interior
Summary
Biomolecular computing is concerned with the engineering of devices made from biomolecules showing some computational behavior. It was initially conceived with the idea of addressing computationally difficult problems [1]–[3] but, nowadays, research endeavors have moved towards the creation of simple computational devices that can be interconnected in a modular fashion for the assembly of more complex systems [4]–[7] Since both input and output signals in biomolecular computing systems are composed of biological reagents, the field exhibits promising applications in biomedicine and biotechnology including in vitro diagnostics [8]–[11] and, the in vivo integration of devices to deliver molecular payloads [12], [13].
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