Abstract
DNA strand displacement technology performs well in sensing and programming DNA segments. In this work, we construct DNA molecular systems based on DNA strand displacement performing computation of logic gates. Specifically, a class of so-called “DNA neurons” are achieved, in which a “smart” way inspired by biological neurons encoding information is developed to encode and deliver information using DNA molecules. The “DNA neuron” is bistable, that is, it can sense DNA molecules as input signals, and release “negative” or “positive” signals DNA molecules. We design intelligent DNA molecular systems that are constructed by cascading some particularly organized “DNA neurons”, which could perform logic computation, including AND, OR, XOR logic gates, automatically. Both simulation results using visual DSD (DNA strand displacement) software and experimental results are obtained, which shows that the proposed systems can detect DNA signals with high sensitivity and accretion; moreover, the systems can process input signals automatically with complex nonlinear logic. The method proposed in this work may provide a new way to construct a sensitive molecular signal detection system with neurons spiking behavior in vitro, and can be used to develop intelligent molecular processing systems in vivo.
Highlights
Biomolecular computation refers to the study of exploiting biological macromolecules to implement relatively standard methods of computation, including molecular computing [1,2,3], membrane computing [4,5], storage media using bacteria rhodopsin [6,7] and biologically altered cells that do rudimentary operations within the paradigm of traditional computation, etc
In recent years, computing with programming DNA molecular has become a hot research topic and lot of work have contributed to this field, such as helical molecular programming [8], tabletop molecular communications with chemical signals [9], molecular computing methods to improve the accuracy of insertion site analysis in tumors [10], DNA selfassembly for computation [11,12], DNA strand displacement (DSD) technology [13,14]
In bio-molecular signal processing systems proposed in [23,24,25,26], single-stranded DNA molecules are generally used as input and output signals; all the strands needed for the computation are mixed together, and the computation proceeds according to the design of DNA sequences without further intervention
Summary
Biomolecular computation refers to the study of exploiting biological macromolecules to implement relatively standard methods of computation, including molecular computing [1,2,3], membrane computing [4,5], storage media using bacteria rhodopsin [6,7] and biologically altered cells that do rudimentary operations within the paradigm of traditional computation, etc. In bio-molecular signal processing systems proposed in [23,24,25,26], single-stranded DNA molecules are generally used as input and output signals; all the strands needed for the computation are mixed together, and the computation proceeds according to the design of DNA sequences without further intervention. The energy for this procedure is provided by the Watson-Crick complementary mechanism of DNA structures themselves, so whole system can run in basic wet labs. Of another DNA strand reactions, which in some sense can process information like functioning unit performing chain reactions
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