The development of conventional, silicon-based computers has several limitations,
including some related to the Heisenberg uncertainty principle and the von
Neumann “bottleneck”. Biomolecular computers based on DNA and proteins are
largely free of these disadvantages and, along with quantum computers, are
reasonable alternatives to their conventional counterparts in some applications.
The idea of a DNA computer proposed by Ehud Shapiro’s group at the Weizmann
Institute of Science was developed using one restriction enzyme as hardware and
DNA fragments (the transition molecules) as software and input/output signals.
This computer represented a two-state two-symbol finite automaton that was
subsequently extended by using two restriction enzymes. In this paper, we
propose the idea of a multistate biomolecular computer with multiple
commercially available restriction enzymes as hardware. Additionally, an
algorithmic method for the construction of transition molecules in the DNA
computer based on the use of multiple restriction enzymes is presented. We use
this method to construct multistate, biomolecular, nondeterministic finite
automata with four commercially available restriction enzymes as hardware. We
also describe an experimental applicaton of this theoretical model to a
biomolecular finite automaton made of four endonucleases.
Great advances in biotechnology have allowed the construction of a computer from DNA. One of the proposed solutions is a biomolecular finite automaton, a simple two-state DNA computer without memory, which was presented by Ehud Shapiro's group at the Weizmann Institute of Science. The main problem with this computer, in which biomolecules carry out logical operations, is its complexity - increasing the number of states of biomolecular automata. In this study, we constructed (in laboratory conditions) a six-state DNA computer that uses two endonucleases (e.g. AcuI and BbvI) and a ligase. We have presented a detailed experimental verification of its feasibility. We described the effect of the number of states, the length of input data, and the nondeterminism on the computing process. We also tested different automata (with three, four, and six states) running on various accepted input words of different lengths such as ab, aab, aaab, ababa, and of an unaccepted word ba. Moreover, this article presents the reaction optimization and the methods of eliminating certain biochemical problems occurring in the implementation of a biomolecular DNA automaton based on two endonucleases.
In the paper we present a theoretical analysis of extension of the finite automaton built on DNA (introduced by the Shapiro team) to an arbitrary number of states and symbols. In the implementation we use a new idea of several restriction enzymes instead of one. We give arithmetical conditions for the existence of such extensions in terms of ingredients used in the implementation.
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