Biomolecular computers with multiple restriction enzymes.

Sebastian Sakowski,Janusz Blasiak,Jacek Waldmajer,Joanna Sarnik,Tomasz Poplawski,Tadeusz Krasinski

doi:10.1590/1678-4685-gmb-2016-0132

Sebastian Sakowski, Janusz Blasiak + Show 4 more

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https://doi.org/10.1590/1678-4685-gmb-2016-0132

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Abstract

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.

Highlights

Biomolecular computers are the answer to problems associated with the development of traditional, siliconbased computers, their miniaturization, as implied by the Heisenberg uncertainty principle, and to limitations in data transfer to and from the main memory by the central processing unit (Amos, 2005)
We present an algorithm for the construction of transition molecules in biomolecular automata with multiple restriction enzymes
The main idea of this general method relies on dividing the set of states Q of finite automaton M into disjoint subsets of states Qi Ì Q (Figure 6) and assigning only one restriction enzyme ei Î E to each Qi in the following way

Summary

Introduction

Biomolecular computers are the answer to problems associated with the development of traditional, siliconbased computers, their miniaturization, as implied by the Heisenberg uncertainty principle, and to limitations in data transfer to and from the main memory by the central processing unit (Amos, 2005). Some of this research provided only theoretical solutions without practical laboratory implementation, e.g., biomolecular representations of the Turing machine (Rothemund, 1995) or the pushdown automaton (Cavaliere et al, 2005; Krasinski et al, 2012), there have been prominent exceptions, including a stochastic automaton (Adar et al, 2004) and a finite automaton (Benenson et al, 2001, 2003) These first constructions of DNA computers used one restriction enzyme (RE) as the hardware and DNA fragments as the software and input/output signals. These DNA computers represent a class of devices known as nondeterministic finite automata that can solve simple computational problems. Benenson et al (2001) designed and implemented a model of a two-state two-symbol (Figure 1A) nondeterministic finite state automaton – the simplest model of a computer (Hopcroft et al, 2001)

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