Towards an autonomous multistate biomolecular devices built on DNA

Krasiński, Tadeusz; Sakowski, Sebastian; Popławski, Tomasz

doi:10.1109/nabic.2014.6921899

Cited by 4 publications

(2 citation statements)

References 17 publications

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“…We also have considered and presented certain arithmetic estimates concerning the possibilities of theoretical extension of a biomolecular DNA automaton using two or more REs [36]. An extended model based on many REs creates an opportunity to implement, in the laboratory, more complex NFA [39] and even other theoretical models of computers: pushdown automata [28] and Turing machines [27].…”

Section: Discussionmentioning

confidence: 99%

A detailed experimental study of a DNA computer with two endonucleases

Sakowski

Krasiński

Sarnik

et al. 2017

Zeitschrift Für Naturforschung C

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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.

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Section: Discussionmentioning

confidence: 99%

A detailed experimental study of a DNA computer with two endonucleases

Sakowski

Krasiński

Sarnik

et al. 2017

Zeitschrift Für Naturforschung C

Self Cite

View full text Add to dashboard Cite

show abstract

“…The structures of DNA and RNA are represented using the concept of classical automata theory [50,51]. Krasinski et al [52] represented the restricted enzyme in DNA with pushdown automata in circular mode. Khrennikov and Yurova [53] modeled the behavior of protein structures using classical automata theory and investigated the resemblance between the quantum systems and modeling behavior of proteins.…”

Section: Prior Workmentioning

confidence: 99%