6533b82bfe1ef96bd128d6d8
RESEARCH PRODUCT
A detailed experimental study of a DNA computer with two endonucleases
Joanna SarnikSebastian SakowskiJanusz BlasiakTomasz PoplawskiJacek WaldmajerTadeusz Krasińskisubject
0301 basic medicineTheoretical computer scienceDNA LigasesComputer scienceCarry (arithmetic)Oligonucleotides0102 computer and information sciencesBioinformatics01 natural sciencesGeneral Biochemistry Genetics and Molecular Biologylaw.inventionAutomationComputers Molecular03 medical and health sciencesDNA computinglawA-DNADeoxyribonucleases Type II Site-Specificchemistry.chemical_classificationDNA ligaseFinite-state machineBase Sequencebiomolecular computers; DNA computing; finite automataProcess (computing)DNAModels TheoreticalEndonucleasesAutomaton030104 developmental biologychemistry010201 computation theory & mathematicsWord (computer architecture)description
Abstract 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.
year | journal | country | edition | language |
---|---|---|---|---|
2017-03-01 | Zeitschrift für Naturforschung C |