A DNA-based computational model using a specific type of restriction enzyme

Yasubumi Sakakibara, Hiroshi Imai

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

The restriction enzyme is an important device which provides cutting operations of DNA strands to construct a DNA-based computational model such as splicing systems [3]. In this paper, we employ a specific type of restriction enzyme which cut on both sides of their recognition sequences [6], and propose a new DNA-based computational model which has several advantages compared with conventional models. The new computational model is shown to achieve universal computability using only natural DNA-based methods such as annealing, cut, ligation and circular strands without any practically hard assumption. Furthermore, while the generative power of the computational model is shown to be universal, the parsing (accepting) computation ability is more appealed. That is, given any string, the model computes whether it accepts the string, and most conventional DNA-based model have not offer this accepting process. We show that the new computational model efficiently computes the parsing process for context-free grammars and finite sequential transducers.

Original languageEnglish
Pages (from-to)315-325
Number of pages11
JournalLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume2568
Publication statusPublished - 2003

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Computational Model
Enzymes
DNA
Restriction
Parsing
Strings
Context-free Grammar
Computability
Transducers
Annealing
Transducer
Ligation
Context free grammars
Model
Equipment and Supplies

ASJC Scopus subject areas

  • Computer Science(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Theoretical Computer Science

Cite this

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