A probabilistic model of the DNA conformational change

Masashi Shiozaki, Hirotaka Ono, Kunihiko Sadakane, Masafumi Yamashita

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)


Predicting the behavior of DNA molecules in vitro is one of the most fundamental issues on DNA computing, but is also known to be quite difficult. Shiozaki et al. proposed a probabilistic model that can simulate many features of biochemical experiments in terms of the reaction rate [7], although there are several differences between the biochemical experiments and the computational simulations on the model. In this paper, we extend the model to support base pairs construction among k DNA sequences, which plays an essential role in realizing branch migrations. The simulation results have much more similarities to the biochemical experiments results than ones on the previous model, which implies that the analysis of the model may give some insight about the reaction rate. Through the analysis, we conclude this paper by giving a guideline for designing DNA sequences that can quickly react.

Original languageEnglish
Title of host publicationDNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers
Number of pages12
Publication statusPublished - 2006
Event12th International Meeting on DNA Computing, DNA12 - Seoul, Korea, Republic of
Duration: Jun 5 2006Jun 9 2006

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4287 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349


Other12th International Meeting on DNA Computing, DNA12
Country/TerritoryKorea, Republic of

All Science Journal Classification (ASJC) codes

  • Theoretical Computer Science
  • Computer Science(all)


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