TY - GEN
T1 - A probabilistic model of the DNA conformational change
AU - Shiozaki, Masashi
AU - Ono, Hirotaka
AU - Sadakane, Kunihiko
AU - Yamashita, Masafumi
PY - 2006
Y1 - 2006
N2 - 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.
AB - 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.
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U2 - 10.1007/11925903_21
DO - 10.1007/11925903_21
M3 - Conference contribution
AN - SCOPUS:49949116652
SN - 3540490248
SN - 9783540490241
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 274
EP - 285
BT - DNA Computing - 12th International Meeting on DNA Computing, DNA12, Revised Selected Papers
T2 - 12th International Meeting on DNA Computing, DNA12
Y2 - 5 June 2006 through 9 June 2006
ER -