Result: Specificity of hybridization between DNA sequences based on free energy

Title:
Specificity of hybridization between DNA sequences based on free energy
Authors:
TANAKA, Fumiaki, KAMEDA, Atsushi, YAMAMOTO, Masahito, OHUCHI, Azuma
Source:
DNA computing (11th international workshop on DNA computing, DNA11, London, ON, Canada, June 6-9, 2005)0DNA 11. :371-379
Publisher Information:
Berlin; New York: Springer, 2006.
Publication Year:
2006
Physical Description:
print, 13 ref 1
Original Material:
INIST-CNRS
Subject Terms:
Computer science, Informatique, Sciences exactes et technologie, Exact sciences and technology, Sciences appliquees, Applied sciences, Informatique; automatique theorique; systemes, Computer science; control theory; systems, Informatique théorique, Theoretical computing, Algorithmique. Calculabilité. Arithmétique ordinateur, Algorithmics. Computability. Computer arithmetics, Calcul ADN, DNA computation, Càlculo ADN, Calcul moléculaire, Molecular computation, Càlculo molecular, DNA, Electrophorèse gel, Gel electrophoresis, Electroforesis gel, Energie libre, Free energy, Energía libre, Energie minimale, Minimum energy, Energía mínima, Hybridation, Hybridization, Hibridación, Raisonnement basé sur cas, Case based reasoning, Razonamiento fundado sobre caso, Simulation ordinateur, Computer simulation, Simulación computadora
Document Type:
Conference Conference Paper
File Description:
text
Language:
English
Author Affiliations:
Graduate School of Engineering, Hokkaido University, North 13, West 8, Kita-ku, Sapporo 060-8628, Japan
CREST, Japan Science and Technology Corporation, 4-1-8, Honmachi, Kawaguchi, Saitama 332-0012, Japan
Graduate School of Information Science and Technology, Hokkaido University, North 14, West 9, Kita-ku, Sapporo 060-0814, Japan
ISSN:
0302-9743
Access URL:
http://pascal-francis.inist.fr/vibad/index.php?action=search&terms=19130918
Rights:
Copyright 2007 INIST-CNRS
CC BY 4.0
Sauf mention contraire ci-dessus, le contenu de cette notice bibliographique peut être utilisé dans le cadre d’une licence CC BY 4.0 Inist-CNRS / Unless otherwise stated above, the content of this bibliographic record may be used under a CC BY 4.0 licence by Inist-CNRS / A menos que se haya señalado antes, el contenido de este registro bibliográfico puede ser utilizado al amparo de una licencia CC BY 4.0 Inist-CNRS
Notes:
Computer science; theoretical automation; systems
Accession Number:
edscal.19130918
Database:
PASCAL Archive

Further Information

We investigated the specificity of hybridization based on a minimum free energy (ΔGmin) through gel electrophoresis analysis. The analysis, using 94 pairs of sequences with length 20, showed that sequences that hybridize each other can be separated using the constraint ΔGmin ≤ -14.0, but cannot be separated using the number of base pairs (BP) in the range from 9 to 18. This demonstrates that the ΔGmin is superior to the BP in terms of the capability to separate specific from non-specific sequences. Furthermore, the comparison between sequence design based on ΔGmin, and that based on the BP, done through a computer simulation, showed that the former outperformed the latter in terms of the number of sequences designed successfully as well as the ratio of successfully designed sequences to the total number of sequences checked.