LNCS 2950 - Aspects of Molecular Computing (Frontmatter Pages)

An Algorithm for Testing Structure Freeness of
Biomolecular Sequences
Satoshi Kobayashi 1 , Takashi Yokomori 2 , and Yasubumi Sakakibara 3
1 Dept. of Computer Science, Univ. of Electro-Communications
Yokohama, Japan
satoshi@cs.uec.ac.jp
2 Dept. of Mathematics, School of Education
Waseda University, Tokyo, Japan
CREST, JST (Japan Science and Technology Corporation)
yokomori@waseda.jp
3 Dept. of Biosciences and Informatics, Keio University, Chofu, Japan
CREST, JST (Japan Science and Technology Corporation)
yasu@bio.keio.ac.jp
Abstract. We are concerned with a problem of checking the structure
freeness of S + for a given set S of DNA sequences. It is still open whether
or not there exists an efficient algorithm for this problem. In this paper,
we will give an efficient algorithm to check the structure freeness of S +
under the constraint that every sequence may form only linear secondary
structures, which partially solves the open problem.
1 Introduction
In the Adleman’s pioneering work on the biomolecular experimental solution to
the directed Hamiltonian path problem ([1]) and in many other works involving
wet lab experiments performed afterward, it has been recognized to be very
important how to encode information on DNA sequences, in order to guarantee
the reliability of those encoded DNA sequences to avoid mishybridization. The
problem of finding a good set of DNA sequences to use for computing is called
the DNA sequence design problem. In spite of the importance of this problem,
it seems that only rather recently research efforts have been paid to develop
systematic methods for solving this problem. An excellent survey on this topic
of DNA sequence design issues can be found in [6].
Being currently engaged in a research activity called molecular programming
project in Japan, we are aiming as a final goal at establishing a systematic
methodology for embodying desired molecular solutions within the molecular
programming paradigm in which designing not only DNA sequences but also
molecular reaction sequences of molecular machines are targeted as major goals
([12]). Here, by designing DNA sequences we mean a broader goal than the one
mentioned above, e.g., the DNA sequence design may generally deal with the
inverse folding problem, too, the problem of designing sequences so as to fold
themselves into intended structural molecules.
N. Jonoska et al. (Eds.): Molecular Computing (Head Festschrift), LNCS 2950, pp. 266–277, 2004.
c○ Springer-Verlag Berlin Heidelberg 2004