Abstract
A DNA computation model by DNA tiles needs sequence design in order to correctly form tile structure and self-assembly. We design sequence, demonstrate biochemical experiments by a trial and error approach, and, repeatedly analyze tiles. Because no integrated sequence design system computes data that indicates properties of sequences, we must analyze designed sequences by hand and many types of software. In this paper, we develop a sequence design support system for 4× 4 DNA tiles that analyzes and optimizes tile sequences to support sequence design. The most remarkable feature of this system is optimization based on free energy. The optimization strategy is developed so that the energy of perfect tile is the stablest.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Winfree, E., Liu, F., Wenzler, L.A., Seeman, N.C.: Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998)
Yan, H., Feng, L., LaBean, T.H., Reif, J.H.: Parallel Molecular Computations of Pairwise Exclusive-Or (XOR) Using DNA ”String Tile” Self-Assembly. J. Am. Chem. Soc. 125(47), 14246–14247 (2003)
Seeman, N.C.: De Nove Design of Sequence for Nucleic Acid Structual Engineering. Jornal of Biomolecular Structure & Dynamics 8, 739–1102 (1990)
Wei, B., Wang, Z., Mi, Y.: Uniquimer: Software of De Novo DNA Sequence Generation for DNA Self-Assembly -An Introduction and the Related Applications in DNA Self-Assembly. Journal of Computational and Theoretical Nanoscience 4(1), 133–141 (2007)
Zuker, A.M., Mathews, B.D.H., Turner, C.D.H.: Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide. In: Barciszewski, J., Clark, B.F.C. (eds.) RNA Biochemistryand Biotechnology. NATO ASI Series, Kluwer Academic Publisers, Dordrecht (1999)
Zuker, M.: Mfold web server for nulceic acid folding and hybridization prediction. Nucleic Acids Reserch 31(13), 3406–3415 (2003)
Andronescu, M., Aguirre-Hernandez, R., Condon, A., Hoos, H.H.: RNA soft: A suite of RNA secondary structure prediction and design software tools. Nucleic Acids Research 31(13), 3416–3422 (2003)
Hofacker, I.L.: Vienna RNA secondary structure server. Nucleic Acids Research 31(13), 3429–3431 (2003)
Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., LaBean, T.H.: DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 301, 1882–1884 (2003)
Park, S.H., Yan, H., Reif, J.H., LaBean, T.H., Finkelstein, G.: Electronic nanostructures templated on self-assembled DNA scaffolds. Nanotechnology 15, S525–S527 (2004)
Tanaka, F., Kameda, A., Yamamoto, M., Ohuchi, A.: Design of nucleic acid sequences for DNA computing based on a thermodynamic approach. Nucleic Acids Research 33(3), 903–911 (2005)
Author information
Authors and Affiliations
Editor information
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Iimura, N., Yamamoto, M., Tanaka, F., Ohuchi, A. (2008). Sequence Design Support System for 4 × 4 DNA Tiles. In: Garzon, M.H., Yan, H. (eds) DNA Computing. DNA 2007. Lecture Notes in Computer Science, vol 4848. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77962-9_14
Download citation
DOI: https://doi.org/10.1007/978-3-540-77962-9_14
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-77961-2
Online ISBN: 978-3-540-77962-9
eBook Packages: Computer ScienceComputer Science (R0)