An Educational Tool for
Visualize DNA Structures in vivo
Shigehiro Fukase 1

fukase@mon.hitachi-sk.co.jp
12

Masato Wayama 2
wayama@jomon.ne.jp

3rd Application Systems Department, Hitachi Software Engineering Co., Ltd., 5-79,Onoe-cho, Naka-ku, Yokohama 231-0015, Japan
Open System Sales Department, Bussiness Service Corporation, 2-6-29, Shinmachi,
Aomori 030-0801, Japan

1 Introduction
Recently, we can use computer graphics and GUI very easily on personal computers. In biology eld,many programs are developed to show biochemical molecules. And these are used by many biologists
and students.
But, these tools are almost visualize only crystal formed molecules, so it's not help for learning
molecules' movement and chemical reactions.
Thus we aim at DNA is balanced with temperature conditions in vivo, we developed an simulation
tool for DNA's attitude. This tool helps to understanding that molecules are not stable crystal formin nature and molecules' attitude with temperature changes.

2 System and Methods
DNA molecules consist of two long chains held together by complementary base pairs [1](Fig. 1). Twochains repeat dissociate and associate while temperature changings because of these are connectedwith hydrogen bonds between them [3]. A parts which having many A-T pairs dissasociate easily.
Because G-C pair is more balanced than A-T pair [2]. This tool diplays DNA's status changes withtemperature changings as graphic animations using OpenGL library [4, 5]. And users can set any
temperature by thermostatic control bar.
We handle not a static molecule (such as crystal) but dynamic changing model. In this reason,
we have to simulate not only structure but also the environment in which molecules exist. If wewill have to calculate all actions and desoxyribose's position and movement, calculation and drawing
processes are very dicult. So we implemented as easy model with limited information. First, wehave to represent to transformation of DNA forms easily. DNAs having phosphatic backbone arerepresented to geometrical many sided gures. Second, \bracket joint model" is represented to eachcovalent bonds. Last, And last, hydrogen bonds between base pairs will appears \binding model" withdistance between base pairs to calculate DNAs twist easily.
Furthermore, this tool requires less calculation time than calculation time for all vectors of variation. Because, our tool calculates coordinates from probability of changing radius on every temperature.

3 Future Works
We developed simpli ed biochemical simulation system. However, this system will support to learning
molecular biologies. Our future objective is to evolve this simulation system. This system will lead to276

Figure 1: DNA's dissociation and association.
simulate inexpensive molecular biological laboratories, and easy biochemical experiments are going todo in this system.

Acknowledgements
The authors would like to thank Shinji Noso of NOSO Institute for his invaluable suggestions, helpfulcomments and economical supports.

References[1] Alberts, B., Bray, D. and Lewis, J., Ra , M., Roberts, K., and Watson, J.D., MOLECULAR
BIOLOGY OF THE CELL, THIRD EDITION, Garland Publishing, Inc. New York & London,
1983, 1989, 1994.
[2] Branden, C. and Tooze, J., Introduction to Protein Structure, Garland Publishing, Inc. New York& London, 1991.
[3] Watson, J.D., Gilman, M., Witkowski, and J., Zoller, M., Recombinant DNA, second edition, W.
H. Freeman and Company, New York, N.Y. and Oxford.
[4] Woo, M., Neider, J., and Davis, T., OpenGL Architecture Review Board, three-dimensional
structure: The Ocial Guide to Learning OpenGL, Version 1.1, Addison-Wesley Publishers
Japan, January 1997.
[5] Kilgard, M.J., OpenGL Programming for the X Window System, Addison-Wesley Developers
Press, January 1997.
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