Scientific Journal of Information Engineering

February 2013, Volume 3, Issue 1, PP.13-18

Research Expectation of Self-Assembled Model

Based on Molecular Beacon
Zhixiang Yin, Wenyi Zhang#
Department of Mathematics and Physics, Anhui University of Science and Technology, Huainan China, 232001
#

Email: zxyin66@163.com

Abstract
DNA computing using Self-Assembly and its model based on molecular beacon has been the focus in the research of DNA
Computing in the recent years. Self-Assembled DNA computing is the result of the combination of DNA Computing, the theory of
tiling and nanotechnology, and moreover, molecular beacon has the advantages of simple structure, high sensitivity, easilymeasured and fast reaction rate. The combination of molecular beacon and Self-Assembly will provide a new effective method of
studying DNA Computing. Introduce the significance of research about Self-Assembled model based on molecular beacon,
researchful actuality of Self-Assembled DNA computing model and DNA computing model based on molecular beacon, as well as
researchful track of Self-Assembled model based on molecular beacon. The first of all, research about the characteristics of
structure about molecular beacon and its capacity of the information expressed and handled, the deep research on the assembly
rules about the theory of Self-Assembled DNA computing and optimal design, discuss the Self-Assembled methods of molecular
beacon and its complexity analysis in detail, create its model. Secondly, establish the Self-Assembled model based on molecular
beacon, which contains many combinatorial optimization problems. Furthermore, we make a further discussion on the advantages
and the disadvantages about Self-Assembled model based on molecular beacon in order to design a new model with universality.
Keywords: Self-Assembly; Molecular Beacon; DNA Computing; Matrix Addition; Combinatorial Optimization

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REFERENCES
[1] Lipton R. J. DNA solution of hard computation problems. Science, 1995, 268(4): 542-545
[2] Ouyang Q., Kaplan P.D, Liu S, et al. DNA solution of the maximal clique problem. Science, 1997, 278(17): 446-449
[3] Liu Q, Wang L, Frutos A, et al. DNA computing on surfaces. Nature, 2000, 403: 175-179
[4] Braich R.S, Chelyapov N, Johnson C, et al. Solution of a 20-variable 3-SAT problem on a DNA computer. Science, 2002,
296(5567): 430-434
[5] He Y, Mao C, et al. Hierarchical self-assembly of DNA into symmetric supra-molecular polyhedra. Nature, 2008, 452: 198-202
[6] Winfree E, Liu F, Seeman N.C, et al. Design and self-assembly of two-dimensional DNA crystals. Nature, 1998, 394:539-544
[7] Paul W.K. Folding DNA to create nanoscale shapes and patterns. Nature, 2006, 440: 297-302
[8] , , , . DNA . . 2006, 51(24): 2860-2863
[9] Gehani A, LaBean T H, and Reif J H . DNA-based Cryptography.5th DIMACS Workshop on DNA Based Computers, MIT, 1999
[10] Adleman L. Toward a mathematical theory of self-assembly, USC Tech Report, 2000
[11] Mao C, LaBen T H, Relf J H, et al. Logical computation using algorithmic self-assembly of DNA triple-crossover molecules.
Nature, 2000, 407(6803): 493-496
[12] Benenson Y, Paz-Elizur T, Adar R, et al. Programmable and autonomous computing machine made of biomolecules. Nature, 2001,
414(6862): 430-434
[13] Braich R. S, Chelyapov N, Johnson C, Rothemund P.W.K, Adleman L. Solution of a 20-Variable 3-SAT Problem on a DNA
Computer. Science, 2002, 296: 499-502
[14] Adleman L, Cheng Q, Goel A, et al. Combinatorial optimization problems in self-assemblyl, Thirty-Fourth Annual

ACM

Symposium on Theory of Computing, Montreal, Quebec, Canada, May 2002, 19-21

[15] Rothemund W.K, Papadakis N, Winfree E. Algorithmic self-assembly of DNA Sierpinski triangles. PLOS Bioll, 2004, 2(12): e424
[16] Robert B, Paul R, Erik W, Two computational primitives for algorithmic self-assembly: Copying and counting. Nano Letters, 2005,
5(12): 2586-2592
[17] Brun Y. Arithmetic computation in the tile assembly model: Addition and multiplication. Theoretical Computer Science, 2006, 378:
17-31
[18] Brun Y. Nondeterministic polynomial time factoring in the tile assembly model. Theoretical Computer Science, 2008, 395(1): 3-23
[19] Brun Y. Solving NP-complete problems in the tile assembly model. Theoretical Computer Sciience, 2008, 395(1): 31 46
[20] Chen Z, Xu J. One-Time-Pads encryption in the tile assembly model. BICTA 2008, 2008, 23-30
[21] Zhang X, Niu Y, Gui G, et al. Breaking the NTRU Public-key Cryptosystem Using Self-Assembly of DNA Tilings. Chinese
Journal of computers, 2008,12: 2129-2137
[22] Zhang X.C, Wang Y. F, Gui G. Z, et al. Arithmetic computation using self-assembly of DNA tiles: subtraction and division.
Progress in Natural Science, 2009, 3: 377-388
[23] Zhang X. C, Niu Y, Cui G. Z, Xu J. Application of DNA Self-assembly on Graph Coloring Problem. Journal of Computational and
Theoretical Nanoscience, 2009, 6(5): 1067-1074
[24] Zhang X. C, Niu Y, Gui G. Z, Xu J. Application of DNA Self-assembly on 0-1 Integer Programming Problem. Journal of
Computional and Theoretical Nanoscience , 2010, 7(1): 165- 172
[25] Zhen C, Huang Y. F, Xu J, Zhang X. C. Algorithm of Elliptic Cure Diffe-Hellman key Exchange Based on DNA Tile Selfassembly. Journal of Computional and Theoretical Nanoscience, 2010, 7(5): 856- 861
[26] Tyagi S, Kramer F R. Molecular beacons: probes that fluoresce upon hybridization. Nat Biotech, 1996, 14(3): 303-308
[27] , , . DNA . , 2003, 18(4) 497-501
[28] , , . DNA . , 2003, 30(3): 412-415
[29] Chung W. Y, Chu C.P, Wu K.R. Molecular solutions to the binary integer programming problem based on DNA computation.
- 17 http://www.sjie.org

Biosystems, 2006, 83: 56-66

[30] Wang Y.X, Li J.S, Tang H X. Strategy for Molecular Beacon Binding Readout: Separating Molecular Recognition Element and
Signal Reporter. Analytical Chemistry, 2009, 81(23): 9703-9708
[31] LaBean T. H, Reif J. H, Seeman N. C, et al. Construction, analysis, ligation, and self assembly of DNA triple crossover complexes.
Journal of the Americal Chemical Society, 2000, 122: 1848-1860
[32] Yan H, LaBean T. H, et al. DNA-templated self-assembly of protein aeeays and highly conductive nanowires. Science, 2003, 301:18821884
[33] Park S H, Finkelstein G, Labean T H. Stepwise Self-Assembly of DNA Tile Lattices Using da DNA Bridges. journal of the
American Chemical Society, 2008, 130: 40-41
[34] He Y, Mao C, et al. Self-Assembly of Hexagonal DNA Two-Dimensional Arrays. Journal of the American Chemical Society, 2005,
127: 12202-12203
[35] Goodman R. P. Reconfigurable braced three-dimensional DNA nanostructures. Nature nanotechnology, 2008, 3: 93-96

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