Computational design of reaction-diffusion patterns using DNA-based chemical reaction networks

被引：13
作者：
Dalchau, Neil [1 ]
Seelig, Georg [2 ]
Phillips, Andrew [1 ]
机构：
[1] Microsoft Research, Cambridge
[2] University of Washington, WA
来源：
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 2014年 / 8727卷
基金：
美国国家科学基金会;
关键词：
Approximate majority; Autocatalysis; Consensus; DNA strand displacement; Oscillators; Reaction-diffusion; Travelling waves;
D O I：
10.1007/978-3-319-11295-4_6
中图分类号：
学科分类号：
摘要：
DNA self-assembly is a powerful technology for controlling matter at the nanometre to micron scale, with potential applications in high-precision organisation and positioning of molecular components. However, the ability to program DNA-only self-organisation beyond the microscopic scale is currently lacking. In this paper we propose a computational method for programming spatial organisation of DNA at the centimetre scale, by means of DNA strand displacement reaction diffusion systems. We use this method to analyse the spatiotemporal dynamics of an autocatalytic system, a predator-prey oscillator and a two-species consensus network. We find that both autocatalytic and oscillating systems can support travelling waves across centimetre distances, and that consensus in a spatial context results in the spontaneous formation of distinct spatial domains, in which one species is completely eliminated. Together, our results suggest that programmed spatial self-organisation of DNA, through a reaction diffusion mechanism, is achievable with current DNA strand displacement technology. © 2014 Springer International Publishing Switzerland.
引用
收藏
页码：84 / 99
页数：15
相关论文
共 32 条
  • [1] Hagan M.F., Chandler D., Dynamic pathways for viral capsid assembly, Biophysical J., 91, pp. 42-54, (2006)
  • [2] Murray J.D., Mathematical biology, (2003)
  • [3] Sheth R., Marcon L., Bastida M.F., Junco M., Quintana L., Dahn R., Kmita M., Sharpe J., Ros M.A., Hox genes regulate digit patterning by controlling the wavelength of a turing-type mechanism, Science, 338, pp. 1476-1480, (2012)
  • [4] Reif J., Chandran H., Gopalkrishnan N., LaBean T., Self-assembled DNA nanostructures and DNA devices, Nanofabrication Handbook, pp. 299-328, (2012)
  • [5] Winfree E., Liu F., Wenzler L.A., Seeman N.C., Design and self-assembly of twodimensional DNA crystals, Nature, 394, pp. 539-544, (1998)
  • [6] Um S.H., Lee J.B., Park N., Kwon S.Y., Umbach C.C., Luo D., Enzyme-catalysed assembly of DNA hydrogel, Nat. Mater., 5, pp. 797-801, (2006)
  • [7] Zaikin A., Zhabotinsky A., Concentration wave propagation in two-dimensional liquid-phase self-oscillating system, Nature, 225, pp. 535-537, (1970)
  • [8] Bauer G., McCaskill J., Otten H., Traveling waves of in vitro evolving RNA, Proc. Natl. Acad. Sci., 86, pp. 7937-7941, (1989)
  • [9] Isalan M., Lemerle C., Serrano L., Engineering gene networks to emulate Drosophila embryonic pattern formation, PLoS Biology, 3, (2005)
  • [10] Simpson Z.B., Tsai T.L., Nguyen N., Chen X., Ellington A.D., Modelling amorphous computations with transcription networks, J. R. Soc. Interface, 6, 4, pp. S523-S533, (2009)
1234