Abstract
In recent years, various types of DNA nanomachines driven by DNA hybridizations have been developed as one of remarkable applications of DNA computer for nanotechnology. Here, we propose an oscillator as a nanosystem to control the nanomachines. It was modeled after a circadian rhythm in life systems and utilized DNA/RNA and their molecular reactions. The molecular reactions were composed of nucleic-acid hybridization, RNA transcription, DNA extension, RNA degradation, and uracil-containing DNA degradation. Results of numerical analyses of rate equations for the reactions demonstrated that oscillatory condition of the system was decided by balance between RNA influx into the system and RNA degradation out of the system. The analytical results will provide much important information when the oscillator is constructed in in vitro experiments.
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
Adleman, L.M.: Science 266, 1021–1024 (1994)
Seeman, N.C.: Nature 421, 427–431 (2003)
Seeman, N.C., Lukeman, P.S.: Rep. Prog. Phys. 68, 237–270 (2005)
Bath, J., Turberfield, A.J.: Nat. Nanotechnol. 2, 275–284 (2007)
Simmel, F.C., Dittmer, W.U.: Small 1, 284–299 (2005)
Mao, C., Sun, W., Shen, Z., Seeman, N.C.: Nature 397, 144–146 (1999)
Yurke, B., Turberfield, A.J., Mills Jr., A.P., Simmel, F.C., Neumann, J.L.: Nature 406, 605–608 (2000)
Yan, H., Zhang, X., Shen, Z., Seeman, N.C.: Nature 415, 62–65 (2002)
Shin, J.S., Pierce, N.A.: J. Am. Chem. Soc. 126, 10834–10835 (2004)
Tian, Y., Mao, C.: J. Am. Chem. Soc. 126, 11410–11411 (2004)
Sherman, W.B., Seeman, N.C.: Nano Lett. 4, 1203–1207 (2004)
Chen, Y., Mao, C.: J. Am. Chem. Soc. 126, 8626–8627 (2004)
Yin, P., Yan, H., Daniell, X.G., Turberfield, A.J., Reif, J.H.: Angew. Chem. Int. Ed. 43, 4906–4911 (2004)
Tian, Y., He, Y., Chen, Y., Yin, P., Mao, C.: Angew. Chem. Int. Ed. 44, 2–5 (2005)
Turberfield, A.J., Mitchell, J.C., Yurke, B., Mills Jr., A.P., Blakey, M.I., Simmel, F.C.: Phys. Rev. Lett. 90, 118102 (2003)
Seelig, G., Yurke, B., Winfree, E.: J. Am. Chem. Soc. 128, 12211–12220 (2006)
Murray, J.D.: Springer, New York (2002)
Fall, C.P., Marland, E.S., Wagner, J.M., Tyson, J.J.: Springer, New York (2002)
Martint, C.T., Coleman, J.E.: Biochemistry 26, 2690–2696 (1987)
Hirano, N., Haruki, M., Morikawa, M., Kanaya, S.: Biochemistry 39, 13285–13294 (2000)
Varshney, U., van de Sande, J.H.: Biochemistry 30, 4055–4061 (1991)
Dittmer, W.U., Simmel, F.C.: Nano Lett. 4, 689–691 (2004)
Dittmer, W.U., Kempter, S., Radler, J.O., Simmel, F.C.: Small 1, 709–712 (2005)
Elowitz, M.B., Leibler, S.: Nature 403, 335–338 (2000)
Fung, E., Wong, W.W., Suen, J.K., Bulter, T., Lee, S.G., Liao, J.C.: Nature 435, 118–122 (2005)
Atkinson, M.R., Savageau, M.A., Myers, J.T., Ninfa, A.J.: Cell 113, 597–607 (2003)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2009 Springer Tokyo
About this paper
Cite this paper
Takinoue, M., Kiga, D., Shohda, Ki., Suyama, A. (2009). Design and Numerical Analysis of RNA Oscillator. In: Suzuki, Y., Hagiya, M., Umeo, H., Adamatzky, A. (eds) Natural Computing. Proceedings in Information and Communications Technology, vol 1. Springer, Tokyo. https://doi.org/10.1007/978-4-431-88981-6_18
Download citation
DOI: https://doi.org/10.1007/978-4-431-88981-6_18
Publisher Name: Springer, Tokyo
Print ISBN: 978-4-431-88980-9
Online ISBN: 978-4-431-88981-6
eBook Packages: Computer ScienceComputer Science (R0)