{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,8]],"date-time":"2025-09-08T06:34:29Z","timestamp":1757313269639},"reference-count":28,"publisher":"Springer Science and Business Media LLC","issue":"2","license":[{"start":{"date-parts":[[2009,2,1]],"date-time":"2009-02-01T00:00:00Z","timestamp":1233446400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["New Gener. Comput."],"published-print":{"date-parts":[[2009,2]]},"DOI":"10.1007\/s00354-008-0057-5","type":"journal-article","created":{"date-parts":[[2009,4,18]],"date-time":"2009-04-18T10:18:41Z","timestamp":1240049921000},"page":"107-127","source":"Crossref","is-referenced-by-count":9,"title":["RNA Oscillator: Limit Cycle Oscillations based on Artificial Biomolecular Reactions"],"prefix":"10.1007","volume":"27","author":[{"given":"Masahiro","family":"Takinoue","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Daisuke","family":"Kiga","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Koh-ichiroh","family":"Shohda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Akira","family":"Suyama","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2009,4,19]]},"reference":[{"key":"57_CR1","doi-asserted-by":"crossref","unstructured":"Alberts, B., Johnson, A., Lewis, J., Raff, M. and Roberts, K., Molecular Biology of the Cell, Garland Science, 2008.","DOI":"10.1201\/9780203833445"},{"key":"57_CR2","doi-asserted-by":"crossref","first-page":"597","DOI":"10.1016\/S0092-8674(03)00346-5","volume":"113","author":"M. R. Atkinson","year":"2003","unstructured":"Atkinson, M. R., Savageau, M. A., Myers, J. T. and Ninfa, A. J., \u201cDevelopment of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli,\u201d Cell, 113, pp. 597\u2013607, 2003.","journal-title":"Cell"},{"key":"57_CR3","doi-asserted-by":"crossref","first-page":"8626","DOI":"10.1021\/ja047991r","volume":"126","author":"Y. Chen","year":"2004","unstructured":"Chen, Y. and Mao, C., \u201cPutting a Brake on an Autonomous DNA Nanomotor,\u201d J. Am. Chem. Soc., 126, pp. 8626\u20138627, 2004.","journal-title":"J. Am. Chem. Soc.,"},{"key":"57_CR4","doi-asserted-by":"crossref","first-page":"709","DOI":"10.1002\/smll.200500074","volume":"1","author":"W. U. Dittmer","year":"2005","unstructured":"Dittmer, W. U., Kempter, S., Radler, J. O. and Simmel, F. C., \u201cUsing Gene Regulation to Program DNA-Based Molecular Devices,\u201d Small, 1, pp. 709\u2013712, 2005.","journal-title":"Small"},{"key":"57_CR5","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1021\/nl049784v","volume":"4","author":"W. U. Dittmer","year":"2004","unstructured":"Dittmer, W. U. and Simmel, F. C., \u201cTranscriptional Control of DNA-Based Nanomachines,\u201d Nano Lett., 4, pp. 689\u2013691, 2004.","journal-title":"Nano Lett."},{"key":"57_CR6","doi-asserted-by":"crossref","first-page":"335","DOI":"10.1038\/35002125","volume":"403","author":"M. B. Elowitz","year":"2000","unstructured":"Elowitz, M. B. and Leibler, S., \u201cA synthetic oscillatory network of transcriptional regulators,\u201d Nature, 403, pp. 335\u2013338, 2000.","journal-title":"Nature"},{"key":"57_CR7","unstructured":"Fall, C. P., Marland, E. S., Wagner, J. M. and Tyson, J. J., Computational Cell Biology, Springer, 2002."},{"key":"57_CR8","first-page":"1877","volume":"60","author":"R. J. Field","year":"1974","unstructured":"Field, R. J. and Noyes, R. M., \u201cOscillations in chemical systems. IV. Limit cycle behavior in a model of a real chemical reaction,\u201d J. Chem. Phys., 60, pp. 1877\u20131884, 1974.","journal-title":"Limit cycle behavior in a model of a real chemical reaction,\u201d. J. Chem. Phys."},{"key":"57_CR9","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1038\/nature03508","volume":"435","author":"E. Fung","year":"2005","unstructured":"Fung, E., Wong, W. W., Suen, J. K., Bulter, T., Lee, S.-g. and Liao, J. C., \u201cA synthetic gene-metabolic oscillator,\u201d Nature, 435, pp. 118\u2013122, 2005.","journal-title":"Nature"},{"key":"57_CR10","doi-asserted-by":"crossref","first-page":"13285","DOI":"10.1021\/bi0015008","volume":"39","author":"N. Hirano","year":"2000","unstructured":"Hirano, N., Haruki, M., Morikawa, M. and Kanaya, S., \u201cEnhancement of the Enzymatic Activity of Ribonuclease HI from Thermus thermophilus HB8 with a Suppressor Mutation Method,\u201d Biochemistry, 39, pp. 13285\u201313294, 2000.","journal-title":"Biochemistry"},{"key":"57_CR11","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1038\/16437","volume":"397","author":"C. Mao","year":"1999","unstructured":"Mao, C., Sun, W., Shen, Z. and Seeman, N. C., \u201cA nanomechanical device based on the B-Z transition of DNA,\u201d Nature, 397, pp. 144\u2013146, 1999.","journal-title":"Nature"},{"key":"57_CR12","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1021\/bi00384a006","volume":"26","author":"C. T. Martint","year":"1987","unstructured":"Martint, C. T. and Coleman, J. E., \u201cKinetic Analysis of T7 RNA Polymerase-Promoter Interactions with Small Synthetic Promoters,\u201d Biochemistry, 26, pp. 2690\u20132696, 1987.","journal-title":"Biochemistry,"},{"key":"57_CR13","doi-asserted-by":"crossref","unstructured":"Murray, J. D., Mathematical Biology I: An Introduction, 3rd ed., Springer, 2002.","DOI":"10.1007\/b98868"},{"key":"57_CR14","unstructured":"Nicolis, G. and Prigogine, I., Self-Organization in Nonequilibrium Systems -From Dissipative Structures to Order through Fluctuations, John Wiley & Sons, 1977."},{"key":"57_CR15","doi-asserted-by":"crossref","first-page":"12211","DOI":"10.1021\/ja0635635","volume":"128","author":"G. Seelig","year":"2006","unstructured":"Seelig, G., Yurke, B. and Winfree, E., \u201cCatalyzed Relaxation of a Metastable DNA Fuel,\u201d J. Am. Chem. Soc., 128, pp. 12211\u201312220, 2006.","journal-title":"Chem. Soc."},{"key":"57_CR16","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1021\/nl049527q","volume":"4","author":"W. B. Sherman","year":"2004","unstructured":"Sherman, W. B. and Seeman, N. C., \u201cA Precisely Controlled DNA Biped Walking Device,\u201d Nano Lett., 4, pp. 1203\u20131207, 2004.","journal-title":"Nano Lett."},{"key":"57_CR17","doi-asserted-by":"crossref","first-page":"10834","DOI":"10.1021\/ja047543j","volume":"126","author":"J. S. Shin","year":"2004","unstructured":"Shin, J.-S. and Pierce, N. A., \u201cA Synthetic DNA Walker for Molecular Transport,\u201d J. Am. Chem. Soc., 126, pp. 10834\u201310835, 2004.","journal-title":"J. Am. Chem. Soc."},{"key":"57_CR18","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1002\/smll.200400111","volume":"1","author":"F. C. Simmel","year":"2005","unstructured":"Simmel, F. C. and Dittmer, W. U., \u201cDNA Nanodevices,\u201d Small, 1, pp. 284\u2013299, 2005.","journal-title":"Small"},{"key":"57_CR19","unstructured":"Strogatz, S. H., Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering, Westview Pr, 2001."},{"key":"57_CR20","doi-asserted-by":"crossref","unstructured":"Takinoue, M., Kiga, D., Shohda, K.-i. and Suyama, A., \u201cDesign and numerical analysis of RNA oscillator,\u201d Proceedings in Information and Communications Technology: Natural Computing, 1, pp. 201\u2013212, 2008.","DOI":"10.1007\/978-4-431-88981-6_18"},{"key":"57_CR21","doi-asserted-by":"crossref","unstructured":"Takinoue, M., Kiga, D., Shohda, K.-i. and Suyama, A., \u201cExperiments and simulation models of a basic computation element of an autonomous molecular computing system,\u201d Phys. Rev. E., 78, article no. 041921, 2008.","DOI":"10.1103\/PhysRevE.78.041921"},{"key":"57_CR22","first-page":"2","volume":"44","author":"Y. Tian","year":"2005","unstructured":"Tian, Y., He, Y., Chen, Y., Yin, P. and Mao, C., \u201cA DNAzyme That Walks Processively and Autonomously along a One-Dimensional Track,\u201d Angew. Chem. Int. Ed., 44, pp. 2\u20135, 2005.","journal-title":"Angew. Chem. Int. Ed."},{"key":"57_CR23","doi-asserted-by":"crossref","first-page":"11410","DOI":"10.1021\/ja046507h","volume":"126","author":"Y. Tian","year":"2004","unstructured":"Tian, Y. and Mao, C., \u201cMolecular Gears: A Pair of DNA Circles Continuously Rolls against Each,\u201d J. Am. Chem. Soc., 126, pp. 11410\u201311411, 2004.","journal-title":"J. Am. Chem. Soc."},{"key":"57_CR24","doi-asserted-by":"crossref","unstructured":"Turberfield, A. J., Mitchell, J. C., Yurke, B., Mills Jr., A. P., Blakey, M. I. and Simmel, F. C., \u201cDNA Fuel for Free-Running Nanomachines\u201d, Phys. Rev. Lett., 90, article no. 118102, 2003.","DOI":"10.1103\/PhysRevLett.90.118102"},{"key":"57_CR25","doi-asserted-by":"crossref","first-page":"4055","DOI":"10.1021\/bi00230a033","volume":"30","author":"U. Varshney","year":"1991","unstructured":"Varshney, U. and Sande, J. H. v. d., \u201cSpecificities and Kinetics of Uracil Excision from Uracil-Containing DNA Oligomers by Escherichia coli Uracil DNA Glycosylase,\u201d Biochemistry, 30, pp. 4055\u20134061, 1991.","journal-title":"Biochemistry"},{"key":"57_CR26","doi-asserted-by":"crossref","first-page":"62","DOI":"10.1038\/415062a","volume":"415","author":"H. Yan","year":"2002","unstructured":"Yan, H., Zhang, X., Shen, Z. and Seeman, N. C., \u201cA robust DNA mechanical device controlled by hybridization topology,\u201d Nature, 415, pp. 62\u201365, 2002.","journal-title":"Nature"},{"key":"57_CR27","doi-asserted-by":"crossref","first-page":"4906","DOI":"10.1002\/anie.200460522","volume":"43","author":"P. Yin","year":"2004","unstructured":"Yin, P., Yan, H., Daniell, X. G., Turberfield, A. J. and Reif, J. H., \u201cA Unidirectional DNAWalker That Moves Autonomously along a Track,\u201d Angew. Chem. Int. Ed., 43, pp. 4906\u20134911, 2004.","journal-title":"Angew. Chem. Int. Ed."},{"key":"57_CR28","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/35020524","volume":"406","author":"B. Yurke","year":"2000","unstructured":"Yurke, B., Turberfield, A. J., Mills Jr., A. P., Simmel, F. C. and Neumann, J. L., \u201cA DNA-fuelled molecular machine made of DNA,\u201d Nature, 406, pp. 605\u2013608, 2000.","journal-title":"Nature"}],"container-title":["New Generation Computing"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00354-008-0057-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s00354-008-0057-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s00354-008-0057-5","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T21:37:43Z","timestamp":1684964263000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s00354-008-0057-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2009,2]]},"references-count":28,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2009,2]]}},"alternative-id":["57"],"URL":"https:\/\/doi.org\/10.1007\/s00354-008-0057-5","relation":{},"ISSN":["0288-3635","1882-7055"],"issn-type":[{"value":"0288-3635","type":"print"},{"value":"1882-7055","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,2]]}}}