Keck Subbasement:Reading

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Oscillators

1. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |

2. Vilar JM, Kueh HY, Barkai N, and Leibler S. Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):5988-92. DOI:10.1073/pnas.092133899 |

3. Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, and Ferrell JE Jr. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science. 2008 Jul 4;321(5885):126-9. DOI:10.1126/science.1156951 |

Delays

This theory paper investigates how delays destabilize fixed points. This is a fundamentally different analysis, quite the opposite of trying to use delays to make limit cycles more attractive.

4. Bratsun D, Volfson D, Tsimring LS, and Hasty J. Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci U S A. 2005 Oct 11;102(41):14593-8. DOI:10.1073/pnas.0503858102 |

This is not transcriptional delay, but rather delay through intermediate species, which is the principle that dominates previous delay studies.

5. Monk NA. Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr Biol. 2003 Aug 19;13(16):1409-13. DOI:10.1016/s0960-9822(03)00494-9 |

This experimental paper uses a plasmid that effectively contains a delay, used for another purpose entirely, but might be a good starting point for design.

6. Golding I, Paulsson J, Zawilski SM, and Cox EC. Real-time kinetics of gene activity in individual bacteria. Cell. 2005 Dec 16;123(6):1025-36. DOI:10.1016/j.cell.2005.09.031 |

Plasmid Design

7. Lutz R and Bujard H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 1997 Mar 15;25(6):1203-10. DOI:10.1093/nar/25.6.1203 |

Testing delays

This paper measures transfer curves and dynamics of a simple circuit

8. Canton B, Labno A, and Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 2008 Jul;26(7):787-93. DOI:10.1038/nbt1413 |

Metastable hairpins

9. Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, and Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Res. 2005;33(13):4090-5. DOI:10.1093/nar/gki721 |