IGEM:Harvard/2006/Background Reading

Synthetic Biology

1. Endy D. Foundations for engineering biology. Nature. 2005 Nov 24;438(7067):449-53. DOI:10.1038/nature04342 |
2. Gardner TS, Cantor CR, and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature. 2000 Jan 20;403(6767):339-42. DOI:10.1038/35002131 |
3. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature. 2000 Jan 20;403(6767):335-8. DOI:10.1038/35002125 |

DNA Nanotechnology

4. Shih WM, Quispe JD, and Joyce GF. A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron. Nature. 2004 Feb 12;427(6975):618-21. DOI:10.1038/nature02307 |
5. Rothemund PW, Papadakis N, and Winfree E. Algorithmic self-assembly of DNA Sierpinski triangles. PLoS Biol. 2004 Dec;2(12):e424. DOI:10.1371/journal.pbio.0020424 |
6. Rothemund PW, Ekani-Nkodo A, Papadakis N, Kumar A, Fygenson DK, and Winfree E. Design and characterization of programmable DNA nanotubes. J Am Chem Soc. 2004 Dec 22;126(50):16344-52. DOI:10.1021/ja044319l |
7. Mathieu F, Liao S, Kopatsch J, Wang T, Mao C, and Seeman NC. Six-helix bundles designed from DNA. Nano Lett. 2005 Apr;5(4):661-5. DOI:10.1021/nl050084f |
8. Nutiu R and Li Y. A DNA-protein nanoengine for "on-demand" release and precise delivery of molecules. Angew Chem Int Ed Engl. 2005 Aug 26;44(34):5464-7. DOI:10.1002/anie.200501214 |
9. Rothemund PW. Folding DNA to create nanoscale shapes and patterns. Nature. 2006 Mar 16;440(7082):297-302. DOI:10.1038/nature04586 |

Circadian Rhythm in Cyanobacteria

10. Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M, and Ishiura M. Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol. 2005 Mar;187(6):2190-9. DOI:10.1128/JB.187.6.2190-2199.2005 |
11. Kondo T and Ishiura M. The circadian clock of cyanobacteria. Bioessays. 2000 Jan;22(1):10-5. DOI:10.1002/(SICI)1521-1878(200001)22:1<10::AID-BIES4>3.0.CO;2-A |
12. Lemeille S, Latifi A, and Geiselmann J. Inferring the connectivity of a regulatory network from mRNA quantification in Synechocystis PCC6803. Nucleic Acids Res. 2005;33(10):3381-9. DOI:10.1093/nar/gki654 |
13. Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV, Golden SS, Ishiura M, and Kondo T. Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 1995 Jun 15;9(12):1469-78. DOI:10.1101/gad.9.12.1469 |
14. Nishiwaki T, Satomi Y, Nakajima M, Lee C, Kiyohara R, Kageyama H, Kitayama Y, Temamoto M, Yamaguchi A, Hijikata A, Go M, Iwasaki H, Takao T, and Kondo T. Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942. Proc Natl Acad Sci U S A. 2004 Sep 21;101(38):13927-32. DOI:10.1073/pnas.0403906101 |
15. Nakajima M, Imai K, Ito H, Nishiwaki T, Murayama Y, Iwasaki H, Oyama T, and Kondo T. Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science. 2005 Apr 15;308(5720):414-5. DOI:10.1126/science.1108451 |
16. Tsinoremas NF, Ishiura M, Kondo T, Andersson CR, Tanaka K, Takahashi H, Johnson CH, and Golden SS. A sigma factor that modifies the circadian expression of a subset of genes in cyanobacteria. EMBO J. 1996 May 15;15(10):2488-95.
17. Xu Y, Mori T, and Johnson CH. Cyanobacterial circadian clockwork: roles of KaiA, KaiB and the kaiBC promoter in regulating KaiC. EMBO J. 2003 May 1;22(9):2117-26. DOI:10.1093/emboj/cdg168 |
18. Wang J. Recent cyanobacterial Kai protein structures suggest a rotary clock. Structure. 2005 May;13(5):735-41. DOI:10.1016/j.str.2005.02.011 |
19. Naef F. Circadian clocks go in vitro: purely post-translational oscillators in cyanobacteria. Mol Syst Biol. 2005;1:2005.0019. DOI:10.1038/msb4100027 |

This is just scratching the surface - do a PubMed search for "circadian cyanobacteria" and you'll find hundreds of papers.