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Reference

cre recombinase

1.Cre recombinase‐mediated inversion using lox66 and lox71: method to introduce conditional point mutations into the CREB‐binding protein
Zuwen Zhang and Beat Lutz, Nucleic Acids Research, 30, e90 (2002)

2.Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination.
Lee G and Saito I, Gene, 216, 55-65

3.In vitro characterization of the site-speciWc recombination system based on actinophage TG1 integrase
Kentaro Morita, Tomoyuki Yamamoto, Naoki Fusada, Mamoru Komatsu, Haruo Ikeda, Nobutaka Hirano and Hideo Takahashi, Mol Genet Genomics, 282, 607-16

as RNA

1.Artificial antisense RNAs silence lacZ in E. coli by decreasing target mRNA concentration
Stefan Alessandra, Tonelli Alessandro, Schwarz Flavio and Hochkoeppler Alejandro, BMB reports, 568-74 (2008)

2.Kill the messenger: bacterial antisense RNA promotes mRNA decay
E Gerhart H Wagner, nature structural & molecular biology, 16, 804-6 (2009)

3.Distance between RBS and AUG plays an important role in overexpression of recombinant proteins
Sunil K. Berwal, R.K. Sreejith and Jayanta K. Pal, Analytical Biochemistry, 405, 275-7 (2010)

4.Antisense RNA Control of Plasmid R1 Replication
Charlotta Malmgren, E. Gerhart H. Wagner, Chantal Ehresmann, Bernard Ehresmann and Pascale Romby, The Journal of Biologycal Chemistry, 272, 12508-12 (1997)

5.Paired termini stabilize antisense RNAs and enhance conditional gene silencing in Escherichia coli
Nobutaka Nakashima, Tomohiro Tamura and Liam Good, Nucleic Acids Research, 34, e138 (2006)

6.The Influence of Antisense Oligonucleotide-induced RNA Structure on Escherichia coli RNase H1 Activity
Walt F. Lima, Venkatraman Mohan and Stanley T. Crooke, The Journal of Biological Chemistry, 272, 18191-8 (2010)

MS2 phage

1.Studies on Sex Pili: Mutants of the Sex Factor F in Escherichia coli Defective in Bacteriophage-Adsorbing Function of F Pili
Munemitsu Tomoeda, Akemi Shuta and Manabu Inuzuka, Journal of Bacteriology, 112, 1358-63 (1972)

2.Crystal structure of an RNA bacteriophage coat protein-operator complex
Karin Valegard, James B. Murray, Peter G. Stockley, Nicola J. Stonehouse and Lars Liljas, Nature, 371, 626 (1994)

3.Ribonucleoprotein Complexes of R17 Coat Protein and a Translational Operator Analog
Dorothy Beckett and Olke C. Uhlenbeck, Journal of Molecular Biology, 204, 927-38 (1988)

4.A unique mechanism regulating gene expression: Translational inhibition by a complementary RNA transcript (micRNA)
Takeshi Mizuno, Mei-Yin Chou and Masayori Inoue, Proc. Nail. Acad. Sci. USA, 81, 1966-70 (1984)

5.Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene
R.A.Kastelein, E.Remaut, W.Fiers and J.van Duin, Nature, 295, 35-41

6.微生物学講義録 前国立感染症研究所長 吉倉　廣 著 第14章 　RNAファージ
http://jsv.umin.jp/microbiology/main_014.htm

T7 RNA polymerase

1.Characterization of two types of termination signal for bacteriophage T7 RNA polymerase
Macdonald LE, Durbin RK, Dunn JJ and McAllister WT, Journal of molecular biology, 238, 145-58 (1994)

To write introduction

1.The second wave of synthetic biology: from modules to systems
Purnick P.E. and Weiss R., Nat. Rev. Mol. Cell. Biol. 10, 410-22, (2009).

2.Construction of a genetic toggle switch in Escherichia coli
Gardner, T. S., Cantor, C. R. & Collins and J. J., Nature 403, 339-42 (2000).

3.Environmentally controlled invasion of cancer cells by engineered bacteria
Anderson, J. C., Clarke, E. J., Arkin, A. P. and Voigt, C. A., J. Mol. Biol., 355, 619-27 (2006).

4.Anderson, J.C., Voigt, C.A. & Arkin, A.P. Environmental signal integration by a modular AND gate. Mol. Syst. Biol. 3, 133 (2007).

5.Win, M. N. & Smolke, C. D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-60 (2008).

6.Ham, T. S., Lee, S. K., Keasling, J. D. & Arkin, A. P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 3, e2815 (2008).

7.Friedland, A. et al. Synthetic gene networks that count. Science 324, 1199?1202 (2009).

modeling

1.Alon, U. Introduction to Systems Biology: Design Principles Of Biological Circuits (CRC, Boca Raton,2006).

2.Ringrose, L. et al. Comparative Kinetic Analysis of FLP and Cre Recombinases: Mathematical Models for DNA Binding and Recombination J. Mol. Biol. (1998) 284, 363-384

3.Bionumbers the database of useful biological numbers. http://bionumbers.hms.harvard.edu/