Light-controlled synthetic gene circuits

Current Opinion in Chemical Biology

Volumn 16, Issue 3-4, 2012, Pages 292-299

  Gardner, Laura ^a   Deiters, Alexander ^a  

^a NORTH CAROLINA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

OLIGONUCLEOTIDE; SYNTHETIC DNA;

GENE CONTROL; GENE EXPRESSION; HUMAN; LIGHT; PHOTOCHEMISTRY; PROTEIN DOMAIN; REVIEW;

ANIMALS; CELL LINE; GENE REGULATORY NETWORKS; GENETIC ENGINEERING; HUMANS; LIGHT; PHOTOCHEMICAL PROCESSES;

BACTERIA (MICROORGANISMS); MAMMALIA;

EID: 84865285923     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2012.04.010     Document Type: Review

References (47)

1. Agapakis C.M., Silver P.A. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst 2009, 5:704-713.
2. Tanouchi Y., Pai A., You L. Decoding biological principles using gene circuits. Mol Biosyst 2009, 5:695-703.
3. Weber W., Fussenegger M. Molecular diversity - the toolbox for synthetic gene switches and networks. Curr Opin Chem Biol 2011, 15:414-420.
4. Deiters A. Light activation as a method of regulating and studying gene expression. Curr Opin Chem Biol 2009, 13:678-686.
5. Deiters A. Principles and applications of the photochemical control of cellular processes. Chembiochem 2010, 11:47-53.
6. Riggsbee C.W., Deiters A. Recent advances in the photochemical control of protein function. Trends Biotechnol 2010, 28:468-475.
7. Buskirk A.R., Liu D.R. Creating small-molecule-dependent switches to modulate biological functions. Chem Biol 2005, 12:151-161.
8. Cruz F., Koh J., Link K. Light-activated gene expression. J Am Chem Soc 2000, 122:8777-8778.
9. Lin W., Albanese C., Pestell R.G., Lawrence D.S. Spatially discrete, light-driven protein expression. Chem Biol 2002, 9:1347-1353.
10. Young D.D., Deiters A. Photochemical activation of protein expression in bacterial cells. Angew Chem Int Ed Engl 2007, 46:4290-4292.
11. Young D.D., Garner R.A., Yoder J.A., Deiters A. Light-activation of gene function in mammalian cells via ribozymes. Chem Commun (Camb) 2009, 568-570.
12. Cambridge S.B., Geissler D., Keller S., Cürten B. A caged doxycycline analogue for photoactivated gene expression. Angew Chem Int Ed Engl 2006, 45:2229-2231.
13. Sadovski O., Jaikaran A.S., Samanta S., Fabian M.R., Dowling R.J., Sonenberg N., Woolley G.A. A collection of caged compounds for probing roles of local translation in neurobiology. Bioorg Med Chem 2010, 18:7746-7752.
14. Karginov A., Zou Y., Shirvanyants D., Kota P., Dokholyan N., Young D., Hahn K., Deiters A. Light regulation of protein dimerization and kinase activity in living cells using photocaged rapamycin and engineered FKBP. J Am Chem Soc 2011, 133:420-423.
15. Umeda N., Ueno T., Pohlmeyer C., Nagano T., Inoue T. A photocleavable rapamycin conjugate for spatiotemporal control of small GTPase activity. J Am Chem Soc 2011, 133:12-14.
16. Cambridge S.B., Geissler D., Calegari F., Anastassiadis K., Hasan M.T., Stewart A.F., Huttner W.B., Hagen V., Bonhoeffer T. Doxycycline-dependent photoactivated gene expression in eukaryotic systems. Nat Methods 2009, 6:527-531.
17. Sauers D.J., Temburni M.K., Biggins J.B., Ceo L.M., Galileo D.S., Koh J.T. Light-activated gene expression directs segregation of co-cultured cells in vitro. ACS Chem Biol 2010, 5:313-320.
18. Gardner L., Zou Y., Mara A., Cropp T.A., Deiters A. Photochemical control of bacterial signal processing using a light-activated erythromycin. Mol Biosyst 2011, 7:2554-2557.
19. Mikat V., Heckel A. Light-dependent RNA interference with nucleobase-caged siRNAs. RNA 2007, 13:2341-2347.
20. Tang X., Maegawa S., Weinberg E.S., Dmochowski I.J. Regulating gene expression in zebrafish embryos using light-activated, negatively charged peptide nucleic acids. J Am Chem Soc 2007, 129:11000-11001.
21. Blidner R.A., Svoboda K.R., Hammer R.P., Monroe W.T. Photoinduced RNA interference using DMNPE-caged 2'-deoxy-2'-fluoro substituted nucleic acids in vitro and in vivo. Mol Biosyst 2008, 4:431-440.
22. Tang X., Swaminathan J., Gewirtz A.M., Dmochowski I.J. Regulating gene expression in human leukemia cells using light-activated oligodeoxynucleotides. Nucleic Acids Res 2008, 36:559-569.
23. Young D.D., Lusic H., Lively M.O., Yoder J.A., Deiters A. Gene silencing in mammalian cells with light-activated antisense agents. Chembiochem 2008, 9:2937-2940.
24. Ouyang X., Shestopalov I.A., Sinha S., Zheng G., Pitt C.L., Li W.H., Olson A.J., Chen J.K. Versatile synthesis and rational design of caged morpholinos. J Am Chem Soc 2009, 131:13255-13269.
25. Jain P.K., Shah S., Friedman S.H. Patterning of gene expression using new photolabile groups applied to light activated RNAi. J Am Chem Soc 2011, 133:440-446.
26. Tang X., Su M., Yu L., Lv C., Wang J., Li Z. Photomodulating RNA cleavage using photolabile circular antisense oligodeoxynucleotides. Nucleic Acids Res 2010, 38:3848-3855.
27. Young D.D., Lively M.O., Deiters A. Activation and deactivation of DNAzyme and antisense function with light for the photochemical regulation of gene expression in mammalian cells. J Am Chem Soc 2010, 132:6183-6193.
28. Govan J.M., Lively M.O., Deiters A. Photochemical control of DNA decoy function enables precise regulation of nuclear factor κB activity. J Am Chem Soc 2011, 133:13176-13182.
29. Qian L., Winfree E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 2011, 332:1196-1201.
30. Prokup A., Hemphill J., Deiters A. DNA computation: a photochemically controlled AND gate. J Am Chem Soc 2012, 134:3810-3815.
31. Liu C.C., Schultz P.G. Adding new chemistries to the genetic code. Annu Rev Biochem 2010, 79:413-444.
32. Chin J.W. Reprogramming the genetic code. EMBO J 2011, 30:2312-2324.
33. Edwards W.F., Young D.D., Deiters A. Light-activated Cre recombinase as a tool for the spatial and temporal control of gene function in mammalian cells. ACS Chem Biol 2009, 4:441-445.
34. Wu N., Deiters A., Cropp T.A., King D., Schultz P.G. A genetically encoded photocaged amino acid. J Am Chem Soc 2004, 126:14306-14307.
35. Lemke E.A., Summerer D., Geierstanger B.H., Brittain S.M., Schultz P.G. Control of protein phosphorylation with a genetically encoded photocaged amino acid. Nat Chem Biol 2007, 3:769-772.
36. Gautier A., Deiters A., Chin J.W. Light-activated kinases enable temporal dissection of signaling networks in living cells. J Am Chem Soc 2011, 133:2124-2127.
37. Chou C., Young D.D., Deiters A. Photocaged T7 RNA polymerase for the light activation of transcription and gene function in pro- and eukaryotic cells. Chembiochem 2010, 11:972-977.
38. Rockwell N.C., Su Y.S., Lagarias J.C. Phytochrome structure and signaling mechanisms. Annu Rev Plant Biol 2006, 57:837-858.
39. Hahn K.M., Kuhlman B. Hold me tightly LOV. Nat Methods 2010, 7:595-597.
40. Toettcher J.E., Gong D., Lim W.A., Weiner O.D. Light-based feedback for controlling intracellular signaling dynamics. Nat Methods 2011, 8:837-839.
41. Fenno L., Yizhar O., Deisseroth K., Hyman S., Jessell T., Shatz C., Stevens C., Zoghbi H. The development and application of optogenetics. Annu Rev Neurosci 2011, 34:389-412.
42. Tabor J.J., Salis H.M., Simpson Z.B., Chevalier A.A., Levskaya A., Marcotte E.M., Voigt C.A., Ellington A.D. A synthetic genetic edge detection program. Cell 2009, 137:1272-1281.
43. Tabor J.J., Levskaya A., Voigt C.A. Multichromatic control of gene expression in Escherichia coli. J Mol Biol 2011, 405:315-324.
44. Levskaya A., Weiner O.D., Lim W.A., Voigt C.A. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 2009, 461:997-1001.
45. Georgianna W.E., Deiters A. Reversible light switching of cell signalling by genetically encoded protein dimerization. Chembiochem 2010, 11:301-303.
46. Wu Y.I., Frey D., Lungu O.I., Jaehrig A., Schlichting I., Kuhlman B., Hahn K.M. A genetically encoded photoactivatable Rac controls the motility of living cells. Nature 2009, 461:104-108.
47. Zhang F., Vierock J., Yizhar O., Fenno L.E., Tsunoda S., Kianianmomeni A., Prigge M., Berndt A., Cushman J., Polle J., et al. The microbial opsin family of optogenetic tools. Cell 2011, 147:1446-1457.