Bright Ideas for Chemical Biology

Overview

Journal ACS Chem Biol

Publisher American Chemical Society

Specialties Biochemistry
Biology

Date 2008 Mar 22

PMID 18355003

Citations 327

Authors

Luke D Lavis

Ronald T Raines

Affiliations

Soon will be listed here.

Abstract

Small-molecule fluorescent probes embody an essential facet of chemical biology. Although numerous compounds are known, the ensemble of fluorescent probes is based on a modest collection of modular "core" dyes. The elaboration of these dyes with diverse chemical moieties is enabling the precise interrogation of biochemical and biological systems. The importance of fluorescence-based technologies in chemical biology elicits a necessity to understand the major classes of small-molecule fluorophores. Here, we examine the chemical and photophysical properties of oft-used fluorophores and highlight classic and contemporary examples in which utility has been built upon these scaffolds.

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References

Yang F, Moss L, Phillips Jr G . The molecular structure of green fluorescent protein. Nat Biotechnol. 1996; 14(10):1246-51. DOI: 10.1038/nbt1096-1246. View

Yang X, Ye S, Bai Q, Wang X . A fluorescein-based fluorogenic probe for fluoride ion based on the fluoride-induced cleavage of tert-butyldimethylsilyl ether. J Fluoresc. 2006; 17(1):81-7. DOI: 10.1007/s10895-006-0140-6. View

Smalley M, Silverman S . Fluorescence of covalently attached pyrene as a general RNA folding probe. Nucleic Acids Res. 2006; 34(1):152-66. PMC: 1326244. DOI: 10.1093/nar/gkj420. View

Schobel U, Egelhaaf H, Brecht A, Oelkrug D, Gauglitz G . New donor-acceptor pair for fluorescent immunoassays by energy transfer. Bioconjug Chem. 1999; 10(6):1107-14. DOI: 10.1021/bc990073b. View

Diwu Z, Chen C, Zhang C, Klaubert D, Haugland R . A novel acidotropic pH indicator and its potential application in labeling acidic organelles of live cells. Chem Biol. 1999; 6(7):411-8. DOI: 10.1016/s1074-5521(99)80059-3. View

Petit J, Ratinaud M . Assessment of fluorochromes for cellular structure and function studies by flow cytometry. Biol Cell. 1993; 78(1-2):1-13. DOI: 10.1016/0248-4900(93)90109-r. View

Whitaker J, Moore P, Hewitt P, Reese M, Haugland R . Cascade blue derivatives: water soluble, reactive, blue emission dyes evaluated as fluorescent labels and tracers. Anal Biochem. 1991; 198(1):119-30. DOI: 10.1016/0003-2697(91)90515-u. View

Liu J, Bhalgat M, Zhang C, Diwu Z, Hoyland B, Klaubert D . Fluorescent molecular probes V: a sensitive caspase-3 substrate for fluorometric assays. Bioorg Med Chem Lett. 1999; 9(22):3231-6. DOI: 10.1016/s0960-894x(99)00566-1. View

Shaner N, Patterson G, Davidson M . Advances in fluorescent protein technology. J Cell Sci. 2007; 120(Pt 24):4247-60. DOI: 10.1242/jcs.005801. View

10.

Ghosh P, Whitehouse M . 7-chloro-4-nitrobenzo-2-oxa-1,3-diazole: a new fluorigenic reagent for amino acids and other amines. Biochem J. 1968; 108(1):155-6. PMC: 1198782. DOI: 10.1042/bj1080155. View

11.

Beechem J, Brand L . Time-resolved fluorescence of proteins. Annu Rev Biochem. 1985; 54:43-71. DOI: 10.1146/annurev.bi.54.070185.000355. View

12.

Zimmerman M, ASHE B, Yurewicz E, Patel G . Sensitive assays for trypsin, elastase, and chymotrypsin using new fluorogenic substrates. Anal Biochem. 1977; 78(1):47-51. DOI: 10.1016/0003-2697(77)90006-9. View

13.

Gao W, Xing B, Tsien R, Rao J . Novel fluorogenic substrates for imaging beta-lactamase gene expression. J Am Chem Soc. 2005; 125(37):11146-7. DOI: 10.1021/ja036126o. View

14.

Gruber H, Hahn C, Kada G, Riener C, Harms G, Ahrer W . Anomalous fluorescence enhancement of Cy3 and cy3.5 versus anomalous fluorescence loss of Cy5 and Cy7 upon covalent linking to IgG and noncovalent binding to avidin. Bioconjug Chem. 2000; 11(5):696-704. DOI: 10.1021/bc000015m. View

15.

Livet J, Weissman T, Kang H, Draft R, Lu J, Bennis R . Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system. Nature. 2007; 450(7166):56-62. DOI: 10.1038/nature06293. View

16.

Kim J, Raines R . Dibromobimane as a fluorescent crosslinking reagent. Anal Biochem. 1995; 225(1):174-6. DOI: 10.1006/abio.1995.1131. View

17.

Ormo M, Cubitt A, Kallio K, Gross L, Tsien R, Remington S . Crystal structure of the Aequorea victoria green fluorescent protein. Science. 1996; 273(5280):1392-5. DOI: 10.1126/science.273.5280.1392. View

18.

de Silva A, Gunaratne H, Gunnlaugsson T, Huxley A, McCoy C, Rademacher J . Signaling Recognition Events with Fluorescent Sensors and Switches. Chem Rev. 1997; 97(5):1515-1566. DOI: 10.1021/cr960386p. View

19.

Lumbierres M, Palomo J, Kragol G, Roehrs S, Muller O, Waldmann H . Solid-phase synthesis of lipidated peptides. Chemistry. 2005; 11(24):7405-15. DOI: 10.1002/chem.200500476. View

20.

Mitchison T, Sawin K, Theriot J, Gee K, Mallavarapu A . Caged fluorescent probes. Methods Enzymol. 1998; 291:63-78. DOI: 10.1016/s0076-6879(98)91007-2. View