Abstract
A caged fluorescent nucleic acid probe, which contains a nucleotide modified with one photolabile nitrobenzyl unit and two hybridization-sensitive thiazole orange units, has been synthesized for area-specific fluorescence imaging of RNA in a cell. The probe emits very weak fluorescence regardless of the presence of the complementary RNA, whereas it shows hybridization-sensitive fluorescence emission after photoirradiation for uncaging. Such probes are generated via several chemical synthetic steps and are applicable to area-specific RNA imaging in a cell. Only probes that exist in the defined irradiation area are activated via uncaging irradiation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Tokunaga K, Tani T (2008) Monitoring mRNA export. Curr Protoc Cell Biol 22:1–20
Bancaud A, Huet S, Rabut G, Ellenberg J (2010) Fluorescence perturbation techniques to study mobility and molecular dynamics of proteins in live cells: FRAP, photoactivation, photoconversion, and FLIP. In: Goldman RD, Swedlow JR, Spector DL (eds) Live cell imaging: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory Press, New York
Lippincott-Schwartz J, Snapp E, Kenworthy A (2001) Studying protein dynamics in living cells. Nat Rev Mol Cell Biol 2:444–456
Cole NB, Smith CL, Sciaky N, Terasaki M, Edidin M, Lippincott-Schwartz J (1996) Diffusional mobility of Golgi proteins in membranes of living cells. Science 273:797–801
Dundr M, McNally JG, Cohen J, Misteli T (2002) Quantitation of GFP-fusion proteins in single living cells. J Struct Biol 140:92–99
Dantzig JA, Higuchi H, Goldman YE (1998) Studies of molecular motors using caged compounds. Methods Enzymol 291:307–348
Adams SR, Tsien RY (1993) Controlling cell chemistry with caged compounds. Annu Rev Physiol 55:755–784
Sando S, Kool ET (2002) Imaging of RNA in bacteria with self-ligating quenched probes. J Am Chem Soc 124:9686–9687
Mhlanga MM, Tyagi S (2006) Using tRNA-linked molecular beacons to image cytoplasmic mRNAs in live cells. Nat Protoc 1:1392–1398
Ikeda S, Kubota T, Wang DO, Yanagisawa H, Umemoto T, Okamoto A (2011) Design and synthesis of caged fluorescent nucleotides and application to live cell RNA imaging. Chembiochem 12:2871–2880
Dyer RG, Turnbull KD (1999) Hydrolytic stabilization of protected p-hydroxybenzyl halides designed as latent quinone methide precursors. J Org Chem 64:7988–7995
Ikeda S, Okamoto A (2008) Hybridization-sensitive on–off DNA probe: application of the exciton coupling effect to effective fluorescence quenching. Chem Asian J 3:958–968
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media, New York
About this protocol
Cite this protocol
Okamoto, A. (2013). Application of Caged Fluorescent Nucleotides to Live-Cell RNA Imaging. In: Kolpashchikov, D., Gerasimova, Y. (eds) Nucleic Acid Detection. Methods in Molecular Biology, vol 1039. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-535-4_24
Download citation
DOI: https://doi.org/10.1007/978-1-62703-535-4_24
Published:
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-1-62703-534-7
Online ISBN: 978-1-62703-535-4
eBook Packages: Springer Protocols