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Many strategies have surfaced for the caging of oligonucleotides using photochemically labile groups. Caging the nucleobase is particularly attractive.(1) One of the most promising strategies for doing so involves the use of the 6-nitropiperonyloxymethyl (NPOM) group, installed at N1 of thymidine, as developed by Deiters and co-workers at North Carolina State University.(2) Thus, NPOM-Caged-dT CE-Phosphoramidite (BA0317) was incorporated into oligonucleotides using standard automated DNA synthesis protocols, resins, and reagents. The bulky NPOM group was found to effectively block hydrogen-bond formation in duplexes, blocking DNAzyme activity, DNA/RNA hybridization, and allowing the control of PCR amplification. The caged thymidine is stable to a wide range of chemical and physiological conditions, but the NPOM caging group is removed within minutes by irradiation with 365 nm UV light, restoring normal biological function in all cases. This can be achieved using a standard fluorescent microscope, UV LED fiberoptic instruments, or even with a simple hand-held 25 watt UVA lamp. This wavelength is long enough to avoid damage to the oligonucleotides or cells.
Also in our collection of photolabile tools for oligonucleotide research is the phosphoramidite Caged Strand-Breaker (BA0315), a monomer that allows the light-induced cleavage of oligonucleotides into two phosphate-terminated daughter strands.
- (a) Mayer, G.; Heckel, A. Angew. Chem. Int. Ed. 2006, 45, 4900-4921. (b) Young, D. D.; Deiters, A. Org. Biomol. Chem. 2007, 5, 999-1005. © Tang, X. Dmochowski, I. J. Mol. BioSyst. 2007, 3, 100-110. (c) Ting, R.; Lermer, L.; Perrin, D. M. J. Am. Chem. Soc. 2004, 126, 12720-12721. (d) Heckel, A.; Meyer, G. J. Am. Chem. Soc. 2005, 127, 822-823. (e) Krock, L.; Heckel, A. Angew. Chem. Int. Ed. 2005, 44, 471-473. (f) Tang, X.; Dmochowski, I. J. Org. Lett. 2005, 7, 279-282. (g) Wenter, P.; Furtig, B.; Hainard, A.; Schwalbe, H.; Pitsch, S. Angew. Chem. Int. Ed. 2005, 44, 2600-2603. (h) Hobartner, C.; Silverman, S. K. Angew. Chem. Int. Ed. 2005, 44, 7305-7309.
- (a) Lusic, H.; Young, D. D.; Lively, M. O.; Deiters, A. Org. Lett. 2007, 9, 1903-1906. (b) Young, D. D.; Edwards, W. F.; Lusic, H.; Lively, M. O.; Deiters, A. Chem. Commun. 2008, 462-464. (c) Lusic, H.; Deiters, A., Synthesis 2006, 2147-2150.