PC Spacer CE-Phosphoramidite
PC Spacer CE-Phosphoramidite
Key featuresShow Hide
- Incorporates a mid-sequence spacer that can be photo cleaved from an oligonucleotide
- Results in a 5'-monophosphate on the released oligonucleotide
- Useful for mass markers
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The general design of the PC monomers is based on an α-substituted 2-nitrobenzyl group.(1) The photo-reactive group is derivatised as a cyanoethyl phosphoramidite for use in automated DNA synthesis.(2)
The PC 5'-Biotin-CE Phosphoramidite contains a biotinyl moiety that bears a trityl group on the N-1 nitrogen atom. This is primarily for N-protection rather than to facilitate coupling efficiency monitoring by trityl cation assay. However, the N-DMTr group enables cartridge purification of the oligo.
5’ Addition of PC Amino-Modifier-CE Phosphoramidite to an oligonucleotide, followed by cleavage from the support and deprotection, results in an aminolinker separated from the oligo by a photocleavable linker. The amino group is then used in post-synthetic modification with amine reactive reagents or to attach synthetic oligonucleotides to activated solid supports. This is particularly useful for capturing DNA or RNA where the oligonucleotide/DNA duplex is cleaved from the surface by photolysis of the PC linker.
While the biotin and amino modifiers are both 5'-terminus modifiers, both the PC Spacer and PC Linker phosphoramidites can be used as mid-sequence modifiers (for example for use with mass markers).
Upon irradiating a PC-modified oligo with near-UV light, the phosphodiester bond between the linker and the phosphate is cleaved, resulting in the formation of a 5'-monophosphate on the released oligonucleotide. PC Linker has the added advantage in that photocleavage results in monophosphate fragments at both the 3'- and 5'-termini.
Photocleavable modifiers have a wide range of applications including in affinity conjugation and purification, oligonucleotide isolation and purification, and photo-triggered strand cleavage. For further detailed information see our catalogue.
- 213 (a) Photocleavage of a 2-nitrobenzyl linker bridging a fluorophore to the 5’ end of DNA, X. Bai, Z. Li, S. Jockusch, N. J. Turro, and J. Ju, PNAS, 100, 409–413, 2003; (b) Model studies for new o-nitrobenzyl photolabile linkers: substituent effects on the rates of photochemical cleavage, C.P. Holmes, J. Org. Chem., 62, 2370-2380, 1997.
- For examples of applications of related, non-phosphoramidite, molecules see: (a) Photochemical control of the infectivity of adenoviral vectors using a novel photocleavable biotinylation reagent, M.W. Pandori, D.A. Hobson, J. Olejnik, S. Sonar, E. Krzymañska-Olejnik, K.J. Rothschild, A.A. Palmer, T.J. Phillips and T. Sano, Chemistry & Biology, 9, 567-573, 2002; and (b) Design and synthesis of a photocleavable biotinylated nucleotide for DNA analysis by mass spectrometry, X. Bai, S. Kim, Z. Li, N. J. Turro, and J. Ju, Nucleic Acids Research, 32, 535-541, 2004.