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Me-dC Brancher CE-Phosphoramidite

Me-dC Brancher CE-Phosphoramidite

Phosphoramidite used to incorporate a methyl-dC base that can be used for branched DNA synthesis.
  • Useful to synthesise branched DNA (bDNA)
  • Can achieve multiplicity of labelled probe hybridisation to target sequences leading to enhanced signals.
  • The levulinyl group is removed with buffered hydrazine at neutral pH.
  • Does not degrade during storage and synthesis, unlike Fmoc protection found in other similar products.
  • Nucleosidic, thereby preserving internucleotide distance.
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Product information

Branched DNA (bDNA) has become a significant tool in diagnostics research and, in particular, gene expression analysis.(1) For example, branching possibilities can be exploited to achieve multiplicity of labelled probe hybridisation to target sequences leading to enhanced signals. 5-Me-dC-Brancher CE Phosphoramidite(2) has been designed to provide a facile route to incorporate branching capability into an oligonucleotide.

The levulinyl group on the branching chain is removed with buffered hydrazine at neutral pH—conditions that do not affect any other groups (e.g. it does not cleave from the support)—yet it does not degrade during storage and synthesis, unlike the Fmoc protection used on other commercially available branching phosphoramidites. This product has the advantage of being nucleosidic, thereby preserving internucleotide distance, therefore perturbs DNA structure less than, for example, a non-nucleosidic doubler or trebler molecule.

It must be noted that, although visually this structure resembles Me-dC, the linker on the N-4 position results in hybridisation akin to dT. Therefore if hybridisation is required at the branching point, this modifier must replace a T base within the natural DNA sequence.

Ref:

  1. (a) Nucleic Acid Detection Technologies—Labels, Strategies, and Formats, L.J. Kricka, Clinical Chemistry, 45, 453-458, 1999; (b) Signal amplification through nucleotide extension and excision on a dendritic DNA platform, S. Capaldi, R.C. Getts, and S.D. Jayasena, Nucleic Acids Research, 28, e21, 2000.
  2. (a) Forks and combs and DNA: The synthesis of branched oligodeoxyribonucleotides, T. Horn and M.S. Urdea, Nucleic Acids Research, 17, 6959-6967, 1989; (b) An improved divergent synthesis of comb-type branched oligodeoxyribonucleotides (bDNA) containing multiple secondary sequences, T. Horn, C-A. Chang and M.S. Urdea, Nucleic Acids Research, 25, 4835-4841, 1997; (c) Chemical synthesis and characterization of branched oligodeoxynucleotides (bDNA) for use as signal amplifiers in nucleic acid quantification assays, T. Horn, C-A. Chang and M.S. Urdea, Nucleic Acids Research, 25, 4842-4849, 1997.
Brand LINK
Type Phosphoramidites
Base dC
Modification Brancher
Sequence Internal

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