8-Br-dA (dmf) CE-Phosphoramidite
8-Br-dA (dmf) CE-Phosphoramidite
Key featuresShow Hide
- Part of the set of the four photoactive bases required to examine base to amino acid contact pairs (along with Br-dG, Br-dC and Br-dU).
- dmf protection allows widest compatibility with deprotection conditions.
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Halogenated nucleosides are versatile reagents in oligo applications. We provide a wide range of halogenated nucleoside phosphoramidites and CPG supports.
Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes.(1) Photoactive bases may also be used to probe the crystal structure of the protein-DNA complexes.(2) Photoactive analogues of dC (5-Iodo- and 5-Bromo-dC), and dT analogues (5-Iodo- and 5-Bromo-dU) are available.
8-Br-dA(3) and 8-Br-dG phosphoramidites have been proposed to complete the set of the four photoactive bases required to examine base to amino acid contact pairs, although work in this regard has been limited. 8-Br-dG is also useful in promoting the formation of Z-form DNA structures and for locating subtle differences in DNA polymerases and repair enzymes.(4)
The three-dimensional structure of DNA can be probed by x-ray crystallography using several halogenated nucleoside phosphoramidites, including 5-Br-U and 5-I-U.(5) In addition, antibodies exist which are specific for Br-dU so that oligonucleotides containing Br-dU can be used as probes.
5-F-dU is a base analogue that has the potential to bind to A and G. It does not destabilise duplex formation, and is an alternative to using mixed bases A/G for degeneracy.
- Photocross-linking of nucleic acids to associated proteins, K.M. Meisenheimer and T.H. Koch, Critical Reviews in Biochemistry and Molecular Biology, 32, 101-140, 1997.
- Crystal structure of chromomycin-DNA complex, C.M. Ogata, W.A. Hendrickson, X. Gao and D. Patel, J. Abstr. Amer. Cryst. Assoc. Mtg. Ser., 2, 1753, 1989.
- Synthesis of photoactive DNA: Incorporation of 8-bromo-2'-deoxyadenosine into synthetic oligonucleotides, J. Liu and G.L. Verdine, Tetrahedron Lett., 33, 4265-4268, 1992.
- Synthesis and properties of oligonucleotides containing 8-bromo-2'-deoxyguanosine, C. Fàbrega, M.J. Macías and R. Eritja, Nucleosides, Nucleotides & Nucleic Acids, 20, 251-260, 2001.
- Effects of cationic charge on three-dimensional structures of intercalative complexes: structure of a bis- intercalated DNA complex solved by MAD phasing, X. Shui, M.E. Peek, L.A. Lipscomb, Q. Gao, C. Ogata, B.P. Roques, C. Garbay-Jaureguiberry, A.P. Wilkinson and L.D. Williams, Curr. Med. Chem., 7, 5971, 2000.
|LK2325||5-Br-dU SynBase™ CPG 1000/110|
Physical & Dilution Data
Dilution volumes (in ml) are for 0.1M solutions in dry acetonitrile (LK4050). Adjust accordingly for other concentrations. For µmol pack sizes, products should be diluted as 100µmol/ml to achieve 0.1M, regardless of molecular weight.
No changes are required from the standard method recommended by the synthesiser manufacturer. Coupling is as per standard nucleoside amidites and supports.
To avoid ammonolysis at the halogenated site, a mild deprotection step is recommended using ammonium hydroxide for 24h at room temperature, or AMA for 2h at room temperature provided dmf-dG and Ac-dC are used. Bz-protected C amidites are not compatible with AMA deprotection.
Storage & Stability
Store the solid phosphoramidites refrigerated, dry, at a maximum of 2-8°C. Store the monomers in solution for no longer than 24h, although 8-Br-dG (LK2055) and 5-Br-dU (LK2012) are stable for 2-3 days. Halogenated nucleosides tend to be photosensitive therefore retain the amidites in amber vials.