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5-Br-dC CE-Phosphoramidite

5-Br-dC CE-Phosphoramidite

CAS No.:178925-43-4

Phosphoramidite used to incorporate a bromo-modified deoxycytidine internally or at the 5' end of an oligonucleotide.
  • Photoactive analogue useful in photo-crosslinking studies.
  • Useful in x-ray crystallography studies.
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Product information

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.

Ref:

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.

Applicable Products

LK2009 5-I-dC-CE Phosphoramidite
LK2010 5-F-dU-CE Phosphoramidite
LK2011 5-Br-dC-CE Phosphoramidite
LK2012 5-Br-dU-CE Phosphoramidite
LK2014 5-I-dU-CE Phosphoramidite
LK2054 8-Br-dA-CE Phosphoramidite
LK2055 8-Br-dG-CE Phosphoramidite
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.

Item

Mol. Formula

Mol. Wt.

Unit Wt.

250mg

500mg

1g

LK2009 C46H51N5O8PI 959.83 415.08 2.60 5.21 10.42
LK2010 C39H46N4O8PF 748.79 308.16 3.34 6.68 13.35
LK2011 C46H51N5O8PBr 912.82 368.08 2.74 5.48 10.96
LK2012 C39H46N4O8PBr 809.69 369.07 3.09 6.18 12.35
LK2014 C39H46N4O8PI 856.69 416.07 2.92 5.84 11.67
LK2054 C43H52N8O6PBr 887.81 392.11 2.82 5.63 11.26
LK2055 C43H52N8O7PBr 903.90 408.10 2.77 5.53 11.06
LK2325 - - 369.07 - - -

Coupling

No changes are required from the standard method recommended by the synthesiser manufacturer. Coupling is as per standard nucleoside amidites and supports.

Deprotection

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.

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