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.