Halogenated Bases Applications

Halogenated Bases Applications

Currently, the primary use of bromo- and iodo-halogenated bases (for example, 5-iodo-dU, 5-bromo-dG) is to facilitate DNA, or protein-DNA, structure determination in either X-ray crystallography or UV-crosslinking studies. For X-ray crystallography, incorporation of such halogenated bases into DNA permits the use of the multi-wavelength anomalous dispersion (MAD) technique to obtain the phase information necessary to calculate the electron density of the molecule’s unit cell. The chief advantage of the MAD technique compared to the traditional multiple isomorphous replacement (MIR) method is simplicity. MAD allows for the measurement of all the diffraction data with the same sample, whereas MIR requires synthesis of, and collection of diffraction data from, multiple heavy-atom isomorphic derivatives of the original molecule (4). For UV-crosslinking, the photo-lability of halogenated nucleotides makes their incorporation into DNA useful for investigational studies into protein-DNA complexes, for example, to help determine the binding location and characteristics of a DNA binding protein for its target.

References

(1) Hendrickson, W.; Ogata, C. Phase determination from multiwavelength anomalous diffraction measurements. Meth. Enzymol.. (1997), 276: 494-523.
(2) Herbert, A.G.; Rich, A. A method to identify and characterize Z-DNA binding proteins using a linear oligodeoxynucleotide. Nucleic Acids Res. (1993), 21: 2669-2672.
(3) Schneider, D.J.; Wilcox, S.K.; Zichi, D.; Nieuwlandt, D.; Carter, J.; Gold, L. Improved SELEX and Photo-SELEX. (2008), PCT/US2008/070371 (WO/2009/012410).
(4) Walsh M.A.; Evans G.; Sanishvili R.; Dementieva I.; Joachimiak, A. MAD data collection - current trends. Acta Cryst. (1999), D55: 1726-1732.