Halogenated nucleotides are used for several kinds of things. The base is derivatized at one or another postion depending on the nucleotide. Sometimes halogenated nucleotides are used as mutagens or as a density label (bromo-deoxy uridine, for example) People who like to do crystal structures of nucleic acids, either of oligonucleotides or as complexes with proteins, will use halogenated bases to help identify the nucleic acids in the electron density maps; halogens are electron-rich and diffract x-rays more strongly than C or N or O atoms and so should have stronger peaks in the map where the bromines or iodines are located compared to more ordinary elements, but the downside is that they (halogenated bases) are also more susceptible to x-ray-induced damage, and so more easily lost. I don’t know if there is any special property of brominated ATP as opposed to any other brominated nucleotide. I don’t know if brominated ATP can replace ATP in a kinase reaction, for example. Depending on the kinase, I imagine it could, but I don’t really know that, nor do I see any reason why you would want to do that anyway.
