The method relies on the fluorimetric detection of free Mg2+. There are a few fluorophores with enhanced affinity for Mg2+. These are:
1) Mag-indo-1. Not preferred, discontinued item by most major vendors.
2) Mag-fura-2, tetrapotassium salt. The great advantage of this dye is that it is ratiometric, thus it does not suffer from signal drifts (among other things). The disadvantage of Mag-fura 2 is that its affinity constant (Kd) for Mg2+ is around 1.9 mM, which makes it a bit insensitive for measuring ADP-ATP exchange if the nucleotides are in the low millimolar range.
3) Mag-fluo-4, potassium salt. I don't suggest it for measuring ADP-ATP exchange rate in mitochondria because its Kd for Mg2+ is 4.7 mM, thus very insensitive to alterations of ADP and ATP in the low millimolar range.
4) Magnesium Green, pentapotassium salt (MgG). This would be my choice because of the low Kd for Mg2+, around 0.9 mM. Unfortunately, it is a single excitation (~505 nm)/single emission (~535 nm) dye, thus the user may experience signal drifts. Under the 'Under the hood' advices I suggest a few tricks to alleviate these drifts.
CAUTION: please note that all Mg2+-sensitive dyes also bind Ca2+. The Kd of Mag-fura-2 for Ca2+ is ~ 20-50 mM, and that of MgG is ~ 6 mM. This means that if you choose MgG, you must keep [Ca2+] to less than 1 mM.