Interpretation of fluorescence decay kinetics in 3-methylbenzimidazolyl(5'-5')guanosine dinucleotides: exponential dependence on the number of phosphates in the polyphosphate bridge.

The number of phosphate groups in the 5',5'-polyphosphate bridge of mRNA-cap dinucleotide analogues affects kinetics of long-range electron transfer (ET) responsible for 3-methylbenzimidazole (m(3)B) fluorescence quenching in model dinucleotides. For instance, 3-methylbenzimidazolyl(5'-5')guanosine dinucleotides (m(3)Bp( n )G, n = 2, 3, 4) having m(3)B donor, 5'-5' polyphosphate bridge, and guanine (G) acceptor, exhibit exponential dependence of the ET rate on the number of phosphates, i.e. donor-acceptor distance. Involvement of the 5'-5' polyphosphate bridge in the ET is strongly indicated by lack of m(3)B-G stacking effect on the exponential factor, which is the same at 20 degrees C, where m(3)B-G intramolecular stacking dominates, as that at 75 degrees C where stacking-unstacking equilibrium is shifted in favour of the unstacked structure.