Fluorescence quenching of 2-aminopurine in dinucleotides

2-Aminopurine is a fluorescent base analog that probes local dynamics in DNA because its fluorescence is quenched by the surrounding bases. But, the underlying mechanisms are still under investigation. We have studied fluorescence decay of 2-aminopurine in dinucleotides and found a similar heterogeneity as was previously observed in larger oligonucleotides. This indicates that dinucleotides could function as model for local dynamics of intact DNA. We also found that fast (21–35 ps) quenching could be induced by all natural bases. Our results confirm that the product of this fast transition has the characteristics of a dark state.