Sequence Dependence of Fluorescent Quenching of Chromophores Covalently Bonded to Oligo-DNAs before and after Duplex Formation

The labeling of oligo- and polynucleotides with fluorescent probes is an important technique for the analysis of DNAs and RNAs. The effect of duplex formation with complementary oligo-DNA on the quenching behavior of two fluorescent chromophores (eosin, Eo and tetramethylrhodamine, TMR) attached to the 5′-terminal of various 10mer oligo-DNAs was investigated and the dependence of the quenching on DNA base sequence is discussed. We found that guanine residues played a major role in the quenching of the fluorescence of the chromophores. Guanine residues on the complementary DNA near the chromophores, in particular, had a significant influence on the quenching.