Molecular dynamics of labeled oligonucleotide probes used for the detection of point mutations in DNA

The fluorescent label BODIPY 576-589 linked to the 5-end of an oligonucleotide via alkyl chain linkers can be used as a probe to detect point mutations in DNA. We have employed fluorescence anisotropy decay and dynamic fluorescence resonance energy transfer (FRET) in order to investigate the molecular origin of the fluorescence lifetime aberrations of BODIPY in the presence of a mismatched base. The results show that both, an increased flexibility of the alcyl chain linker to the BODIPY molecule as well as relaxation of the secondary structure of the whole complex, contribute to the decreased fluorescence lifetimes reported previously.