Adaptation of inorganic quantum dots for stable molecular beacons

We have developed semiconductor quantum dots (QDs)-conjugated molecular beacons (MBs). The organic fluorophores are replaced with inorganic fluorescent ZnS-capped CdSe quantum dots covered with mercaptoacetic acid monolayer. We confirmed the overlap between emission spectrum of the QD after the surface modification and the absorption spectrum of 4-(4'-dimethylaminophenylazo) benzoic acid (DABCYL) as an organic quencher molecule. About 90% overlap between QDs and DABCYLs' spectra promotes fluorescent resonance energy transfer (FRET). FRET efficiency between QD-DABCYL and 6-FAM (organic fluorophore)-DABCYL are compared by using 3-D molecular modeling. The farthest and nearest possible separation between the fluorophore and the quencher are predicted using 3-D molecular model considering the rotational freedom of the bonds defined by the type of chemical linker between MB-fluorophore and MB-DABCYL. Finally, QD-modified MBs are tested with their complementary target deoxyribonucleic acid (DNA) sequence and for non-specific sequences. The use of QDs instead of organic fluorophores may offer multiplexed imaging during DNA or RNA analysis due to their broad UV absorption spectrum. (C) 2004 Elsevier B.V. All rights reserved.