Enhancement of fluorescent resonant energy transfer and the antenna effect in DNA structures with multiple fluorescent dyes

Abstract

This study examines the use of surfactants and metal cations for the enhancement of long range fluorescent resonant energy transfer (FRET) and the antenna effect in double-stranded (ds) DNA structures formed by hybridization of 21mer oligonucleotides with three fluorescent TAMRA donor dyes and complementary 21mer oligonucleotides with one fluorescent Texas Red acceptor dye. In FRET ds-DNA structures, hydrophobic interactions between the fluorescent dyes in close proximity produces dimerization and quenching which reduces fluorescent emissions. For the neutral surfactant Triton X-100, dimerization and emission quenching in the FRET ds-DNA structures remain unaffected. The cationic surfactant CTAB (>100 μM), which neutralizes the negatively charged ds-DNA backbone reduces TAMRA dye dimerization and emission quenching, and improves the Texas Red quantum yield, FRET efficiency and the antenna effect. While the negatively charged SDS surfactant does not reduce dimerization and emission quenching, addition of sodium cations (Na⁺) and magnesium cations (Mg²⁺) lead to a significant reduction in dimerization and emission quenching, and produce higher FRET efficiency and enhanced antenna effect. This study provides a viable strategy for using combinations of surfactants and cations to reduce fluorescent dye and other quenching mechanisms and improve the overall long distance FRET efficiency and the antenna effect in ds-DNA structures.