Polyfluorophore Excimers and Exciplexes as FRET Donors in DNA

Abstract

We describe studies aimed at testing whether oligomeric exciplex-and excimer fluorophores conjugated to DNA have the potential to act as donors for energy transfer by the Förster mechanism. Oligodeoxyfluorosides (ODFs) are composed of stacked, electronically interacting fluorophores replacing the bases on a DNA scaffold. The monomer chromophores in the twenty tetramer-length ODFs studied here include pyrene (Y), benzopyrene (B), perylene (E), dimethylaminostilbene (D), and a nonfluorescent spacer (S); these are conjugated in varied combinations at the 3' end of a 14mer DNA probe sequence. In the absence of an acceptor chromophore, many of the ODF-DNAs show broad, unstructured long-wavelength emission peaks characteristic of excimer and exciplex excited states, similar to what has been observed for unconjugated ODFs. Although such delocalized excited states have been widely studied, we know of no prior report of their use in FRET. We tested the ability of the twenty ODFs to donate energy to Cy5 and TAMRA dyes conjugated to a complementary strand of DNA, with these acceptors oriented either at the near or far end of the ODF-conjugated probes. Results showed that a number of the ODF fluorophores exhibited relatively efficient energy transfer characteristic of the Förster mechanism, as judged by drops in donor emission quantum yield and fluorescence lifetime, accompanied by increases in intensity of acceptor emission bands. Excimer/exciplex bands in the donors were selectively quenched while shorter-wavelength monomer emission stayed relatively constant, consistent with the notion that the delocalized excited states, rather than individual fluorophores, are the donors. Interestingly, only specific sequences of ODFs were able to act as donors, while others did not, even though their emission wavelengths were similar. The new FRET donors possess large Stokes shifts, which can be beneficial for multiple applications. In addition, all ODFs can be excited at a single wavelength; thus, ODFs may be candidates as "universal FRET donors", thus allowing multicolor FRET of multiple species to be carried out with one excitation.

Molecular Interactions in Organic Nanoparticles for Phototheranostic Applications

“…62 DNA fluorotags were also shown to be excellent FRET donors. 63 Conjugating a FRET acceptor (Cy5) at the end of the DNA oligomer resulted in efficient energy transfer from the two dyes with transfer efficiencies reaction over 70% in the 5′-EYYSS-Cy5−3′ sequence. 63 Further demonstrating the applicability of their DNA platform, Wang et al showed high-speed, multicolored tracking of various single and multicellular organisms.…”

Efficient synthesis of fluorescent alkynyl C-nucleosides via Sonogashira coupling for the preparation of DNA-based polyfluorophores

“…another Y or E) 45, 46 and it can also potentially function as a FRET donor for through-space energy transfer to an appropriate acceptor dye. 47, 48 If the styryl-pyran dye K was incorporated, the respective ODFs showed yellow to orange emission. Beads with red emission were found rather frequently, but the brightness of those beads was typically limited.…”

Fluorescence resonance energy transfer in AOT/4-chlorophenol/m-xylene organogels

“…Since R 0 typically lies in the range 10-100 Å, FRET offers a convenient method for estimating distances in the molecular length-scale, especially in materials where the local environment changes drastically over only a few nm. Hence, FRET studies have been conducted in micelles [12], reverse micelles [13,14], vesicles [15], liposomes [16], ionic liquids [17,18], supramolecular assemblies [19], DNA [20], quantum dots and cyclodextrins [21], etc. Recently, there has been a spurt in energy transfer studies aimed for the development of novel white light emitting organogels like [22][23][24][25][26][27].…”