Naphthalenyl- and anthracenyl-ethynyl dT analogues as base discriminating fluorescent nucleosides and intramolecular energy transfer donors in oligonucleotide probes

Xiao, Qiang, Ranasinghe, Rohan T., Tang, Adrian M.P. and Brown, Tom (2007) Naphthalenyl- and anthracenyl-ethynyl dT analogues as base discriminating fluorescent nucleosides and intramolecular energy transfer donors in oligonucleotide probes. Tetrahedron, 63 (17), 3483-3490. (doi:10.1016/j.tet.2006.10.090).

Abstract

Fluorescent thymidine analogues functionalised in the 5-position with the moieties naphthalenylethynyl (NeT), anthracenylethynyl (AeT) and anthracenylbuta-1,3-diynyl (AeeT) have been incorporated into oligonucleotides. The modified oligonucleotides undergo significant emission enhancement when hybridised to fully complementary strands and a decrease in fluorescence emission when the modified thymine is paired with guanine. Thus these analogues are potentially useful as base discriminating fluorescent nucleosides (BDFs). When a fluorescein dT monomer is incorporated into the same oligonucleotide strand as the modified base, energy transfer enhances the fluorescein emission, particularly upon duplex formation. These dual-labelled probes may be useful for genetic analysis to detect point mutations and SNPs and could provide multiplexing capability.

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