A fluorescent 3,7-bis-(naphthalen-1-ylethynylated)-2′-deoxyadenosine analogue reports thymidine in complementary DNA by a large emission Stokes shift

The new environmentally responsive fluorescent nucleosides, 3,7-bis-(naphthalen-1-ylethynyl)-8-aza-3,7-dideaza-2′-deoxyadenosine ( 3n7nz A , 1 ) and 7-(naphthalen-1-ylethynyl)-8-aza-3,7-dideaza-2′-deoxyadenosine ( 37nz A , 2 ), have been synthesized. Both 3n7nz A ( 1 ) and 37nz A ( 2 ) possess large π-conjugated systems which extend into both the minor and major grooves or the major groove alone, respectively. The nucleosides exhibited large solvatochromic shifts ( 3n7nz A : Δ λ = 45 nm, 37nz A : Δ λ = 78 nm) and were examined for their ability to fluorimetrically report hybridization events. When incorporated into ODN probes, the bis-substituted 3n7nz A ( 1 ) selectively recognized thymidine on target strands which was reported by a distinct change in its emission wavelength in the long wavelength region, whereas 37nz A ( 2 ) showed a preference for pairing to cytidine and a smaller wavelength shift. Thus, 3n7nz A ( 1 ) has the potential for use as a fluorescent probe for structural studies of DNAs/RNAs including the detection of single-base alterations in target DNA sequences. The first example of a fluorescent adenosine analogue possessing simultaneous major- and minor-groove substitution selectively reports base-pairing to thymidine.