Sequence specific recognition of ssDNA by fluorophore 3-hydroxyflavone

A fully water soluble 3-hydroxyflavone (3HF) derivative, N-(3-hydroxy-4'-flavonyl)-N,N,N-trimethylammonium sulfate (3HFNMe3) was synthesized. Investigation of its emissions at varying wavelengths revealed that it had three emission bands of normal (N*), anionic (A*) and tautomeric (T*), in ultrapure water. Recognition of single-stranded ten ssDNA chains, having different nucleotide sequences was studied, using the ratiometric change of the intensities of the two bands (A*/T*), depending upon the varying environment of the 3HFNMe3 with different ssDNA chains. Addition of the ssDNA chains to the 3HFNMe3 solution caused gradual quenching of the A* band and had almost no effect on the T*. band. As the ratios of the two bands (A*/T*) vs increasing amount of the ssDNAs generated characteristic curves for each ssDNA chain, it became possible to identify the chains with their characteristic curves. (C) 2015 Elsevier B.V. All rights reserved.