A theoretical and experimental study of two thiazole orange derivatives with single- and double-stranded oligonucleotides, polydeoxyribonucleotides and DNA

The effect of interaction with DNA and oligonucleotides on the photophysica l properties of two thiazole orange (TO) derivatives, with different side c hains (-(CH2)(3)-N+ (CH3)(3) and -(CH2)(6)-I) linked to the nitrogen of the quinoline ring of the thiazole orange, is presented here. The first one ca lled TO-PRO1 is a commercially available dye, whereas the second one called TO-MET has been specially synthesized for further covalent binding to olig onucleotides with the aim of being used for specific in situ detection of b iomolecular interactions. Both photophysical measurements and molecular cal culations have been done to assess their possible mode of interaction with DNA. When dissolved in buffered aqueous solutions both derivatives exhibit very low fluorescence quantum yields of 8 X 10(-5) and 2 X 10(-4), respecti vely. However, upon binding to double-stranded DNA, large spectroscopic cha nges result and the quantum yield of fluorescence is enhanced by four order s of magnitude, reaching values up to phi(F)=0.2 and 0.3, respectively, as a result of an intercalation mechanism between DNA base pairs. A modulation of the quantum yield is observed as a function of the base sequence. The t wo derivatives also bind with single-stranded oligonucleotides, bur the flu orescence quantum yield is not so great as that when bound to double-strand ed samples. Typical fluorescence quantum yields of 7 x10(-3) to 3 x 10(-2) are observed when the dyes interact with short oligonucleotides, whereas th e fluorescence quantum yield remains below 10(-2) when interacting with sin gle-stranded oligonucleotides. This slight but significant quantum-yield in crease is interpreted as a folding of the single strand around the dye, whi ch reduces the internal rotation of the two heterocycles around the central methine bridge that links the two moieties of the dye. From these properti es, it is proposed to link monomer covalently to oligonucleotides for the s ubsequent detection of target sequences within cells. (C)1999 Elsevier Scie nce S.A. All rights reserved.