OLIGONUCLEOTIDES CONTAINING FLUORESCENT 2'-DEOXYISOINOSINE - SOLID-PHASE SYNTHESIS AND DUPLEX STABILITY

Abstract

The fluorescent nucleoside 2'-deoxyisoinosine (2, isol(d)) has been incorporated into oligonucleotides, For this purpose the phosphonate 3a and the phosphoramidite 3b, as well as the polymer-linked 3d, have been synthesized and oligonucleotides were prepared by P(III) solid-phase chemistry. One or two isol(d)-residues were introduced into the oligomer d(T-12), replacing dT either in the middle or at the 3'- and 5'-ends, The isol(d)-containing oligomers were hybridized with a modified d(A)12 containing the conventional nucleosides (dA, dT, dG and dC) opposite to isol(d), The replacement of one dT by isol(d) in the centre of the duplex reduced the T-m value by similar to 15 degrees C and a decrease of similar to 25 degrees C was found when two isol(d) residues were incorporated, Thermodynamic data were determined from the melting curves, The destabilization was almost independent of the four naturally occurring nucleosides located opposite to sol(d). The isol(d) (2) seems to be stacked in the duplex when dT-dA base pairs are the nearest neighbours; an internal loop is formed in the case of oligomers containing two consecutive isol(d) residues.