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Nucleic Acids Research, 1995, Vol. 23, No. 13 2499-2505
© 1995

CHEMISTRY

Oligonucleotides containing fluorescent 2'-deoxyisoinosine: solid-phase synthesis and duplex stability

Frank Seela* and Yaoming Chen

Laboratorium für Organische and Bioorganische Chemie, Institut fü Chemie, Universität Osnabrück Barbaratrasse 7, D-49069 Osnabrück, Germany

*To whom correspondence should be addressed

Received March 14, 1995. Accepted May 24, 1995.

The fluorescent nucleoside 2'-deoxyisoinosine (2,isold)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(lll) solid-phase chemistry. One or two Isoldresidues were introduced into the oligomer d(T12),replacing dT either in the middle or at the 3'- and 5'-ends. The Isold-containing oligomers were hybridized with a modified d(A)12 containing the conventional nucleosides (dA, dT, dG and dC) opposite to isold. The replacement of one dT by isold in the centre of the duplex reduced the Tm value by ~15°C and a decrease of ~25°C was found when two Isold 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 isold. The isold (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 Isold residues.


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