G/C-modified oligodeoxynucleotides with selective complementarity: Synthesis and hybridization properties

Modified oligodeoxyribonucleotides (ODNs) that have unique hybridization properties were designed and synthesized for the first time, These ODNs, called selective binding complementary ODNs (SEC ODNs), are unable to form stable hybrids with each other, yet are able to form stable, sequence specific hybrids with complementary unmodified strands of nucleic acid, To make SEC ODNs, deoxyguanosine (dG) and deoxycytidine (dC) were substituted with deoxyinosine (dl) and 3-(2'-deoxy-beta-D-ribofuranosyl)pyrrolo-[2,3-d]-pyrimidine-2-(3H)-one (dP), respectively, The hybridization properties of several otherwise identical complementary ODNs containing one or both of these nucleoside analogs were studied by both UV monitored thermal denaturation and non-denaturing PAGE, The data showed that while dl and dP did form base pairs with dC and dG, respectively, dl did not form a stable base pair with dP A self-complementary ODN uniformly substituted with dl and dP acquired single-stranded character and was able to strand invade the end of a duplex DNA better than an unsubstituted ODN, This observation implies that SEC ODNs should effectively hybridize to hairpins present in single-stranded DNA or RNA.