OLIGONUCLEOTIDES CONTAINING 2-AMINOADENINE AND 2-THIOTHYMINE ACT AS SELECTIVELY BINDING COMPLEMENTARY AGENTS

A pair of complementary oligodeoxynucleotides (ODNs) uniformly substit uted with 2-aminoadenine (A') in place of adenine and 2-thiothymine (T ') in place of thymine did not hybridize to each other but did form ve ry stable hybrids with unmodified complementary ODNs. These unusual pr operties were a consequence of the hydrogen-bonding properties of the two base analogs. Thermal denaturation studies of short duplexes which contained these bases demonstrated that the A'-T and A-T' doublets fo rmed stable base pairs whereas the A'-T' doubler acted like a mismatch . Complementary ODNs substituted with these base analogs are referred to as SEC or selectively binding complementary ODNs. When used as a pa ir, these single-stranded ODNs invaded the ends of homologous duplexes and formed stable three-al-m junctions under conditions where unmodif ied ODNs failed to give a product. SEC ODNs have a fundamental thermod ynamic advantage in hybridizing to short segments of double-stranded n ucleic acid and represent a new approach for the design of oligomeric probes and antisense agents. Many secondary structure features present in long single-stranded nucleic acids should be accessible to these r eagents.