Hybridization of two oligodeoxynucleotides to both strands of an RNA hairpin structure increases the efficiency of RNA-DNA duplex formation.

Hybridization of two oligodeoxyribonucleotides (ON1 and ON2), complementary to opposite strands of the apical domain of Escherichia coli 4.5S RNA, was studied. ON1, complementary to bases 58-71, was not able to form a stable RNA-DNA hybrid whereas ON2, complementary to bases 38-53, was. Addition of both oligonucleotides at the same time resulted in the formation of a ternary complex permitting hybridization of ON1 and increasing hybridization of ON2. Under this condition, binary complexes of ON1 or ON2 with 4.5S RNA were not observed. The data demonstrate that hybridization of oligonucleotides to both strands of an RNA hairpin structure increases the efficiency of hybridization of either oligonucleotide.