Recognition of hairpin-containing single-stranded DNA by oligonucleotides containing internal acridine derivatives

Oligodeoxynucleotides with an internal intercalating agent have been target ed to single-stranded sequences containing hairpin structures. The oligonuc leotide binds to nonadjacent single-stranded sequences on both sides of the hairpin structure in such a way as to form a three-way junction. The acrid ine derivative is inserted at a position that allows it to interact with th e three-way junction. The melting temperature (T-m) of complexes formed bet ween the hairpin-containing target and oligonucleotides containing one inte rnal acridine derivative was higher than that obtained with the same target and an unmodified oligonucleotide (Delta T-m = +13 degrees C). The interna l acridine provided the oligonucleotide with a higher affinity than covalen t attachment to the 5' end. Oligonucleotides could also be designed to reco gnize a hairpin-containing single-stranded nucleic acid by formation of Wat son-Crick hydrogen beads with a single-stranded part and Hoogsteen hydrogen bonds with the stem of the hairpin. An internal acridine derivative was in troduced at the junction between the two domains, the double helix domain w ith Watson-Crick base pairs and the triple helix domain involving Hoogsteen base triplets in the major groove of the hairpin stem. Oligonucleotides wi th an internal acridine or an acridine at their 5' end have similar binding affinities for the stem-loop-containing target. The bis-modified oligonucl eotide containing two acridines, one at the 5' end and one at an internal s ite, did not exhibit a higher affinity than the oligonucleotides with only one intercalating agent. The design of oligonucleotides with an internal in tercalating agent might be of interest to control gene expression through r ecognition of secondary structures in single-stranded targets.