Padlock oligonucleotides for duplex DNA based on sequence-specific triple helix formation

An oligonucleotide was circularized around double-stranded DNA thanks to tr iple helix formation. Short oligonucleotides are known to be able to form D NA triple helices by binding into the DNA major groove at an oligopurine ol igopyrimidine sequence. After sequence-specific recognition of a double-str anded DNA target through triple helix formation, the ends of the tripler-fo rming oligonucleotide were joined through the action of T4 DNA ligase, thus creating a circular DNA molecule catenated to the plasmid containing the t arget sequence. The labeling of the double-stranded DNA sequence has been c arried out without any chemical or enzymatic modification of this sequence. These "padlock" oligonucleotides provide a tool to attach a noncovalent ta g in an irreversible way to supercoiled plasmid or other double-stranded DN As. Such a complex may find applications in the development of new techniqu es for duplex DNA detection or plasmid delivery methods for gene therapy.