title: P-loop catalytically assisting the enzymatic cleavage of single-stranded DNA.
abstract: We demonstrated that a P-loop, a looped complex formed inside duplex DNA by adding peptide nucleic acids (PNA), acts catalytically as a template for enzymatic cleavage of single-stranded probe oligodeoxynucleotides (ODN). A PD-loop complex formed from P-loop and probe ODN was digested efficiently by a restriction enzyme, and the truncated probe ODN was released. The P-loop nicked by the enzyme can form PD-loop again with another probe ODN, and then assisted the enzymatic cleavage of an excess of probe ODN. In addition, by using dumbbell-formed ODN as a probe ODN, the efficiency of the P-loop-assisted ODN cleavage was enhanced considerably as compared with that of linear ODN. Thus, the method utilizing P-loop will make it possible to amplify the sequence information of duplex DNA via a catalytic cleavage of probe ODNs.
authors.affiliation: Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University and SORST, Japan Science and Technology Corporation, 606-8501, Kyoto, Japan.
authors.forename: Akimitsu
authors.initials: A
authors.lastname: Okamoto
authors.forename: Kazuhito
authors.initials: K
authors.lastname: Tanabe
authors.forename: Isao
authors.initials: I
authors.lastname: Saito
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D004277:DNA, Single-Stranded / Q000378:metabolism*; D008969:Molecular Sequence Data; D015345:Oligonucleotide Probes / Q000378:metabolism*; D020135:Peptide Nucleic Acids / Q000737:chemistry / Q000378:metabolism*
chemical_list: D004277:DNA, Single-Stranded; D015345:Oligonucleotide Probes; D020135:Peptide Nucleic Acids