title: Strand-invading linear probe combined with unmodified PNA.
abstract: Efficient strand invasion by a linear probe to fluorescently label double-stranded DNA has been implemented by employing a probe and unmodified PNA. As a fluorophore, we utilized ethynylperylene. Multiple ethynylperylene residues were incorporated into the DNA probe via a d-threoninol scaffold. The ethynylperylene did not significantly disrupt hybridization with complementary DNA. The linear probe self-quenched in the absence of target DNA and did not hybridize with PNA. A gel-shift assay revealed that linear probe and PNA combination invaded the central region of double-stranded DNA upon heat-shock treatment to form a double duplex. To further suppress the background emission and increase the stability of the probe/DNA duplex, a probe containing anthraquinones as well as ethynylperylene was synthesized. This probe and PNA invader pair detected an internal sequence in a double-stranded DNA with high sensitivity when heat shock treatment was used. The probe and PNA pair was able to invade at the terminus of a long double-stranded DNA at 40°C at 100mM NaCl concentration.
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan. Electronic address: asanuma@nubio.nagoya-u.ac.jp.
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Asanuma
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Rie
authors.initials: R
authors.lastname: Niwa
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Mariko
authors.initials: M
authors.lastname: Akahane
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Keiji
authors.initials: K
authors.lastname: Murayama
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Hiromu
authors.initials: H
authors.lastname: Kashida
authors.affiliation: Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan.
authors.forename: Yukiko
authors.initials: Y
authors.lastname: Kamiya
mesh_terms: D000880:Anthraquinones / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D015342:DNA Probes / Q000737:chemistry*; D005456:Fluorescent Dyes / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D020135:Peptide Nucleic Acids / Q000737:chemistry*; D010569:Perylene / Q000031:analogs & derivatives; D013050:Spectrometry, Fluorescence
chemical_list: D000880:Anthraquinones; D015342:DNA Probes; D005456:Fluorescent Dyes; D020135:Peptide Nucleic Acids; D010569:Perylene; D004247:DNA
keywords: DNA; Linear probe; PNA; Strand invader