Bis-pyrene-labeled molecular beacon: a monomer-excimer switching probe for the detection of DNA base alteration.
A new bis-pyrene-labeled oligonucleotide probe (BP-probe) has been designed for the detection of a single base mismatch in single strand (ss) DNA as a target. The sequence of BP-probe was chosen to form stem-loop structure similar to a molecular beacon (MB-probe), yielding bis-pyrene-labeled molecular beacon (BP-MB-probe). Partially double stranded (ds) BP-MB-probes were prepared by complexation with oligonucleotides whose sequences are complementary to the loop segment but not to the stem and exchangeable with the target DNA. The partially ds BP-MB-probes were shown to exhibit monomer fluorescence as major fluorescence, while the ss BP-MB-probe in the stem-loop form displays strong excimer fluorescence. The strand exchange reactions between partially ds BP-MB-probe and target ss DNA in the presence of cationic comb-type copolymer as a catalyst were monitored by the excimer fluorescence changes. The existence of a mismatched base can be determined by the slower PASE rates compared with fully matched DNA.
Yamana
Kazushige
K
Department of Materials Science and Chemistry, Graduate School of Engineering, University of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan. yamana@eng.u-hyogo.ac.jp
Ohshita
Yoshikazu
Y
Fukunaga
Yudai
Y
Nakamura
Mitsunobu
M
Maruyama
Atsushi
A
D020137:Base Pair Mismatch; D020029:Base Pairing; D004247:DNA / Q000032:analysis / Q000737:chemistry*; D005453:Fluorescence; D007700:Kinetics; D015336:Molecular Probe Techniques; D009693:Nucleic Acid Hybridization; D015345:Oligonucleotide Probes / Q000737:chemistry*; D011721:Pyrenes
D015345:Oligonucleotide Probes; D011721:Pyrenes; D004247:DNA; C030984:pyrene