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Controlling the Fluorescence of Benzofuran‐Modified Uracil Residues in Oligonucleotides by Triple‐Helix Formation
Author(s) -
Kanamori Takashi,
Ohzeki Hiroki,
Masaki Yoshiaki,
Ohkubo Akihiro,
Takahashi Mari,
Tsuda Kengo,
Ito Takuhiro,
Shirouzu Mikako,
Kuwasako Kanako,
Muto Yutaka,
Sekine Mitsuo,
Seio Kohji
Publication year - 2015
Publication title -
chembiochem
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.05
H-Index - 126
eISSN - 1439-7633
pISSN - 1439-4227
DOI - 10.1002/cbic.201402346
Subject(s) - fluorescence , oligonucleotide , uracil , triple helix , chemistry , benzofuran , dna , biophysics , stereochemistry , biochemistry , biology , physics , quantum mechanics
We developed fluorescent turn‐on probes containing a fluorescent nucleoside, 5‐(benzofuran‐2‐yl)deoxyuridine (dU BF ) or 5‐(3‐methylbenzofuran‐2‐yl)deoxyuridine (dU MBF ), for the detection of single‐stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU MBF achieved superior fluorescence enhancement than that containing dU BF . NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3‐methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3‐methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex‐induced fluorescence enhancement of the oligonucleotide probe containing dU MBF .