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Oligonucleotides Containing Phenoxazine Artificial Nucleobases: Triplex‐Forming Abilities and Fluorescence Properties
Author(s) -
Fujii Akane,
Nakagawa Osamu,
Kishimoto Yuki,
Nakatsuji Yusuke,
Nozaki Natsumi,
Obika Satoshi
Publication year - 2020
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.201900536
Subject(s) - phenoxazine , oligonucleotide , chemistry , thymine , dna , nucleobase , cytosine , moiety , combinatorial chemistry , fluorescence , stereochemistry , phenothiazine , biochemistry , biology , physics , quantum mechanics , pharmacology
1,3‐Diaza‐2‐oxophenoxazine (“phenoxazine”), a tricyclic cytosine analogue, can strongly bind to guanine moieties and improve π–π stacking effects with adjacent bases in a duplex. Phenoxazine has been widely used for improving duplex‐forming abilities. In this study, we have investigated whether phenoxazine and its analogue, 1,3,9‐triaza‐2‐oxophenoxazine (9‐TAP), could improve triplex‐forming abilities. A triplex‐forming oligonucleotide (TFO) incorporating a phenoxazine component was found to show considerably decreased binding affinity with homopurine/homopyrimidine double‐stranded DNA, so the phenoxazine system was considered not to function as either a protonated cytosine or thymine analogue. Alternatively, a 9‐TAP‐containing artificial nucleobase developed by us earlier as a new phenoxazine analogue functioned as a thymine analogue with respect to AT base pairs in a parallel triplex DNA motif. The fluorescence of the 9‐TAP moiety was maintained even in triplex (9‐TAP:AT) formation, so 9‐TAP might be useful as an imaging tool for various oligonucleotide nanotechnologies requiring triplex formation.