pH-Responsive quencher-free molecular beacon systems containing 2′-deoxyuridine units labeled with fluorene derivatives

Abstract

Three fluorescent nucleosides—U^FL, U^AF, and U^DAF, containing fluorene, 2-aminofluorene, and 2-dimethylaminofluorene units, respectively, covalently attached to 2′-deoxyuridine—have been incorporated into the central positions of oligodeoxynucleotides (ODNs) to examine the effects of their flanking bases (FBs) and pH on the emission properties upon hybridization with fully matched and single-base-mismatched targets. The ODN containing U^FL and cytosine-FBs in the pH range from 5.5 to 8.0 and the ODN containing U^DAF and cytosine-FBs under slightly acidic conditions (pH 6.0–6.5) exhibited dramatic increases in fluorescence only upon duplex formation with their fully matched target DNAs.