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

ABSTRACT

Three fluorescent nucleosides-UFL, UAF, and UDAF, 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 UFL and cytosine-FBs in the pH range from 5.5 to 8.0 and the ODN containing UDAF 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.