Benzoquinazoline derivatives as substitutes for thymine in nucleic acid complexes. Use of fluorescence emission of benzo[g]quinazoline-2,4-(1H,3H)-dione in probing duplex and triplex formation.

Triple helix formation obeys structural features that do not allow accommodation of every double-stranded sequence; it requires the occurrence of homopurine stretches. A further constraint comes from the weak energy of interaction between the third strand and the double-stranded target. In an attempt to design bases leading to increased stability of triplexes, we explored the ability of modified bases with an extended aromatic domain to increase third strand binding through stacking interactions. We report here the use of benzo[g]- and benzo[f]quinazoline-2,4-dione-(1H,3H)-dione as substitutes for thymine in the canonical TAT triplet. The synthesis and characterization of the beta nucleoside derivatives of benzoquinazolines are described. Triplex-forming oligonucleotides containing these modified bases have been prepared, and their ability to form triplexes has been evaluated by UV absorption-monitored thermal denaturation measurements. Benzo[g]quinazoline and benzo[f]quinazoline formed triple-stranded structures with slightly decreased stabilities. In addition, benzo[g]quinazoline revealed strong fluorescence emission properties which can be used to monitor selectively the formation of triple-helical structures. Annealing of benzo[g]quinazoline to complementary strands did not produce any fluorescence modification. But when it was introduced into the Hoogsteen strand of PyPuPy complexes, the fluorescence intensity was reduced and the emission maximum was shifted to short wavelengths.