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 acc ommodation of every double-stranded sequence; it requires the occurren ce of homopurine stretches. A further constraint comes from the weak e nergy of interaction between the third strand and the double-stranded target. In an attempt to design bases leading to increased stability o f triplexes, we explored the ability of modified bases with an extende d aromatic domain to increase third strand binding through stacking in teractions. We report here the use of benzo[g]- and benzo[f]quinazolin e-2,4-dione-(1H,3H)-dione as substitutes for thymine in the canonical TAT triplet. The synthesis and characterization of the beta nucleosid e derivatives of benzoquinazolines are described. Triplex-forming olig onucleotides containing these modified bases have been prepared, and t heir ability to form triplexes has been evaluated by UV absorption-mon itored thermal denaturation measurements. Benzo[g]quinazoline and benz o[f]quinazoline formed triple-stranded structures with slightly decrea sed stabilities. In addition, benzo[g]quinazoline revealed strong fluo rescence emission properties which can be used to monitor selectively the formation of triple-helical structures. Annealing of benzo[g]quina zoline to complementary strands did not produce any fluorescence modif ication. But when it was introduced into the Hoogsteen strand of PyPu Py complexes, the fluorescence intensity was reduced and the emission maximum was shifted to short wavelengths.