THE FORMATION AND DETECTION OF TIGHT-TURN IN PYRIMIDINE/PURINE/PYRIMIDINE TYPE DNA TRIPLEXES — NEW FINDINGS ON MOTIFS CC AND TT BY FLUORESCENCE SPECTROSCOPY AT pH 7

Abstract

DNA triplexes with 'tight turns', i.e., sharp turns without any intervening bases, are studied by fluorescence resonance energy transfer process (FRET). The particular turning motifs under consideration are CC and TT imbedded in triplexes (5′- F -( TC )3( CT )3- D + 5′- AGAGAG ) and (5′- F -( CT )3( TC )3- D + 5′- GAGAGA ), where F and D are 6-fluorescein and 4-(4-dimethylaminophenylazo) benzoic acid, respectively. The association equilibrium constants of the above two triplexes ranged from 1.7 × 107 to 2.9 × 104 and 0.75 × 107 to 1.8 × 104 from 10 to 35°C, respectively. The thermodynamic parameters of these two triplexes are comparable (△ H : -46.0 vs. -45.0 Kcal/mol ; △ S : -129 vs -127 cal/mol K ; △ G : -7.5 vs. -7.2 Kcal/mol , respectively). Thus, the stability of the tight-turn triplex with a CC motif is comparable to that with a TT motif, but slightly favored over the latter. This is the first report of a py/pu/py type triplex containing such tight turns studied under pH at 7. The importance is manifested in their stabilities maintained under physiological neutral condition, as opposed to previous studies only obtainable in acidic conditions.