2-Phenanthrenyl-DNA: synthesis, pairing, and fluorescence properties

Three 2'-phenanthrenyl-C-deoxyribonucleosides with donor (phenNH(2)), acceptor (phenNO(2)), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single-modified duplexes can vary between -2.7 to +11.3 degrees C in T(m) and that of triple-modified duplexes from +7.8 to +11.1 degrees C. Van't Hoff analysis suggested that the observed higher thermodynamic stability in phenH- and phenNO(2)-containing duplexes is of enthalpic origin. A single phenH or phenNO(2) residue in a bulge position also stabilizes a corresponding duplex. If a phenNO(2) residue is placed in a bulge position next to a base mismatch this can lead, in a sequence-dependent manner, to duplex destabilization. The phenNO(2) residue was found to be a highly efficient (10-100-fold) quencher of phenH and phenNH(2) fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH(2) residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH(2) fluorescence was found, which is an indicator for electron- or energy-transfer processes between the aromatic units.