Donor/Acceptor Interactions in Systematically Modified RuII−OsII Oligonucleotides

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Abstract
Donor/acceptor (D/A) interactions are studied in a series of doubly modified 19-mer DNA duplexes. An ethynyl-linked RuII donor nucleoside is maintained at the 5‘ terminus of each duplex, while an ethynyl-linked OsII nucleoside, placed on the complementary strands, is systematically moved toward the other terminus in three base pair increments. The steady-state RuII-based luminescence quenching decreases from 90% at the shortest separation of 16 Å (3 base pairs) to ∼11% at the largest separation of 61 Å (18 base pairs). Time-resolved experiments show a similar trend for the RuII excited-state lifetime, and the decrease in the averaged excited-state lifetime for each duplex is linearly correlated with the fraction quenched obtained by steady-state measurements. Analysis according to the Förster dipole−dipole energy transfer mechanism shows a reasonable agreement. Deviation from idealized behavior is primarily attributed to uncertainty in the orientation factor, κ2. Analyzing D/A interactions in an analogous series of doubly modified oligonucleotides, where the ethynyl-linked RuII center is replaced with a saturated two-carbon linked complex, yields an excellent correlation with the Förster mechanism. As this simple change partially relaxes the rigid geometry of the donor chromophore, these results suggest that the deviation from idealized Förster behavior observed for the duplexes containing the rigidly held RuII center originates, at least partially, from ambiguities in the orientation factor. Surprisingly, analyzing both quenching data sets according to the Dexter mechanism also shows an excellent correlation. Although this can be interpreted as strong evidence for a Dexter triplet energy transfer mechanism, it does not imply that this electron exchange mechanism is operative in these D/A duplexes. Rather, it suggests that systems that transfer energy via the Förster mechanism can under certain circumstances exhibit Dexter-like “behavior”, thus illustrating the danger of imposing a single physical model to describe D/A interactions in such complex systems. While we conclude that the Förster dipole−dipole energy transfer mechanism is the dominant pathway for D/A interactions in these modified oligonucleotides, a minor contribution from the Dexter electron exchange mechanism at short distances is likely. This complex behavior distinguishes DNA-bridged RuII/OsII dyads from their corresponding low molecular-weight and covalently attached counterparts.