Good Vibrations Report on the DNA Quadruplex Binding of an Excited State Amplified Ruthenium Polypyridyl IR Probe

Abstract

The nitrile containing Ru(II)polypyridyl complex [Ru(phen) 2 (11,] 2+ (1) is shown to act as a sensitive infrared probe of G-quadruplex (G4) structures. UV−visible absorption spectroscopy reveals enantiomer sensitive binding for the hybrid htel(K) and antiparallel htel(Na) G4s formed by the human telomer sequence d[AG 3 (TTAG 3 ) 3 ]. Time-resolved infrared (TRIR) of 1 upon 400 nm excitation indicates dominant interactions with the guanine bases in the case of Λ-1/htel(K), Δ-1/htel(K), and Λ-1/htel(Na) binding, whereas Δ-1/htel(Na) binding is associated with interactions with thymine and adenine bases in the loop. The intense nitrile transient at 2232 cm −1 undergoes a linear shift to lower frequency as the solution hydrogen bonding environment decreases in DMSO/water mixtures. This shift is used as a sensitive reporter of the nitrile environment within the binding pocket. The lifetime of 1 in D 2 O (ca. 100 ps) is found to increase upon DNA binding, and monitoring of the nitrile and ligand transients as well as the diagnostic DNA bleach bands shows that this increase is related to greater protection from the solvent environment. Molecular dynamics simulations together with binding energy calculations identify the most favorable binding site for each system, which are in excellent agreement with the observed TRIR solution study. This study shows the power of combining the environmental sensitivity of an infrared (IR) probe in its excited state with the TRIR DNA "site effect" to gain important information about the binding site of photoactive agents and points to the potential of such amplified IR probes as sensitive reporters of biological environments.

Nitrile Substituents at the Conjugated Dipyridophenazine Moiety as Infrared Redox Markers in Electrochemically Reduced Heteroleptic Ru(II) Polypyridyl Complexes

“… 12 This study further reveals that the ν(C≡N) vibrations of nitrile substituents on redox-active ligands can be utilized as convenient IR probes in electron-transfer systems despite the initially low IR intensity and Fermi resonances. 30 It is anticipated that the strong increase in molar absorptivity observed during a reduction step or optical excitation localized in their vicinity facilitates the detection of the IR ν(C≡N) absorption at low concentrations, for example, during photoexcitation of Ru–polypyridyl-based probes intercalated in DNA 31 in kinetic studies carried out by time-resolved IR laser spectroscopy. Combined with DFT and TDDFT calculations, the results indicate that both title complexes are promising IR-active tags for monitoring photo-oxidation of DNA by electron transfer from the guanine base 3 to the intercalated complex in its lowest 3 MLCT excited state residing on a single Ru III –tap •– moiety, despite the NN-based π* LUMO of the parent dicationic complexes.…”