Emission kinetics of fluorescent nucleoside analogs

Fluorescent analogs of nucleic acid bases are useful probes for observation of DNA structure, interactions, and dynamics. 2-aminopurine (2AP) and 3-methylisoxanthopterin (3MI) are analogs of adenine and guanine, respectively, which have single exponential fluorescence intensity decay kinetics when free in buffer at neutral pH but complex multi-exponential decays when incorporated into oligonucleotides. We have investigated the mechanisms underlying the complexity of the emission kinetics of these probes in DNA by observing decays as a function of local nucleic acid sequence and emission wavelength. For both probes, the intensity-averaged lifetime increases smoothly with increasing emission wavelength. Analysis of these data as a time-resolved emission spectrum (TRES) demonstrates that the complex decay law can be described as resulting from dipolar relaxation of the local environment of the probe on the same timescale as emission. While the mean fluorescence lifetime shows no dependence on nucleic acid sequence 5' or 3' of the probe, the mean time constant for dipolar relaxation is correlated with the identity of the neighboring bases. These results suggest that 2AP and 3MI may be sensitive probes of the local dynamics of nucleic acids, bound water, and counterions.