pH-dependent spectroscopy and electronic structure of the guanine analogue 6,8-dimethylisoxanthopterin

Fluorescent nucleic acid analogues are valuable tools for studying DNA dynamics, protein-DNA interactions and nucleotide-dependent enzyme activities. The recent development of guanine analogues based on the isoxanthopterin structure offers new opportunities to investigate these dynamics, interactions, and activities. Our combined experimental/theoretical investigation of one such analogue, 6,8-dimethylisoxanthopterin (6,8DMI), has shown that absorbance and fluorescence emission spectra of 6,8DMI shift to lower energies as the pH is increased, yielding pK_a values of 8.3 and 8.5, respectively. We show that these pH-dependent spectral changes result from protonation/deprotonation of the nitrogen at position 3 of 6,8DMI on the basis of pH-dependent iodide ion quenching of 6,8DMI fluorescence and pH-independent absorption and fluorescence properties of 3,6,8-trimethylisoxanthopterin. Quantum mechanical calculations on the neutral and deprotonated forms of 6,8DMI confirm the observed spectral changes.