Excitation and Ground-State Properties of Natural and Modified Nucleic Acid Bases
Doctoral thesis, 1997
The nucleic acid bases are the carriers of genetic information in DNA and RNA. They are also the main chromophores of nucleic acids and determine their optical properties and sensitivity to UV radiation. In order to understand and interpret the optical spectra and photophysical behavior of nucleic acid bases, this thesis focuses on the electronic and vibrational transition moments of the naturally occurring nucleic acid bases uracil and adenine, and two synthetic, fluorescent bases: 1,N6-ethenoadenine and 2-aminopurine. The tools have been linear dichroism, fluorescence anisotropy and magnetic circular dichroism techniques in combination with semi-empirical molecular orbital calculations of electronic spectra, and ab initio and density functional theory (DFT) calculations of vibrational spectra.
The UV spectrum of adenine is concluded to derive from five .pi. - .pi.* transitions whose transition moment directions and band shapes are characterized. The presence of an .pi. - .pi.* transition occurring close to the lowest .pi. - .pi.* transition is inferred from comparisons with other purines and from quantum-chemical calculations. Such an .pi. - .pi.* transition could explain the low fluorescence quantum yield and also the relatively low photochemical reactivity of adenines.
For 1,N6-ethenoadenine and 2-aminopurine, the UV spectra are resolved into contributions from four .pi. - .pi.* transitions. A most remarkable finding in 2-aminopurine is the identification of a low-lying .pi. - .pi.* transition. The determined transition moments should be useful for studies of structure and dynamics of nucleic acids based on absorption and emission anisotropy.
The carbonyl stretching vibrations of 1,3-dimethyluracil are assigned to the in-phase and out-of-phase components of the carbonyl stretching motions. The transition moment directions of the strong amino-group-scissoring and ring-stretching vibrations in adenine and 2-aminopurine are expected to be useful for structural studies of nucleic acids containing adenine or 2-aminopurine bases using IR spectroscopy.
Some of the purines are investigated with respect to their structures and tautomerism in solution using ab initio and DFT calculations. The results allow us to predict relative concentrations of various tautomers, and to identify possible differences between solution and gas-phase structures and those determined by crystallographic methods.