Pyrimidine bases absorption spectra

The close correspondence of the DNA absorption spectrum with that of a mixture of mononucleotides of the same composition illustrates the weak nature of the interactions between neighboring purine and pyrimidine bases guanine (G), cytosine (C), adenine (A), and thymine (T) at an interplanar separation of 3.36 A in the unexcited double-helical configuration. On the other hand the structureless fluorescence band of (calf-thymus) DNA is red-shifted by 3500 cm-1 from the fluorescence spectral origin of the mononucleotides it closely resembles the fluorescence spectrum of the dinocleotide ApT (and of poly dAT) and is accordingly identified131 with the fluorescence... 

Spectral data (Amax and AE, and e x 10 3) for the pyrimidine bases investigated in a few representative papers are collected in Table XXVIII. The absorption bands are denoted by the capital letters A, B, C, etc. In Table XXVIII we have listed the results of the vacuum ultraviolet measurements by Yamada and Fukutome428 (cf. also ref. 429), who measured the spectra of sublimed films of cytosine, thymine, uracil (and also of guanine and adenine) down to 120 nm at room temperature. Several remarkable absorption peaks were found below 190 nm in addition to the already known ones near 260 and 200 nm. A weak absorption at 230-240 nm in cytosine was not indicated in the sublimed films of the molecule,428 but was visible in the stretched polyvinyl alcohol film spectrum.432 Crewe et al.i3° studied the interactions of fast electrons with the five nucleic acid bases and measured the energy-loss spectra of 20 keV electrons transmitted through thin films of these bases. These last data are also listed in Table XXVIII for comparison with the other spectral findings. 

Light exposure within the absorption spectrum of the psoralens (300 to 400 nm) leads to covalent binding of the psoralen to pyrimidine bases in DNA. Monofunctional psoralens, such as angelicines, bind to only one of the DNA strands bifunctional ones (linear psoralens) bind to both strands, and therefore cross-link one strand to the other. This will slow down the rate of cell division, which is abnormally high in psoriatic skin. Psoralens may also act on membranes in a type II process. 

It is generally believed that among the pyrimidine bases, uracil and thymine mainly exist in the keto form. However, the existence of a small amount of the enol form of these compounds has also been indicated in some experiments. Hauswirth and Daniels have explained the observed deviation in the excitation spectrum of thymine firom the corresponding absorption spectrum in terms of the possibility of emission firom the enol tautomer. On the other hand, Vigny and Duquesne observed that both absorption and fluorescence excitation spectra of thymine are in resemblance with each other. Suwaiyan et al. have suggested the existence of a small amount of the enol tautomer in aqueous solutions of 5-chlorouracil at room temperature. The existence of keto-enol tautomerism in uracil, thymine and their derivatives has also been suggested in supersonic jet-cooled spectroscopic studies. ... 

The purine and pyrimidine bases, as a result of their 7c-electrons, absorb strongly in the UV region of the spectrum. The approximate absorption maximum is 260 nm (8260nm = 10" ), which is in contrast to that of proteins at 280 nm. The will be dependent upon the structure of the base (hence the pH of the solution, as different tautomeric structures will predominate at different pH values), and derivatization of the base, but not markedly... 

The hydroxypyrazolo[3,4-d]pyrimidine derivative 306 exists mainly as such based on the absence of a CO band in the IR (61JOC451). The IR spectrum of allopurinol, the C-6 thioxo derivative, and the C-6 0x0 derivative reveal strong CO absorption and an absence of any absorption for enol forms (76MI3). 

A nucleic acid gives more than 40 well-defined absorption bands in the IR spectrum (300-4000 cm region). For elucidating the nature of the normal vibrations of a nucleic acid, it is helpful to examine the effects of base composition on the vibrational frequencies, as well as the intensity and anisotropy of the IR absorption. Three of the four natural bases of a DNA (adenine, guanine, and cytosine) have an amino group w hich is considered to be nearly coplanar, because the purine or pyrimidine rings have aromatic character and the C—N bonds have some double-bond character. 

---