Protonated nucleobases

C. Existence of Protonated Nucleobases in Base Pairs and Triplets / 394... 

As pointed out in the previous section, chemical modification of a nucleobase can lead to the situation that a cationic (protonated) nucleobase is involved in base pairing. Two cases are to be differentiated First, the modified base is cationic. This situation is realized in the base pair between 7,9-dimethylguani-nium (58a) or 7-methylguanosinium (58b) and the corresponding neutral betain (cf. Fig. 2). Second, the modified base forces the complementary base to become protonated in order to form hydrogen bond for increased base pair stability. This situation is realized in the pair formed between 06-alkylguanine and protonated cytosine (59b) or adenine (69), and also in the pair between 3-methylguanine and protonated cytosine (60) (cf. above). Of course, the above differentiation is in a way superficial in that simple proton transfer will interconvert the two cases. 

In summary, protonated nucleobases are stabilized by suitably positioned H acceptors (endocyclic N atom exocyclic O atom). As a consequence the proton in question is less acidic and consequently has a higher apparent pKA. Conversely, a deprotonated nucleobase is efficiently stabilized by hydrogen donors and the proton lost has increased its acidity and consequently the apparent pKA is lowered. 

There are numerous ways to determine experimentally pK values of chemical compounds (205). Classical methods are potentiometric titration and ultraviolet (UV) spectroscopy, among others. These techniques have been widely applied for nucleobases and also for metal-nucleobase complexes. For the extremes such as negative pK values (pK < —2) of singly or multiply protonated nucleobases, or very high pK values (pK >15) for deprotonation of exocyclic amino groups of nucleobases (C, G, A), modifications have to be employed. These include the consideration of the Hammett acidity function in superacidic solvents or solvent mixtures (206), as well as extrapolative techniques according to Bunnett-Olsen and Marziano-Cimino-Passerini to be applied in polar, aprotic solvents (45, 207). 

The phenomenon of shifted pA"a values is now well established in nucleic acid chemistry. By in large, it refers to pA"a shifts of protonated nucleobases to higher values in nucleic acid structures, hence there is an apparent loss in acidity... 

IV. HYBRID SYSTEMS BASED ON METAL-OXALATO AND PROTONATED NUCLEOBASES... 

Hybrid Systems Based on Metal-Oxalato and Protonated Nucleobases 433... 

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