Modification of nucleobases

Phosphoric bis- or trisazolides can also be used for the modification of nucleobases. As mentioned before with ammonia the azolyl group is easily exchanged against the amino group. 

There are numerous other modifications of nucleobases possible, many of which are biologically relevant in that they lead to alternations in p/fa values, changes in tautomer structure as well as their base pairing patterns (55). Examples include ligands such as N6-methoxyadenine, which is a promutagen (66, 67) as well as 8-oxoadenine and 8-oxoguanine (68), which are known mutagens. 

As demonstrated in Figs 22 and 23, phosphoramidites of convertible nucleosides allow introduction of non-natural modifications of nucleobases after solid-phase synthesis. 

Summing up, remote substitution (2003EJOC2577) influences the H-bond energy depending on two separate factors the electron-donating/electron-withdrawing power of the substituent and its location. Such chemical modification of nucleobases can be used to control the stability of unnatural base pairs. 

Eschenmoser and co-workers <20030L2067, 20040L3691, 2005HCA1960> carried out thorough synthetic studies for preparation of some imidazo[l,5-tf][l,3,5]triazines with particular substitution patterns such that these compounds could be considered as nitrogen-positional isomers of some nucleobases. One of the typical synthetic steps is treatment of the diaminotriazine derivative 248 with phosphorus oxychloride to give the cyclized purinoid 249 in high yield (82%). Modification of this procedure also allowed preparation of the various oxo- and amino-related derivatives 250-252. 

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. 

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). 

As mentioned in the Introduction, we are especially interested in the effect of nucleoside modifications on RNA structure. The equilibrium sequences introduced above were selected for this reason. The position of the conformational equilibrium of the sequence constructs is expected to be highly sensitive to chemical alteration, e.g. methylation of nucleobases. 

The use of nonbiological nucleobases to enhance oligonucleotide duplex stability is widespread, and an exhaustive exploration of this field is beyond the scope of this review. At the same time, recent studies exist that go beyond this goal with the aim of understanding the function of base interactions in duplex stability and the impact of unusual nucleobases on both conformation and assembly. Herein, we focus on a few of these examples as representatives of the field and to highlight how modifications at nucleobase sites that are remote from the backbone can have profound architectural effects on... 

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