Guanine canonical forms

The experimental and theoretical investigations of the relative stability of the tautomers of the DNA bases reveal that several tautomers of guanine and cytosine have (in gas phase) the relative stability which is only slightly different (1-2 Kcal-mof ) from the stability of their canonic forms [61, 125]. Such studies qualitatively support the theory of spontaneous mutations in the DNA which considers the appearance of the rare DNA bases tautomers as the natural source of the mutations [130]. On the other hand, the surrounding of the DNA bases in the living cell is definitely different from the gas phase, so the investigations of the role of the polar environment on the stability of the different tautomers are extremely important. 

Figure 10-11. Representative trajectory snapshots showing the nuclear skeleton and the two canonical SOMOs (it hr light grey, it dark grey) at different stages of OH bond dissociation. Top panel isolated G at an OH distance of 1.11 A (a), 1.36 A (b), and 1.62 A (c). Middle panel (i 112O at an OH distance of 1.26 A (d), 1.44 A (e), and 1.62 A (f). Bottom panel G(aq) at an OH distance of 1.21 A (g), 1.59 A (h), and 1.59 A (i) note that the identity of the proton that recombines with N to form 7H-keto guanine in (i) is different from the one that was detached from the 7H-enol tautomer in (g) and that a 11 <() charge defect migrated through water between (h) and (i)...

The picture of prototropic trjinsformations of the nucleic acid base tautomers will never be completed without a knowledge of inter- and intramolecular proton transfer kinetics. The most general data describing the kinetics of proton transfer are the set of temperature dependent rate constants. These data for nucleic acid bases are not yet available from either experimental or theoretical studies except the very recent paper [ 134] where the authors attempt to estimate the water assisted proton transfer rate constant for adenine. However, the calculated values of proton transfer barrier for both non-water assisted and water assisted pathways are available for the adenine, guanine and eytosine [119, 123, 134]. These data are collected in Tables 12 - 16, where, for convenience, we have defined as forward reaction the proton transfer process from the normal (canonical) to the hydroxo- (imino-) form. 

Besides the canonical triplexes formed, for example, between thymine and the adenine-thymine base pair and cytosine and the guanine-cytosine base pair other combinations have been suggested to form stable triplexes, e.g. G-TA, G-GC and T-GC [43], The stability of triplexes depends on pH, ionic strength, temperature, and, in cases where the Watson-Crick duplex is part of a plasmid DNA, it depends on supercoil density [44]. 

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