Nucleobase stacking

The difference in stabilities of cation radicals located on G, GG, and GGG sequences was initially investigated by Sugiyama and Saito [14], who employed ab initio methods to calculate the gas phase ionization potentials of nucleobases stacked in B-DNA geometries. Their results indicated large differences in potential for holes on G vs GG (0.47 eV) and GGG (0.68 eV) sequences. A similar G vs GG difference was calculated by Prat et al. [62]. These values suggest that GG and GGG are, in fact, deep hole traps and they have been widely cited as evidence to that effect [54, 63]. 

Fig. 19. The combination of (a) a strong stereospecific hydrogenbonding interaction of the C60 carbonyl of 9-EtG with an en NH in [Ru(r 6-dha)(en)(9-EtG)]+ and (b) a strong ti-ti arene-nucleobase stacking interaction is responsible for the high preference of G over A observed for such ruthenium—arene complexes.

Figure 34. Hypothetical insertion of vinyl comonomers into vinyl nucleobase-stack matrices, bridging gaps between the vinyl groups and allowing a convenient zipping-up (26, 64,125,135)...

Planar Py and Ptz are expected to stack well among nucleobases, and so were used as the probe molecules to measure the hole transfer rate. The oxidation potentials of Py and Ptz were lower than those of the four nucleobases. We examined the sequence and distance dependences of the hole transfer rate by monitoring the decay and formation of the transient absorption of Py,+ and Ptz + during pulse radiolysis of ODN conjugated with Py and Ptz (PtzPy-(n) (n=l 5)). 

Figure 24 Interactions between the nucleobases involve dimers of stacked AT pairs that are slipped so as to...

It is assumed that tholins also played an important role in the PAH world hypothesis. The PAH world could have existed as a pre-RNA world on the primeval Earth. It is suggested that PAHs can undergo stacking, thus forming structures to which nucleobases are chemically bound (to OH functions which are formed by photochemical derivatisation of the PAHs). The PAH stacks replace the more complex phosphate-D-ribose-phosphate chains in the nucleic acids (Ehrenfreund et al., 2006). 

In the B conformation, the aromatic rings of the nucleobases are stacked at a distance of... 

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