Cytosine nonplanarity

Razskazovskiy et al. employ ESR spectroscopy at low temperatures to investigate electron transfer within brominated DNA [8]. The brominated DNA base electron traps were introduced by bromination of DNA in ice-cooled aqueous solution. The procedure is shown by NMR and GC/MS techniques to modify thymine, cytosine, and guanine, transforming them into 5-bro-mo-6-hydroxy-5,6-dihydrothymine, T(OH)Br, 5-bromocytosine, CBr, and 8-bromoguanine, GBr, derivatives. The bromination products formed in molar ratio close to T(OH)Br/CBr/GBr 0.2 1 0.23 and serve as internal electron scavengers on y-irradiation. Structurally the CBr and GBr are planar, but T(OH)Br is quite nonplanar with the bromine directly above the molecular plane. This disrupts the DNA base stack. Paramagnetic products that result... 

Theoretical and experimental methods are complementary to each other. For example, computational methods have suggested that the amino groups of nucleic acid bases in the ground state are nonplanar [58], However, experimental evidence for amino group nonplanarity was obtained only recently when Dong and Miller [59] measured the vibrational transition moment angles in adenine and three tautomers of cytosine in helium droplets. 

Nonplanarity of the guanine amino group is substantially more pronounced than the nonplanarity of adenine and cytosine. 

Let us start the analysis of the influence of the hydration on the nonplanarity phenomena from the nonplanarity of the first type. There are two important observations here. First of all one may see that the nonplanarity of the first type (sp- hybradization of the amino group) does not depend significantly either on chemical structure of the tautomers or on the interaction with water molecules in the case of guanine and cytosine. 

All complexes of cytosine - isocytosine base pairs dramatically change the geometry when they interact with six water molecules. They become strongly nonplanar and adopt a buckling structure. For example, the buckle angle amounts to 3.6", 6.1 , 3.2" and 31.2" for isolated, two-, four- and six-hydrated iCCl complexes, respectively. The same effect has been observed for seven water molecules hydrating the AU complexes. 

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