Nucleobase methylations

Nucleobases, including 9-methyl-, 9-ethyl-, 1,9-dimethyl-guanine and 2-amino-6-methoxy-9-methylpurine, form complexes of the type Au(N)Cl3 when reacted with [AuCU] in water at pH 3—4. Binding of a AuCh unit to the N (7) position of the purine ring was confirmed by X-ray crystallography [26]. 

There are examples in which base radicals undergo reaction with adjacent base residues. The 5-(2 -deoxyuridinyl)methyl radical (63, Scheme 8.30) can forge an intrastrand cross-link with adjacent purine residues. Cross-link formation is favored with a guanine residue on the 5 -side of the pyrimidine radical and occurs under low-oxygen conditions. A mechanism was not proposed for this process, but presumably the reaction involves addition of the nucleobase alkyl radical to the C8-position of the adjacent purine residue. Molecular oxygen likely inhibits crosslink formation by trapping the radical 63, as shown in Scheme 8.24. The radical intermediate 89 must undergo oxidation to yield the final cross-linked product 90,... 

The effect of the aqueous medium on the reactivity and on the stability of the resulting adducts has been investigated to assess which adduct arises from the kinetically favorable path or from an equilibrating process. The calculations indicate that the most nucleophilic site of the methyl-substituted nucleobases in the gas phase is the guanine oxygen atom, followed by the adenine N1, while other centers exhibit a substantially lower nucleophilicity (see activation Gibbs energies in Table 2.2). 

Two approaches that have been validated for HIV inhibitors, nucleoside 5 -phosphonates [48] and 1,3-dioxolane analogs [49] have proven unsuccessful when applied to HCV inhibitors. Phosphonodiphosphates have been synthesized and are incorporated by NS5B RdRp, but Vmax/Km for these chain terminators is 10-100-fold less than for ATP, and potency must be greatly improved for analogs of this type to have utility [50]. A small series of 1,3-dioxolanes also failed to afford active inhibitors of HCV, or HIV, despite the addition of a 5-methyl substituent to impose the desired conformational preference [51]. Ring expanded nucleobases [52,53] and AICAR analogs have also been synthesized as HCV inhibitors which provide only weak replicon activity [54]. 

Mass fragmentation of modified nucleobases of 6-methyl tetrazolo[l,5-c]pyrimidin-5(6fl)-one and its 7 and 8-methyl derivatives suggested the occurrence of both azide and tetrazole tautomeric forms of M (661 and 662). For the 8-halo derivatives, only the of the tetrazole form was proposed (930MS643) (Scheme 135). 

In their free-radical chemistry, these nucleobases have many properties in common. There are, however, also considerable differences which strongly affect the various reaction pathways. In nucleosides and nucleotides, free-radical attack mainly occurs at the base moiety. These reactions largely involve addition reactions. Only the sugar moiety and the methyl group in Thy can act as H-donors. The C(2 ) -position is the least likely to be attacked because of the stronger BDEs of these hydrogens (Miaskiewicz and Osman 1994 Steenken et al. 2001), but this reaction can become of importance when favored by steric conditions. 

Substitution of the aromatic C(5)H in uracil by a methyl group (to give thymine) decreases the acidity of N(3)H by 0.5 log units (cf. Table I). Replacement of protons of endocyclic N atoms and of exocyclic amino groups by alkyl groups in general has a relatively minor effect on the pkl, values of nucleobases. For example, the pvalues of N1 protonated 9-methyladenine (9-MeA), 6,9-dimethyladenine (6,9-DiMeA), and 6,6,9-trimethyladenine (6,6,9-TriMeA) are... 

The very same philosophy can also be applied to metal complexes. Indeed, metal compounds containing methylated nucleobases [e.g., 1,9-dimethylguanine (1,9-DiMeG) (258), 7,9-DiMeG (131a, 259), 6,9-DiMeG (258), 1,9-DiMeA (260), 6,9-DiMeA (52), or 6,6,9-trimethylguanine (6,6,9-TriMeA) (53)] have been reported, but only in one case has the effect of metal ion coordination on the tautomer equilibrium of a nucleobase (adenine) been measured (52). 

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. 

A more suitable model, mimicking the DNA environment to a better extent, is the 9-methyladenine-l-methylthymine (MAMT) base pair, since in DNA nucleobases are bonded to deoxyribose (through the C-N bond) via these methylated positions. 

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