53294-73-8Relevant academic research and scientific papers
Role of the guanine N1 imino proton in the migration and reaction of radical cations in DNA oligomers
Ghosh, Avik K.,Schuster, Gary B.
, p. 4172 - 4173 (2006)
Oxidation of a guanine nucleobase to its radical cation in DNA oligomers causes an increase in the acidity of the N1 imino proton that may lead to its spontaneous transfer to N3 of the paired cytosine. This proton transfer is suspected of playing an important role in long-distance radical cation hopping in DNA and the decisive product-determining role in the reaction of the radical cation with H2O or O2. We prepared and investigated DNA oligomers in which certain deoxycytidines are replaced by 5-fluoro-2′-deoxycytidines (F5dC). The pKa of F5C was determined to be 1.7 units below that of dC, which causes proton transfer from the guanine radical cation to be thermodynamically unfavorable. Photoinitiated one-electron oxidation of the DNA by UV irradiation of a covalently attached anthraquinone derivative introduces a radical cation that hops throughout the oligomer and is trapped selectively at GG steps. The introduction of F5dC does not affect the efficiency of charge hopping, but it significantly reduces the amount of reaction at the GG sites, as revealed by subsequent reaction with formamidopyrimidine glycosylase. These findings suggest that transfer of the guanine radical cation N1 proton to cytosine does not play a significant role in long-range charge transfer, but this process does influence the reactions with H2O and/or O2. Copyright
Biochemical detection of cytidine protonation within RNA
Oyelere,Strobel
, p. 10259 - 10267 (2007/10/03)
Perturbation of active site functional group pK(a)s is an important strategy employed by protein enzymes to achieve catalysis. There is increasing evidence to indicate that RNAs also utilize functional group pK(a) perturbation for folding and reactivity. One of the best candidates for a functionally relevant pK(a) perturbation is the N3 of C (pK(a) 4.2), which could be sufficiently raised to allow protonation near physiological pH. Here we report the synthesis and use of a series of α-phosphorothioate tagged cytidine analogues whose altered N3 pK(a)s make it possible to efficiently detect functionally relevant protonation events by nucleotide analogue interference mapping. 6-Azacytidine (n6CαS) and 5-fluorocytidine (f5CαS) both have enhanced acidity at the N3 position (pK(a) 2.6 and 2.3, respectively) but leave the hydrogen bonding face of C otherwise unaffected. In contrast, pseudoisocytidine (ΨiCαS) is a charge neutral analogue that mimics the hydrogen bonding character of protonated C. To test the utility of these analogues, we characterized the C300+-G97-C277 mutant form of the Tetrahymena group I intron, which is predicted to require C300 protonation for ribozyme folding and reactivity. At neutral to alkaline pHs, C300 was the only site of n6CαS and f5Cαs interference within the intron, yet both interferences were rescued at acidic pH. Furthermore, ΨiCαS substitution at C300 resulted in enhanced activity at alkaline pHs, consistent with the presence of an N3 proton under the pH conditions studied. Interference mapping with these analogues provides an efficient and sensitive means to identify every site within an RNA where cytidine protonation is important for RNA function and may make it possible to identify C's that participate in general acid/base catalysis within ribozyme active sites.
