The formation of catalytically competent enzyme-substrate complex is not a bottleneck in lesion excision by human alkyladenine DNA glycosylase.

Human alkyladenine DNA glycosylase (AAG) protects DNA from alkylated and deaminated purine lesions. AAG flips out the damaged nucleotide from the double helix of DNA and catalyzes the hydrolysis of the N-glycosidic bond to release the damaged base. To understand better, how the step of nucleotide eversion influences the overall catalytic process, we performed a pre-steady-state kinetic analysis of AAG interaction with specific DNA-substrates, 13-base pair duplexes containing in the 7th position 1-N6-ethenoadenine (εA), hypoxanthine (Hx), and the stable product analogue tetrahydrofuran (F). The combination of the fluorescence of tryptophan, 2-aminopurine, and 1-N6-ethenoadenine was used to record conformational changes of the enzyme and DNA during the processes of DNA lesion recognition, damaged base eversion, excision of the N-glycosidic bond, and product release. The thermal stability of the duplexes characterized by the temperature of melting, Tm, and the rates of spontaneous opening of individual nucleotide base pairs were determined by NMR spectroscopy. The data show that the relative thermal stability of duplexes containing a particular base pair in position 7, (Tm(F/T) < Tm(εA/T) < Tm(Hx/T) < Tm(A/T)) correlates with the rate of reversible spontaneous opening of the base pair. However, in contrast to that, the catalytic lesion excision rate is two orders of magnitude higher for Hx-containing substrates than for substrates containing εA, proving that catalytic activity is not correlated with the stability of the damaged base pair. Our study reveals that the formation of the catalytically competent enzyme-substrate complex is not the bottleneck controlling the catalytic activity of AAG.

Low field photo-CIDNP in the intramolecular electron transfer of naproxen-pyrrolidine dyads.

Photoinduced processes with partial (exciplex) and full charge transfer in donor-acceptor systems are of interest because they are frequently used for modeling drug-protein binding. Low field photo-CIDNP (chemically induced dynamic nuclear polarization) for these processes in dyads, including the drug, (S)- and (R)-naproxen and (S)-N-methyl pyrrolidine in solutions with strong and weak permittivity have been measured. The dramatic influence of solvent permittivity on the field dependence of the N-methyl pyrrolidine (1)H CIDNP effects has been found. The field dependences of both (R,S)- and (S,S)-dyads in a polar medium are the curves with a single extremum in the area of the S-T+ terms intersection. Moreover, the CIDNP field dependences of the same protons measured in a low polar medium present curves with several extrema. The shapes of the experimental CIDNP field dependence with two extrema have been described using the Green function approach for the calculation of the CIDNP effects in the system without electron exchange interactions. The article discusses the possible causes of the differences between the CIDNP field dependence detected in a low-permittivity solvent with the strong Coulomb interactions and in a polar solvent.