Computational studies of electronic circular dichroism spectra predict absolute configuration assignments for the guanine oxidation product 5-carboxamido-5-formamido-2-iminohydantoin

Abstract

Oxidation of the guanine heterocycle by two electrons can yield the chiral product 5-carboxamido-5-formamido-2-iminohydantoin (2Ih). The 2Ih free base enantiomers were synthesized from 2′-deoxyguanosine oxidized with a Cu(II)/H2O2 oxidant system followed by hydrolysis of the N-glycosidic bond. These isomers were each studied by electronic circular dichroism spectroscopy for determination of their absolute configurations. Time-dependent density functional theory calculations of the expected spectra were completed in both the gas phase and with solvent modeling in order to interpret the experimental spectra and provide the absolute configuration assignments.

5-Carboxamido-5-formamido-2-iminohydantoin, in Addition to 8-oxo-7,8-Dihydroguanine, Is the Major Product of the Iron-Fenton or X-ray Radiation-Induced Oxidation of Guanine under Aerobic Reducing Conditions in Nucleoside and DNA Contexts

“…Use of a Hypercarb column allowed separation of the d2Ih and dSp diastereomers for which the absolute configurations and elution order on this HPLC column are known. 42 , 62 In the current studies, the R and S isomers of d2Ih were observed in a 1:2 ratio, respectively, for both oxidation reactions studied, while the R and S isomers of dSp were observed in a 1:1 ratio. Furthermore, these ratios did not change under any of the reaction conditions studied.…”

“… 43 However, our previous time-dependent density functional theory studies on the UV–vis and ECD properties for dSp and d2Ih allow us to use these previous results to determine the relative difference in extinction coefficient between these two compounds at the wavelength monitored. 42 , 43 These calculations determined the ε 240 nm for d2Ih to be ∼30% less than that of dSp ; therefore, the ε 240 nm value used to quantify d2Ih was calculated to be 2290 L·mol –1 ·cm –1 . 45 The Fenton reaction was initially conducted with the Fe(II)/EDTA catalyst and 10 mM H 2 O 2 under aerobic conditions to give 5% conversion to product.…”

Rates of Chemical Cleavage of DNA and RNA Oligomers Containing Guanine Oxidation Products

“… 58 The dSp diastereomers were individually purified while the diastereomers of dGh were studied as a mixture because they readily interconvert. 59 Syntheses of dZ and the ( R )- and ( S )-d2Ih 60 diastereomers were achieved in a 15-mer DNA oligomer containing a single dG site (5′-AAT CCA CGA CAC CTC-3′) following literature methods. 17 , 24 All product oligomers were purified using an analytical ion-exchange HPLC column that resolves diastereomeric products ( Figure S1 ).…”

Guanine Oxidation Product 5-Carboxamido-5-formamido-2-iminohydantoin Induces Mutations When Bypassed by DNA Polymerases and Is a Substrate for Base Excision Repair

“…22,60 Briefly, 10 μM ODN in 20 mM NaP i buffer (pH 7.4) and 100 mM NaCl was incubated with 5 μM NiCR at 37 °C for 20 min prior to the addition of 100 μM KHSO 5 , and the reaction was allowed to progress for 30 min. The reaction was quenched by adding 50 mM HEPES (pH 8).…”

“…The absoluteconfigurations for the diastereomers of 2Ih and Sp have previously been determined, as well as their elution order in an ODN on the ion-exchange HPLC column used in the present studies. 60,61 These ODNs were further purified by HPLC to obtain > 95% purity before use. The ODNs with 2Ih or Sp were characterized by either ESI-MS for ODNs 1 (G: calcd 5357.5, found 5356.9; ( S )-2Ih or ( R )-2Ih): calcd 5391.5, found 5391.0 and 5391.1, respectively; a mixture of the Sp diastereomers: calcd 5389.5, found 5389.6) or MALDI-MS for ODNs 3 (G: calcd 4463.8, found 4464.2; mixture of 2Ih diastereomers: calcd 4497.8, found 4498.2; mixture of Sp diastereomers: calcd 4495.8, found 4496.6).…”