The genetic toxicology of hydroxylamines

Miscoding and DNA Polymerase Stalling by Methoxyamine-Adducted Abasic Sites

Apurinic/apyrimidinic (AP) sites appear in DNA spontaneously and as intermediates of base excision DNA repair. AP sites are noninstructive lesions: they strongly block DNA polymerases, and if bypassed, the nature of the incorporated dNMP is mostly guided by the interactions within the polymerase-DNA active site. Many DNA polymerases follow the "A-rule", preferentially incorporating dAMP opposite to natural AP sites. Methoxyamine (MX), a small molecule, efficiently reacts with the aldehyde moiety of natural AP sites, thereby preventing their cleavage by APEX1, the major human AP endonuclease. MX is currently regarded as a possible sensitizer of cancer cells toward DNA-damaging drugs. To evaluate the mutagenic potential of MX, we have studied the utilization of various dNTPs by five DNA polymerases of different families encountering MX-AP adducts in the template in comparison with the natural aldehydic AP site. The Klenow fragment of Escherichia coli DNA polymerase I strictly followed the A-rule with both natural AP and MX-adducted AP sites. Phage RB69 DNA polymerase, a close relative of human DNA polymerases δ and ε, efficiently incorporated both dAMP and dGMP. DNA polymerase β mostly incorporated dAMP and dCMP, preferring dCMP opposite to the natural AP site and dAMP opposite to the MX-AP site, while DNA polymerase λ was selective for dGMP, apparently via the primer misalignment mechanism. Finally, translesion DNA polymerase κ also followed the A-rule for MX-AP and additionally incorporated dCMP opposite to a natural AP site. Overall, the MX-AP site, despite structural differences, was similar to the natural AP site in terms of the dNMP misincorporation preference but was bypassed less efficiently by all polymerases except for Pol κ.

Oxidation of 5-methylaminomethyl uridine (mnm⁵U) by Oxone Leads to Aldonitrone Derivatives

Oxidative RNA damage is linked to cell dysfunction and diseases. The present work focuses on the in vitro oxidation of 5-methylaminomethyl uridine (mnm⁵U), which belongs to the numerous post-transcriptional modifications that are found in tRNA. The reaction of oxone with mnm⁵U in water at pH 7.5 leads to two aldonitrone derivatives. They form by two oxidation steps and one dehydration step. Therefore, the potential oxidation products of mnm⁵U in vivo may not be only aldonitrones, but also hydroxylamine and imine derivatives (which may be chemically more reactive). Irradiation of aldonitrone leads to unstable oxaziridine derivatives that are susceptible to isomerization to amide or to hydrolysis to aldehyde derivative.

Photoisomerizations of N4-Hydroxycytosines

A series of N4-hydroxycytosines, unsubstituted or substituted with methyl groups at N3 or C5 atoms of the heterocyclic ring, was studied using the matrix-isolation method. Depending on the absence or presence of the methyl substituent at N3 or C5 atoms (or at both of them) the syn or anti form of the compounds (or a mixture of both forms) was trapped from the gas phase into a low-temperature matrix. Upon UV (lambda > 295 nm) irradiation of the matrixes the syn --> anti as well as the anti --> syn photoisomerization reactions were observed. The syn and anti isomers of N4-hydroxycytosines were identified by comparing their experimental IR spectra with the theoretical spectra calculated at the DFT(B3LYP)/6-31G(d,p) level. For the majority of the studied compounds, the UV induced reactions led to a photostationary state. The position of the final photostationary state was found to be a sensitive function of weak interactions of a studied N4-hydroxycytosine with the matrix environment: solid argon or solid nitrogen. However, not all of the studied photoisomerizations led to a classical photostationary state. For some of the investigated N4-hydroxycytosines, the position of the photostationary state was shifted very strongly in favor of the photoproduct, whereas for some others the position was shifted so strongly in favor of the starting isomer that no photoisomerization was observed. These experimental findings were elucidated by theoretical investigations of the potential energy surfaces of the ground (S0) and first excited (S1) electronic states of N4-hydroxycytosine. The crucial result of these calculations (carried out at the CASSCF level) was the localization of a conical intersection between S0 and S1 at a structure with perpendicular orientation of the hydroxylimino group with respect to the heterocyclic ring.

Photochemical syn-anti isomerization reactions in N2-hydroxyisocytosines--an experimental matrix isolation and theoretical study

N2-hydroxyisocytosine and 1-methyl-N2-hydroxyisocytosine were studied using a matrix isolation technique combined with infrared absorption spectroscopy. For N2-hydroxyisocytosine isolated in an Ar matrix (at 10 K), two imino-oxo isomers, one with the hydroxyimino =N-OH group directed toward the N1-H group (the form called further anti) and the second with the =N-OH group directed toward N3-H (syn), were observed in the ratio 1.4:1. The syn isomer is converted totally to the anti form after UV (lambda > 295 nm) irradiation of the matrix. A small amount of the N(3)H-hydroxy-amino tautomer of N2-hydroxyisocytosine was also detected in the matrix. This form did not react photochemically. For 1-methyl-N2-hydroxyisocytosine, only the syn form of the imino-oxo tautomer was observed after deposition of the matrix. UV (lambda > 295 nm) irradiation induced a photoreaction converting this isomer into the anti form. After 15% of the starting material had been converted into the product, a photostationary state was achieved, and no further progress of the reaction was observed. Subsequent UV irradiation (lambda > 335 nm) caused a back reaction, leading to a disappearance of the anti form and to the recovery of the initial syn isomer. All isomers were identified by comparing their experimental IR spectra with the spectra theoretically calculated at the DFT(B3LYP)/6-31G(d,p) level, where DFT is the density functional theory. Good agreement between the observed and predicted patterns of the spectral lines allowed for reliable identification. The experimental IR spectra were interpreted and discussed. The relative energies of the 12 isomers of N2-hydroxyisocytosine were calculated at the MP2/6-31G(d,p) and MP4//MP2/6-31G(d,p) levels. For six isomers of 1-methyl-N2-hydroxyisocytosine, the calculations were carried out at the MP2/6-31G(d,p) level. The anti form of the imino-oxo tautomer of N-hydroxyisocytosine and the syn form of the imino-oxo tautomer of 1-methyl-N2-hydroxyisocytosine were predicted to be the most stable.

Photochemical syn-anti isomerization reaction in N4-hydroxycytosine. An experimental matrix isolation and theoretical study

Infrared spectra of N4-hydroxycytosine isolated in argon and nitrogen low-temperature matrixes are reported. The compound was found to adopt the syn structure of the imino-oxo tautomeric form exclusively. A photoreaction (lambda > 250 nm) converting this form into the anti isomer was observed. The reaction is reversible and leads to a photostationary point. The initial infrared spectrum and the spectrum of the photoproduct were assigned to the syn and anti isomers, respectively. This assignment is based on a close agreement between the experimental spectra and the spectra theoretically simulated at the DFT(B3LYP)/6-31++G** level of theory.

Tautomerism, acid-base properties and conformation of methylated analogues of the promutagenic N4-hydroxycytosine

UV and NMR spectroscopy were employed to study the tautomerism, acid-base properties and conformation of the exocyclic N(4)-OH group in 1-methyl-N(4)-hydroxycytosine (1-mOH(4)C), and its methyl derivatives, viz. the fixed imino forms (1,3-m(2)OH(4)C and 1,3,5-m(3)OH(4)C), the fixed amino form (1,N(4)-m(2)OH(4)C), and analogues sterically constrained to the form syn (1,5-m(2)OH(4)C) or anti (1,3-m(2)OH(4)C) with respect to the ring N(3). Relative to 1,N(4)-m(2)OH(4)C, UV spectroscopy showed that the other analogues were predominantly imino and that all analogues formed a structurally common cation in acid medium, with results pointing to approximately 90% population of the imino species for 1-mOH(4)C and 1,5-m(2)OH(4)C, further supported by NMR spectroscopy. Both exhibited two sequential dissociations in alkaline medium, the first due to N(4)-OH, followed by the N(3)-H. (1)H and (13)C NMR spectroscopy showed 1-mOH(4)C in the conformation syn. With 1,3,5-m(3)OH(4)C, an ;overcrowded' planar molecule with steric constraints to both the syn and anti conformations, a syn-anti equilibrium is observed, with a preference of approximately 75% for the anti rotamer, independently of the polarity of the medium. Exchange between the rotamers is slow on the NMR time-scale, with a minimal barrier to exchange exceeding 100 kJ/mol. In low-polar media, the analogues associate as dimers via O(4)-Hcdots, three dots, centeredO(2) or O(4)-Hcdots, three dots, centeredN(4) hydrogen bonds, with association constants at ambient temperature of 4.6 (1,3-m(2)OH(4)C), 12.8 (anti 1,3,5-m(3)OH(4)C), 36 (1,5-m(2)OH(4)C), 109 (syn 1,3,5-m(3)OH(4)C) M(-1). Implications of the overall findings to the promutagenic activities of OH(4)C and OMe(4)C are examined.

Conditions affecting the mutagenicity of sodium bisulfite in Salmonella typhimurium

Sodium bisulfite is a weak mutagen at pH 5 and 6 in S. typhimurium strains carrying the hisG46 and hisD6610 mutations, but is not mutagenic in strains with the hisC3076 or hisD3052 mutations. The bisulfite-induced base-pair substitution mutations were slightly enhanced by the presence of the plasmid, pKM101, but inhibited by the presence of the uvrB and rfa mutations. The hisO1242 mutation which causes constitutive expression of the histidine operon, produced a slight enhancement of frameshift (hisD6610), but not base-pair substitution (hisG46) mutations. Bisulfite-induced mutations appear to be the result of two different mechanisms which may be a function of the repair capacity of the strains. The data suggest that the deamination of cytosine may not be responsible for frameshift mutations, but may be responsible for base-pair substitution mutagenesis. Because the rate of bisulfite autooxidation appears to play a role in the mutagenic process, we are suggesting that the deamination of cytosine may be the result of oxidative damage rather than through the direct formation of a cytosine-bisulfite adduct. This is further supported by the much lower concentrations of bisulfite needed to cause mutagenicity than the 1 M concentrations cited to produce cytosine-bisulfite adducts.