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PubMed2005

Singlet excited-state dynamics of 5-fluorocytosine and Cytosine: an experimental and computational study.

The photophysics of singlet excited 5-fluorocytosine (5FC) was studied in steady-state and time-resolved experiments and theoretically by quantum chemical calculations. Femtosecond transient absorption measurements show that replacement of the C5 hydrogen of cytosine by fluorine increases the excited-state lifetime by 2 orders of magnitude from 720 fs to 73 +/- 4 ps. Experimental evidence indicates that emission in both compounds originates from a single tautomeric form. The lifetime of 5FC is the same within experimental uncertainty in the solvents ethanol and dimethyl sulfoxide. The insensitivity of the S(1) lifetime to the protic nature of the solvent suggests that proton transfer is not the principal quenching mechanism for the excited state. Excited-state calculations were carried out for the amino-keto tautomer of 5FC, the dominant species in polar environments, in order to understand its longer excited-state lifetime. CASSCF and CAS-PT2 calculations of the excited states show that the minimum energy path connecting the minimum of the (1)pi,pi state with the conical intersection responsible for internal conversion has essentially the same energetics for cytosine and 5FC, suggesting that both bases decay nonradiatively by the same mechanism. The dramatic difference in lifetimes may be due to subtle changes along the decay coordinate. A possible reason may be differences in the intramolecular vibrational redistribution rate from the Franck-Condon active, in-plane modes to the out-of-plane modes that must be activated to reach the conical intersection region.

Absorption↗
PubMed2006

Excited-state structural dynamics of cytosine from resonance Raman spectroscopy.

Cytosine, a nucleobase found in both DNA and RNA, is known to form photoproducts upon UV irradiation, damaging the nucleic acids and leading to cancer and other diseases. To determine the molecular mechanism by which these photoproducts occur, we have measured the resonance Raman spectra of cytosine at wavelengths throughout its 267 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yields both the excited-state structural changes and electronic parameters. From this analysis, we have been able to determine that, at most, 31% of the reorganization energy upon excitation is directed along photochemically relevant modes.

Algorithms↗
PubMed2006

Physical nature of interactions within the active site of cytosine-5-methyltransferase.

The physical nature of interactions within the active site of cytosine-5-methyltransferase (CMT) was studied using a variation-perturbation energy decomposition scheme defining a sequence of approximate intermolecular interaction energy models. These models have been used to analyze the catalytic activity of residues constituting cytosine-5-methyltransferase active site as well their role in the binding group of de novo designed inhibitors. Our results indicate that Glu119, Arg163, and Arg165 appear to play the dominant role in stabilizing the protonated transition state structure and their influence can be qualitatively approximated by electrostatic interactions alone. The stabilization of neutral structures of the alternative reaction pathway is small, which might suggest the protonated pathway as preferred by the enzyme. Exchange and delocalization terms are negligible in most cases, or they cancel each other to some extent. Interactions of inhibitors with the CMT active site are dominated by electrostatic multipole contributions in analogy with previously studied transition state analogue inhibitors of leucyl aminopeptidase.

Arginine↗
PubMed2006

Computational study of the deamination reaction of cytosine with H2O and OH-.

The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.

Computer Simulation↗
PubMed2006

Deprotonated cytosine anions: a theoretical prediction of photoelectron spectra.

Predictions on the photoelectron spectra of deprotonated cytosine anions (cytosinate, Cye(-)) have been made with ab initio electron propagator methods. Two imino-oxo forms are most stable, but four other isomers have energies within 10 kcal/mol. The first vertical electron detachment energies (VEDEs) for the three most stable Cye(-) isomers are approximately 3.4 eV. Imino-oxy VEDEs are about 0.3 eV smaller. For each anion, the lowest VEDE corresponds to a pi Dyson orbital. The order of higher final states is changed when relaxation and correlation effects are considered. Considerable mixing between lone-pair and bonding lobes occurs in the sigma Dyson orbitals.

Anions↗
PubMed2006

A combined ONIOM quantum chemical-molecular dynamics study of zinc-uracil bond breaking in yeast cytosine deaminase.

A QM/MM method that combines ONIOM quantum chemistry and molecular dynamics is developed and applied to a step in the deamination of cytosine to uracil in yeast cytosine deaminase (yCD). A two-layer ONIOM calculation is used for the reaction complex, with an inner part treated at a high level for the chemical reaction (bond breaking) and a middle part treated at a lower level for relevant protein residues that are frozen in the quantum optimization. An outer layer (protein and solvent) is treated using MD. Configurations for the entire system are generated using MD and optimized with ONIOM. The method permits the use of high-level quantum calculations along with sufficient configurational sampling to approximate the potential of mean force for certain bond-breaking reactions. A previously proposed reaction mechanism for deamination (Sklenak, S.; Yao, L. S.; Cukier, R. I.; Yan, H. G. J. Am. Chem. Soc. 2004, 126, 14879) requires breaking the bond between a catalytic zinc and the O4 of uracil in order to permit product release. Using an ONIOM approach, direct bond cleavage was found to be energetically unfavorable. In the work presented here, the combined ONIOM MD method is used to show that the barrier for bond cleavage is small, approximately 3 kcal/mol, and, consequently, should not be the rate-limiting step in the reaction.

Cytosine Deaminase↗
PubMedDate not supplied

Alkylation of guanine and cytosine in DNA by bizelesin. Evidence for a covalent immobilization leading to a proximity-driven alkylation of normally unreactive bases by a (+)-CC-1065 cross-linking compound.

Bizelesin, an intrahelical DNA-DNA interstrand cross-linker related to (+)-CC-1065, has been shown to alkylate DNA through guanine in restriction enzyme sequences in which there is a suitably positioned adenine contained in a highly reactive monoalkylation sequence on the opposite strand. Oligomers containing the sequence 5'-TTTTTN*, in which "N" was either G, C, or T, were synthesized to evaluate the cross-linking potential of bizelesin at nonadenine bases. Kinetic analysis of monoalkylation and cross-linking events demonstrates that it is the reaction at "N" (guanine or cytosine) that results in the cross-link which is the slow step. On the basis of this analysis and the normal unreactivity of guanine and cytosine to alkylation by the cyclopropapyrroloindole alkylating moiety of (+)-CC-1065, we propose that the molecular mechanism for this type of cross-linking reaction most likely involves a covalent immobilization of the second alkylating arm, resulting in a "proximity-driven" reaction.

Alkylating Agents↗
PubMedDate not supplied

Reductive metabolism of 1-nitropyrene accompanies deamination of cytosine.

1-Nitropyrene (1-NP), a common environmental pollutant, is a mutagen and tumorigen. Nitroreduction is a major pathway by which 1-NP is metabolized. In order to study the mutational specificity of reductively activated 1-NP, single-stranded M13mp18 DNA was treated with tritium-labeled 1-nitrosopyrene in the presence of ascorbic acid to generate N-hydroxy-1-aminopyrene in situ. HPLC analysis of the treated DNA, following enzymatic digestion, showed that > 95% of tritium was located in one major adduct, N-(deoxyguanosin-8-yl)-1-aminopyrene. Transfection of these adducted M13 DNA in Escherichia coli indicated a dose-dependent reduction in viability with concomitant enhancement in mutagenesis in the lacZ gene fragment. Without SOS functions, the major type of mutation was C-->T transition (48%). Further studies have shown that cytosine deamination occurred during ascorbic acid-induced nitroreduction, which was likely responsible for the C-->T transitions. Deamination of cytosine alco occurred at a significant frequency when nitroreduction of either 1-NP or 1-nitrosopyrene was catalyzed by xanthine oxidase, a mammalian nitroreductase.

Base Sequence↗
PubMed2002

Conformational changes of a benzo[a]pyrene diol epoxide-N(2)-dG adduct induced by a 5'-flanking 5-methyl-substituted cytosine in a (Me)CG double-stranded oligonucleotide sequence context.

Mutations in p53 genes are one of the most common genetic alterations in human cancers. A disproportionate number of mutations are found in certain codons of the p53 gene, mostly at CpG dinucleotide sequences, which are highly methylated in human tissues. The reactivities of the mutagenic metabolite of benzo[a]pyrene, the bay region diol epoxide r7,t8-dihydroxy-t9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (BPDE), to yield adducts with guanine at the exocyclic amino group (e.g., trans-anti-BPDE-N(2)-dG, or G*), are enhanced when the cytosine in CpG sequences in DNA is methylated at its 5-position ((Me)CpG). However, methylation may also affect the characteristics of these adducts, and we have therefore investigated whether adduct conformations are different in double-stranded DNA in methylated (Me)CpG* and in unmethylated CpG* sequence contexts in the oligonucleotide model system duplex 5'-d(CCAT[(5X)C]GCTACC).d(GGTAGCGATGG) with X = H or -CH(3). The (-)-trans-adduct exhibits a striking conformational change from a minor groove structure external to the DNA duplex in the unmethylated CpG* sequence, to an intercalative conformation in the (Me)CG* sequence context. In contrast, the conformation of the stereoisomeric (+)-trans-adduct is predominantly of the minor groove type in both the methylated and unmethylated sequences. These results indicate that methylation of CpG sequences may affect not only chemical reactivities of chemically reactive intermediates with DNA, but also the conformational properties of the DNA adducts formed. Thus, both factors must be considered in evaluating the effects of cytosine methylation in CpG sequences on the biological consequences of the DNA adducts formed.

5-Methylcytosine↗
PubMed2005

Nitrosative cytosine deamination. An exploration of the chemistry emanating from deamination with pyrimidine ring-opening.

A discussion of nitrosative deamination of cytosine 1 is presented that argues for the formation of 6 by diazotization of 1 to cytosinediazonium ion 2 and its electrostatic complex 3, dediazoniation to 4 <--> 5, and amide-bond cleavage to 6. The reaction channels available to 6 include hydrolytic deglycation to 3-isocyanatoacrylonitrile 7, water addition to carbamic acid 9 with the possibility for re-closure to uracil 13, water addition to carbamic acid 9, and decarboxylation to 3-aminoacrylonitrile 10. With a view to the instability of the carbamic acid 9, the carbamate models ethyl (Z)-2-cyanovinylcarbamate 14 and (Z)-2-cyano-1-tert-butylvinylcarbamate 20 were studied. Acid-catalyzed hydrolysis of 14 leads to 2-amino-carbonylphenylcarbamate 15, and its cyclization yields the benzo-fused uracil quinazoline-2,4-dione 16. In contrast to the aromatic system 14, acid-catalyzed cyclization cannot compete with oligomerization in the case of 20, and 5-tert-butyluracil 22 is accessible only with base-catalysis. It is shown that 23, the parent of 10, also easily polymerizes. The experimental results provide a rationale as to why 9, 10, and 12 would have escaped detection in in vitro studies: they would have oligomerized. In contrast to the in vitro experiments, the oligomerizations of 9, 10, or 12 clearly are not relevant in vivo because of low monomer concentrations. With the exclusion of recyclization and of oligomerization in vivo, attention thus needs to focus on (Z)-3-aminoacrylonitrile 10 as the most likely deamination product of cytosine aside from uracil.

Carbamates↗
PubMedDate not supplied

Deamination of single-stranded DNA cytosine residues in aerobic nitric oxide solution at micromolar total NO exposures.

Deamination of cytosine to uracil is a potential source of mutations in DNA. Here we examine the deaminating ability of aerobic nitric oxide (NO) toward single-stranded DNA at very low (micromolar and below) total exposures, using a sensitive genetic method that allows us to study a single deamination event at a specific site in a 7200-nucleotide DNA molecule within a pool of ca. 100,000 other identical DNA molecules. We incubated gapped C141 M13mp2 DNA with the NO-generating compound, Et2N[N(O)NO]Na (DEA/NO), in aerobic buffer for 16 h to ensure complete autoxidation at pH 7.4 and 37 degrees C. After ultrafiltration to remove small molecules, the DNA was transformed into isogenic Escherichia coli cultures that were either deficient (NR9404, ung-) or proficient (MC1061, ung+) in uracil-DNA glycosylase activity. The gapped DNA was constructed such that the target (CCC) codon was contained in a short single-stranded segment of otherwise double-stranded circular DNA, and the incubation was performed in a closed system to prevent loss of NO to the atmosphere before the reaction was complete. An increase in the reversion frequency in the ung- strain was noted between 0 and 1 microM DEA/NO, and the reversion frequency leveled out between 3 and 30 microM. However, 30 microM "spent" DEA/NO (i.e., that which was similarly incubated for 4 h to complete the autoxidation of NO before the DNA was added) did not increase reversion frequency relative to control. Nearly all (42/43) of the mutations identified after 1 microM DEA/NO treatment were C-->T transitions, and reversion frequency in the isogenic ung+ strain was lower than in the ung- strain. The data are consistent with the hypothesis that total NO exposures in the mumol/L range can lead to C-->T mutations via a mechanism most probably involving deamination of DNA cytosine residues.

Aerobiosis↗
PubMed2000

Role of cytosine deaminase and beta-alanine-pyruvate transaminase in pyrimidine base catabolism by Burkholderia cepacia.

A determination of the possible role of the salvage enzyme cytosine deaminase or beta-alanine-pyruvate transaminase in the catabolism of the pyrimidine bases uracil and thymine by the opportunistic pathogen Burkholderia cepacia ATCC 25416 was undertaken. It was of interest to learn whether these enzymes were influenced by cell growth on pyrimidine bases and their respective catabolic products to the same degree as the pyrimidine reductive catabolic enzymes were. It was found that cytosine deaminase activity was influenced very little by cell growth on the pyrimidines tested. Using glucose as the carbon source, only B. cepacia growth on 5-methylcytosine as a nitrogen source increased deaminase activity by about three-fold relative to (NH4)2SO4-grown cells. In contrast, the activity of beta-alanine-pyruvate transaminase was observed to be at least double in glucose-grown ATCC 25416 cells when pyrimidine bases and catabolic products served as nitrogen sources instead of (NH4)2SO4. Transaminase activity in the B. cepacia glucose-grown cells was maximal after the strain was grown on either uracil or 5-methylcytosine as a nitrogen source compared to (NH4)2SO4-grown cells. A possible role for beta-alanine-pyruvate transaminase in pyrimidine base catabolism by B. cepacia would seem to be suggested from the similarity in how its enzyme activity responded to cell growth on pyrimidine bases and catabolic products when compared to the response of the three reductive catabolic enzymes.

Burkholderia cepacia↗
PubMed1999

Assignment of cytosine N3 resonances in nucleic acids via intrabase three-bond coupling to amino protons.

Coherences were observed between 15N3 of cytosine and its trans amino proton (H42) using a modified gradient-based heteronuclear single quantum coherence (HSQC) pulse sequence optimized for three-bond proton-nitrogen couplings. The method is demonstrated with a 22-nucleotide RNA fragment of the P5abc region of a group I intron uniformly labeled with 15N. Use of intraresidue 15N3-amino proton couplings to assign cytosine 15N3 signals complements the recently proposed JNN HNN COSY [Dingley, A.J. and Grzesiek, S. (1998) J. Am. Chem. Soc., 120, 8293-8297] method of identifying hydrogen-bonded base pairs in RNA.

Animals↗
PubMed2001

Non-expression of HLA-B*5111N is caused by an insertion into the cytosine island at exon 4 creating a frameshift stop codon.

The identification of the "blank" allele HLA-B*5111N, which was detected in German and Czech individuals, is described. In the pedigree analysis this new allele segregates with the serological haplotype HLA-A2; B-; DR4 which is frequent in Czech population. The non-expression of B*5111N is caused by the insertion of an additional cytosine molecule at the cytosine island between the nucleotides 621-626 (codons 183-185, first three codons of exon 4) leading to a frame shift that creates a stop codon at codon 196. This insertion may be explained either by conversion with the pseudogene HLA-J or by slipped-strand mispairing. In order not to overlook the presence of alleles with altered expression in case of hematopoietic stem cell transplantation, both serological and DNA-based typing should be performed (Note).

Alleles↗
PubMed2004

Transduction of yeast cytosine deaminase mediated by HIV-1 Tat basic domain into tumor cells induces chemosensitivity to 5-fluorocytosine.

Enzyme/prodrug approach is one of the actively developing areas for cancer therapy. In an effort to develop more effective enzyme/prodrug systems, cell-permeable cytosine deaminase was produced by fusing yeast cytosine deaminase (yCD) in frame with RKKRRQRRR domain of HIV-1 Tat which is an efficient delivery peptide of the foreign proteins into cells. The purified Tat-yCD fusion protein expressed in Escherichia coli was readily transduced into mammalian cells in a time- and dose-dependent manner. A significant level of the transduced Tat-yCD protein was recovered in the cell and was stable for 24 h as indicated by both results of the enzymatic assay of 5-fluorocytosine (5-FC) conversion to 5-fluorouracil (5-FU) and Western blot analysis. The cells transduced with Tat-yCD become highly sensitive to the cytotoxicity of 5-FC, while cells treated with yCD are unaffected by 5-FC. In addition, a strong bystander effect was observed with conditioned media from cells transduced with Tat-yCD added to non-transduced cells. Tat-yCD fusion protein demonstrated here for its ability to transduce into cells and convert nontoxic prodrug 5-FC to the toxic antimetabolite 5-FU, may be a useful approach for cancer therapy.

Animals↗
PubMed2006

Combination of cytosine deaminase suicide gene expression with DR5 antibody treatment increases cancer cell cytotoxicity.

Combined treatment using adenoviral-directed enzyme/prodrug therapy and immunotherapy has the potential to become a powerful alternative method of cancer therapy. We have developed adenoviral vectors encoding the cytosine deaminase gene (Ad-CD) and cytosine deaminase:uracil phosphoribosyltransferase fusion gene (Ad-CD:UPRT). A monoclonal antibody, TRA-8, specifically binds to death receptor 5, one of two death receptors bound by tumor necrosis factor-related apoptosis-inducing ligand (TRAIL). The purpose of this study was to evaluate cytotoxicity in vitro and therapeutic efficacy in vivo of the combination of Ad-CD:UPRT and TRA-8 against human pancreatic cancer and glioma cell lines. The present study demonstrates that Ad-CD:UPRT infection resulted in increased 5-FC-mediated cell killing, compared with Ad-CD. Furthermore, a significant increase of cytotoxicity following Ad-CD:UPRT/5-FC and TRA-8 treatment of cancer cells in vitro was demonstrated. Animal studies showed significant inhibition of tumor growth of MIA PaCa-2 pancreatic and D54MG glioma xenografts by the combination of Ad-CD:UPRT/5-FC plus TRA-8 as compared with either agent alone or no treatment. The results suggest that the combination of Ad-CD:UPRT/5-FC with TRA-8 produces an additive cytotoxic effect in cancer cells in vitro and in vivo. These data indicate that combined treatment with enzyme/prodrug therapy and TRAIL immunotherapy provides a promising approach for cancer therapy.

Adenoviridae↗
PubMed2003

Mutagenesis of the HMGB (high-mobility group B) protein Cmb1 (cytosine-mismatch binding 1) of Schizosaccharomyces pombe: effects on recognition of DNA mismatches and damage.

Cmb1 (cytosine-mismatch binding 1) is a high-mobility group (HMG) protein of Schizosaccharomyces pombe, which consists of 223 amino acids and has a single HMG domain at the C-terminal end. We have created several mutant and deletion forms of the Cmb1 protein and studied the effects on general DNA binding and specific binding to DNA mismatches and damaged DNA. Cmb1Delta41 (i.e. Cmb1 from which the 41 N-terminal amino acids have been deleted) bound specifically to cytosine-containing mismatches, to the cisplatin-induced intrastrand cross-links cis -GG and cis -AG and to an O (6)-methylguanine lesion. DNA binding was not affected when the 45 N-terminal amino acids were deleted, but was abolished in the absence of the 50 N-terminal amino acids, and was reduced when Cmb1 was truncated by between five and eleven C-terminal amino acids. Cmb1, both with and without the C-terminal truncations, retained its DNA binding affinity after heating at 95 degrees C. The cmb1 gene was induced when S. pombe cells were treated with cisplatin. Mitotic mutation rates were increased in a S. pombe cmb1 null mutant and in a cmb1-(1-212) mutant, which encodes a Cmb1 protein lacking the 11 C-terminal amino acids. We conclude that mutation avoidance by Cmb1 is distinct from Msh2-dependent mismatch repair, but related to nucleotide excision repair.

Antineoplastic Agents↗