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PubMed1997

Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.

We have determined the structure of Pvu II methyltransferase (M. Pvu II) complexed with S -adenosyl-L-methionine (AdoMet) by multiwavelength anomalous diffraction, using a crystal of the selenomethionine-substituted protein. M. Pvu II catalyzes transfer of the methyl group from AdoMet to the exocyclic amino (N4) nitrogen of the central cytosine in its recognition sequence 5'-CAGCTG-3'. The protein is dominated by an open alpha/beta-sheet structure with a prominent V-shaped cleft: AdoMet and catalytic amino acids are located at the bottom of this cleft. The size and the basic nature of the cleft are consistent with duplex DNA binding. The target (methylatable) cytosine, if flipped out of the double helical DNA as seen for DNA methyltransferases that generate 5-methylcytosine, would fit into the concave active site next to the AdoMet. This M. Pvu IIalpha/beta-sheet structure is very similar to those of M. Hha I (a cytosine C5 methyltransferase) and M. Taq I (an adenine N6 methyltransferase), consistent with a model predicting that DNA methyltransferases share a common structural fold while having the major functional regions permuted into three distinct linear orders. The main feature of the common fold is a seven-stranded beta-sheet (6 7 5 4 1 2 3) formed by five parallel beta-strands and an antiparallel beta-hairpin. The beta-sheet is flanked by six parallel alpha-helices, three on each side. The AdoMet binding site is located at the C-terminal ends of strands beta1 and beta2 and the active site is at the C-terminal ends of strands beta4 and beta5 and the N-terminal end of strand beta7. The AdoMet-protein interactions are almost identical among M. Pvu II, M. Hha I and M. Taq I, as well as in an RNA methyltransferase and at least one small molecule methyltransferase. The structural similarity among the active sites of M. Pvu II, M. Taq I and M. Hha I reveals that catalytic amino acids essential for cytosine N4 and adenine N6 methylation coincide spatially with those for cytosine C5 methylation, suggesting a mechanism for amino methylation.

Amino Acid Sequence↗
PubMed1990

Electrostatic properties of cytosine monohydrate from diffraction data.

The charge density distribution in deuterated cytosine monohydrate [4-(2H2)-amino-2(1H)-(1-2H)-pyrimidinone], C4H2D3N3O.D2O, Mr = 134.15, monoclinic, P2(1)/c, a = 7.714 (1), b = 9.825 (1), c = 7.506 (2) A, beta = 100.52 (1) degrees, Z = 4, has been determined from 1432 X-ray reflections [sin theta/lambda less than 1.15 A-1, Mo K alpha, lambda = 0.7093 (1) A] collected at 82 (2) K. Least-squares structure refinement assuming Stewart's rigid pseudoatom model gave R(F) = 0.041, with all nuclear positions and H/D anisotropic thermal parameters having fixed values previously determined by neutron diffraction. The cytosine and water molecules are both electrically neutral within experimental error (0.09 e). Molecular dipole moments are mu = 8.0 (1.4) debye for cytosine and 2.3 (3) debye for water. For the doubly hydrogen-bonded cytosine dimer (N1-D1...N3', N4-D4...O2') isolated from the crystal, the electrostatic energy of interaction is estimated to be -96 (27) kJ mol-1. Maps of the electrostatic potential for molecules isolated from the crystal indicate that the electronegativity of the hydrogen-bonding acceptor sites can be ranked with the water O atom, cytosine N(3) and carbonyl O(2) in decreasing order.

Crystallization↗
PubMed1974

Mutants of the N-3 R-factor conditionally defective in hspII modification and deoxyribonucleic acid-cytosine methylase activity.

The N-3 drug resistance (R) factor specifies a deoxyribonucleic acid (DNA)-cytosine methylase and a DNA restriction-modification (hspII) system. We have isolated three independent mutants that are conditionally defective in their ability to modify bacteriophage lambda and to methylate DNA-cytosine residues. The ratio of 5-methylcytosine to N(6)-methyladenine in bacterial DNA and in the DNA of phages lambda and fd was determined after labeling with [methyl-(3)H]methionine at various growth temperatures. Although the ability of the wild-type N-3 factor to modify phage lambda and to methylate DNA-cytosine residues was unaffected with increasing temperature, two of the mutants exhibited a parallel loss in modification and cytosine methylation ability. The ability of the third mutant to carry out these functions was dependent on the presence or absence of an amber suppressor mutation in the host genome. These results offer further support for the notion that hspII modification is mediated by a DNA-cytosine methylase. Evidence is also presented that the modification methylase is responsible for the in vivo methylation of phage fd DNA (which is not subject to hspII restriction in vivo).

Alanine↗
PubMed1987

Methylation of specific cytosine residues enhances simian virus 40 T-antigen binding to origin region DNA.

Specific binding of simian virus 40 large T antigen to origin region DNA requires the interaction of T antigen with multiples of a consensus recognition pentanucleotide sequence (5'-G[T]-A[G]-G-G-C-3'). To assess the interaction of T antigen with cytosine residues in the recognition sequences, bacterial methylases were used to methylate simian virus 40 form I DNA in vitro at specific cytosine residues. Methylation of a subset of the cytosine residues in the pentanucleotide sequences resulted in enhanced binding of T antigen to origin region DNA. Enhanced binding to the methylated pentanucleotides indicates that the methyl groups introduced on this subset of pentanucleotide cytosine residues could not have sterically interfered with the interaction of T antigen with the recognition sequences. This lack of steric interference suggests that T antigen does not make close contact in the major groove with these particular cytosine residues during normal binding.

5-Methylcytosine↗
PubMed2004

Cytosine arabinoside substitution decreases transcription factor-DNA binding element complex formation.

CONTEXT: The pyrimidine nucleoside analog, cytosine arabinoside (Ara-C), is an effective therapeutic agent for acute leukemia. The phosphorylated triphosphate, cytosine arabinoside triphosphate, competes with deoxycytosine triphosphate as a substrate for incorporation into DNA. Once incorporated into DNA, it inhibits DNA polymerase and topoisomerase I and modifies the tertiary structure of DNA. OBJECTIVE: To determine if the substitution of Ara-C for cytosine in double-stranded oligonucleotides that contain 4 specific transcription factor binding sites (TATA, GATA, C/EBP, and AP-2alpha) alters transcription factor binding to their respective DNA binding elements. DESIGN: Transcription factors were obtained from nuclear extracts from human promyelocytic leukemia HL-60 cells. [32P]-end-labeled double-stranded oligonucleotides that contained 1 or 2 specific transcription factor binding sites with or without Ara-C substitution for cytosine were used to assess transcription factor binding by electrophoretic mobility shift assay. RESULTS: The substitution of Ara-C for cytosine within and outside the transcription factor binding element (AP-2alpha, C/EBP), outside the binding element only (GATA, TATA), or within the binding element only (AP-2alpha) all result in a reduction in transcription factor binding to their respective DNA binding element. CONCLUSION: The reduction of the binding capacity of transcription factors with their respective DNA binding elements may depend on structural changes within oligonucleotides induced by Ara-C incorporation. This altered binding capacity of transcription factors to their DNA binding elements may represent one mechanism for Ara-C cytotoxicity secondary to inhibition of transcription of new messenger RNAs and, subsequently, translation of new proteins.

Binding Sites↗
PubMed1992

Effects of decreased cytosine content on rho interaction with the rho-dependent terminator trp t' in Escherichia coli.

We have introduced multiple cytosine-to-uracil mutations in the rho-dependent transcription terminator trp t' and have characterized a subset of the resulting mutant derivatives in vitro for termination efficiency, affinity for rho, and stimulation of rho-ATPase activity. No specific cytosine residue appears to be required for termination, and at least 13 of the 28 cytosine residues in the 104 nucleotide trp t' region can be mutated with little effect on termination efficiency. One derivative with 11 mutations is significantly less efficient than other derivatives with a similar number of mutations, implying that the pattern of alterations, as well as the number, can affect termination efficiency. Derivatives with 20 and 28 cytosines mutated are non-functional in termination, consistent with the idea that cytosines are required for rho-dependent termination. Our results are inconsistent, however, with the hypothesis that the termination efficiency is directly related to the cytosine/guanine ratio in the nascent transcript. The results support the idea that neither RNA binding affinity nor ATPase activation per se are accurate predictors of rho-dependent termination efficiency.

Adenosine Triphosphatases↗
PubMed1991

Distribution of electron trapping in DNA: protonation of one-electron reduced cytosine.

Electron spin resonance was employed to study one-electron reduced cytosine stabilized in glasses at low temperatures. In a LiCl/H2O glass, deoxycytidine gives an extra approximately 1 mT splitting that is not observed in oligomers. To better understand the source of the extra splitting, 1-methylcytosine (1mC) and N,N-dimethyldeoxycytidine (dmC) were examined in an HCl/H2O glass. The spectrum of 1mC is a quartet and the spectrum of dmC is a triplet. A probable explanation for this is that in both cases N4 is fully protonated prior to electron addition. In the LiCl/H2O glass, monomeric cytosine, after one-electron reduction, appears to protonate at N4. However, oligomeric cytosine, after one-electron reduction, does not protonate at N4 and therefore must protonate at N3. This could be due to the exclusion of Li+ coordination at N3 and/or the constraining of N4 to a planar configuration via stacking interactions. These findings provide additional insight into why cytosine is the major site of electron capture in DNA. Proton transfer across the N1-H...N3 hydrogen bond is expected to stabilize electron addition to cytosine preferentially.

Cytosine↗
PubMed1984

Sequence specificity of isolated DNA-cytosine methylases from Shigella sonnei 47 cells.

Five individual DNA-cytosine methylases differing in pI (isoelectric point) values are present in Shigella sonnei 47-cells. The sequence specificity of each of those was determined 'in vitro' by a highly efficient combined approach that included pyrimidine tract (isostic) analysis, identification of the immediate neighbourhood of the methylated base within the recognition sequence and the calculation method. The enzyme with pI 5.3 (MSso5.3) is the counterpart of the RSso 47 II in the Sso 47 II restriction-modification system and methylates the internal cytosine residue of the 'palindromic' 5'-C-C-N-G-G-3' sequence. The enzymes with pI 6.2 (MSso6.2) and 7.4 (MSso7.4) exhibit identical specificity upon methylation of the 'palindromic' 5'-Py-C-N-G-Pu-3' sequence, but differ in the pI values of the proteins. The enzyme with pI 4.2 (MSso4.2) recognizes the unique tetranucleotide 5'-C-C-C-C-3' sequence and methylates the second cytosine residue at the 5'-end of the sequence. The enzyme with pI 8.4 (MSso8.4) methylates the central cytosine residue within the degenerative trinucleotide 5'-(PuC)-C-C-3' sequence. MSso5.3, MSso6.2, and MSso7.4 are presumed to belong to the 'family' of sequence-specific (Eco RII-like) enzymes. These DNA-cytosine methylases are likely to be evolutionary related to Eco RII and to have undergone a sufficient genetic drift so as to recognize similar (but more degenerative) nucleotide sequences.

Base Sequence↗
PubMed1996

Overproduction of DNA cytosine methyltransferases causes methylation and C --> T mutations at non-canonical sites.

Multicopy clones of Escherichia coli cytosine methyltransferases Dcm and EcoRII methylase (M. EcoRII) cause an approximately 50-fold increase in C --> T mutations at their canonical site of methylation, 5'-CmeCAGG (meC is 5-methylcytosine). These plasmids also cause transition mutations at the second cytosine in the sequences CCGGG at approximately 10-fold lower frequency. Similarly, M. HpaII was found to cause a significant increase in C --> T mutations at a CCAG site, in addition to causing mutations at its canonical site of methylation, CCGG. Using a plasmid that substantially overproduces M. EcoRII, in vivo methylation at CCSGG (S is C or G) and other non-canonical sites could be detected using a gel electrophoretic assay. There is a direct correlation between the level of M. EcoRII activity in cells, the extent of methylation at non-canonical sites and frequency of mutations at these same sites. Overproduction of M. EcoRII in cells also causes degradation of DNA and induction of the SOS response. In vitro, M. EcoRII methylates an oligonucleotide duplex containing a CCGGG site at a slow rate, suggesting that overproduction of the enzyme is essential for significant amounts of such methylation to occur. Together these results show that cytosine methyltransferases occasionally methylate cellular DNA at non-canonical sites and suggest that in E. coli, methylation-specific restriction systems and sequence specificity of the DNA mismatch correction systems may have evolved to accommodate this fact. These results also suggest that mutational effects of cytosine methyltransferases may be much broader than previously imagined.

Base Sequence↗
PubMed1979

Effect of cytosine arabinoside triphosphate on the incorporation of 3H-thymidine in mitochondria isolated from HeLa cells.

HeLa cell mitochondria were allowed to incorporate 3H-thymidine in a cell free system and the effect of ethidium bromide, cytosine arabinoside and cytosine arabinoside triphosphate on the labeling of mitochondrial DNA was studied. The labeled products, isolated by sedimentation velocity in CsCl-ethidium bromide two-step gradients, showed similar sedimentation profiles as in vivo labeled mtDNA. Cytosine arabinoside triphosphate and ethidium bromide strongly inhibited the labeling of mitochondrial DNA, whereas cytosine arabinoside appeared to be much less effective. Tritiated deoxycytidine was found to be incorporated by isolated mitochondria, whereas cytosine arabinoside was shown to enter the mitochondrial acid-soluble pool but not to be incorporated in acid-insoluble form. These results are in agreement with the previously reported findings of in vivo experiments.

Arabinofuranosylcytosine Triphosphate↗
PubMed1976

[Mouse cytomegalovirus infection under cytosine arabinoside treatment].

The antiviral activity of cytosine arabinoside (ARA-C) against the mouse cytomegalovirus was investigated in animal experiments using various dosages. The substance did not exhibit any virostatic effect, but on the contrary fostered the viral infection. The virus concentration in the liver after administration of five dosages of 30 mg/kg of cytosine arabinoside was 35 times higher than that in untreated animals, and after five dosages of 45 mg/kg was 70 times higher. In addition the mortality rate for infected animals treated with cytosine arabinoside was significantly higher in relation to dosage. Cytosine arabinoside also acts as an immunosuppressor in humans. Adverse effects in cytomegalo-infection can therefore not be excluded. The use of cytosine arabinoside in therapy would thus appear to be highly questionable.

Animals↗
PubMed2006

Peripheral neuropathy caused by high-dose cytosine arabinoside treatment in a patient with acute myeloid leukemia.

The central nervous system toxicity of high-dose cytosine arabinoside is well recognized, but the toxicity of cytosine arabinoside in the peripheral nervous system has been infrequently reported. A 49-year-old Japanese man was diagnosed with acute myeloid leukemia. After he achieved complete remission, he received high-dose cytosine arabinoside treatment (2 g/m2 twice a day for 5 days; total, 20 g/m2) as consolidation therapy. The first course of high-dose cytosine arabinoside resulted in no unusual symptoms, but on day 21 of the second course of treatment, the patient complained of numbness in his right foot. Electromyogram and nerve-conduction studies showed peripheral neuropathy in both peroneal nerves. This neuropathy was gradually resolving; however, after the patient received allogeneic bone marrow transplantation, the symptoms worsened, with the development of graft-versus-host disease, and the symptoms subsequently responded to methylprednisolone. Although the mechanisms of peripheral neuropathy are still unclear, high-dose cytosine arabinoside is a therapy that is potentially toxic to the peripheral nervous system, and auto/alloimmunity may play an important role in these mechanisms.

Acute Disease↗
PubMed1986

Phase I-II clinical and pharmacologic studies of high-dose cytosine arabinoside in refractory leukemia.

Sixty-four patients with refractory acute leukemia were treated with high-dose cytosine arabinoside given at a dosage of 3 g/m2 intravenously over two hours every 12 hours for four to 12 doses, repeated at two- to three-week intervals. Complete remissions were observed in 16 patients (25 percent), and the median duration of remission was three months (range, one to 10 months). Remission rates were similar for patients with acute myelogenous and acute lymphocytic leukemia (24 and 27 percent, respectively). Response rates were significantly higher in patients with initial remission durations of more than six months than in those with shorter remissions or those in whom there was no response to front-line therapy (41 and 9 percent; p less than 0.01). Similarly, patients with disease sensitive to conventional cytosine arabinoside had higher response rates than did those with resistant disease (54 and 17 percent; p = 0.03). Serial in vivo measurements of intracellular concentrations of the active metabolite of cytosine arabinoside in peripheral blasts following the initial dose demonstrated considerable individual variation. Favorable intracellular pharmacology of this active metabolite, manifested by its higher intracellular concentrations 12 hours after the first dose, by longer half-lives of active metabolite levels, and by higher values of the measured area under the curve of its accumulation and retention, was associated with higher response rates. Central nervous system toxicity occurred in 24 percent of patients, and pulmonary toxicity occurred in 22 percent; both were dose-limiting and dose-related. Other toxicities included nausea, vomiting, diarrhea, conjunctivitis, photophobia, cytosine arabinoside fever, skin rashes, and hepatic dysfunction. Response rates were similar for schedules utilizing four to six doses at two-week intervals or nine doses at three-week intervals (27 percent versus 25 percent). The schedule of 12 doses had a more rapid antileukemic effect but resulted in significantly higher toxicity and mortality rates during therapy with a similar overall response rate (21 percent). Thus, high-dose cytosine arabinoside is an effective regimen with substantial toxicity in patients with acute leukemia.

Adolescent↗
PubMed1984

Cell differentiation and therapeutic effect of low doses of cytosine arabinoside in human myeloid leukemia.

Bone marrow cells from 2 patients over 60 years of age with acute myeloblastic (AML) or monoblastic (AMoL) leukemia were cultured in the presence of a low dose of cytosine arabinoside. In the cells from the AML patient this treatment induced differentiation to metamyelocytes and a decrease in the number of blasts, so that there was an 11-fold increase in the ratio of differentiated myeloid cells to blasts. In the patient with AMoL there was differentiation to monocytes and macrophages and only a 3-fold increase in the ratio of differentiated myeloid cells to blasts. In the latter patient actinomycin D was a more potent inducer of differentiation than cytosine arabinoside, daunomycin was similar to cytosine arabinoside and adriamycin showed the lowest response. Four courses of low dose treatment with cytosine arabinoside produced remission in the patient with AML and in another patient with AMoL whose cells were not tested in culture. No remission was induced by this low dose treatment in the patient with AMoL whose cells showed only a small decrease in blast cells in culture with cytosine arabinoside. It is suggested that prescreening for effective compounds in patients with myeloid leukemias and the use of low dose therapy can be of help in obtaining remission without serious side effects. This could be especially useful in patients where there may be severe toxic effects after high dose chemotherapy.

Aged↗
PubMed2005

EPR study of a copper center in a single crystal of cytosine monohydrate.

Copper is found incorporated into the crystal structure of cytosine monohydrate grown from aqueous solution of commercially available cytosine. Upon ionizing irradiation, the crystals exhibited the electron paramagnetic resonance (EPR) spectra characteristic of Cu(II) complex. Planar coordination bonding to the cupric ion, having three nitrogen atoms and an oxygen as ligands, is interpreted to bridge two cytosine molecules, replacing the two cytosine-cytosine hydrogen bonds present in pure crystals. The EPR signals are much stronger for crystals grown from the solutions to which small amount of copper powder were added.

Journal Article↗
PubMed1978

Determination of cytosine arabinoside in human plasma by gas chromatography with a nitrogen-sensitive detector and by gas chromatography--mass spectrometry.

A method for the determination of cytosine arabinoside in the plasma of leukemic patients being treated with this drug is described using either gas--liquid chromatography with a nitrogen-sensitive flame ionization detector or gas chromatography--mass spectrometry (GC-MS). To increase volatility, a double derivative of cytosine arabinoside was used, prepared by acetylation and subsequent methylation. Cytidine was used as internal standard for the GC procedure. GC--MS was performed with either cytidine as internal standard and detection by single-ion monitoring or by the use of [2H3] acetate-methyl derivative of cytosine arabinoside as internal standard and subsequent multiple-ion monitoring. Attempted extraction of cytosine arabinoside from plasma with various organic solvents was unsuccessful, but protein precipitation with ethanol or trichloroacetic acid followed by washing of the aqueous residue with organic solvents to remove as many of the interfering substances as possible gave satisfactory results. The minimum detectable quantity of pure cytosine arabinoside was similar for both techniques (approximately 500 pg). However, with GC using a nitrogen-sensitive detector, the lower limit of detection from plasma was found to be approximately 40--70 ng per ml plasma whilst GC--MS showed greater analytical selectivity with a detection limit in some cases as low as 1 ng per ml plasma.

Chromatography, Gas↗
PubMed1998

Synthesis and antiviral activity of prodrugs of the nucleoside 1-[2',3'-dideoxy-3'-C-(hydroxymethyl)-beta-D-erythropentofuranosyl] cytosine.

The synthesis and antiviral evaluation of 21 prodrugs of 1-[2',3'-dideoxy-3'-C-(hydroxymethyl)-beta-D-erythropentofuranosyl ] cytosine 1 is reported. Cytosine N4-imine analogues were prepared by condensation of 1 with selected formamide dimethyl acetals. Amino acid substituted prodrugs were prepared from 1 or imine prodrug 2 by coupling with either N-tert-butoxycarbonyl (t-Boc)-L-valine or N-t-Boc-L- phenylalanine in the presence of dicyclohexycarbodiimide (DCC) and 4-dimethylaminopyridine (4-DMAP). Deprotection of the t-Boc protecting group was achieved with trifluoroacetic acid (TFAA) in methylene chloride. Cytosine N4-amide analogues were prepared by reaction of 1 with appropriate anhydrides in aqueous dioxane. Triacylated analogue 22 was prepared by reaction of 1 with four equivalents of benzoyl chloride in pyridine. Prodrugs were evaluated for activity against duck hepatitis B virus, herpes simplex virus types 1 and 2, human cytomegalovirus, and human immunodeficiency virus. A number of analogues were found comparable in activity to 1 with the cytosine N4-imine series more active than the amino acid substituted and cytosine N4-amide prodrugs. Slight to moderate cellular toxicity was observed with some analogues.

Antiviral Agents↗
PubMed2001

Consolidation therapy for childhood acute lymphoblastic leukaemia: clinical and cellular pharmacology of cytosine arabinoside, epipodophyllotoxins and cyclophosphamide.

The intensification of post-remission induction therapy has been shown to improve the relapse-free survival for childhood acute lymphoblastic leukaemia (ALL), and is now a standard component of the treatment of childhood acute lymphoblastic leukaemia. For cytosine arabinoside (ara-C), methotrexate, vincristine and corticosteroids, in-vitro studies indicate that the extracellular drug concentration and exposure time are important determinants of cytotoxicity for human leukaemia cell lines. For L-asparaginase, epipodopyllotoxins and cyclophosphamide, there have been few studies of the relationship between cellular pharmacology and cytotoxicity in relation to ALL. The clinical and cellular pharmacology of methotrexate and cytosine arabinoside have been studied in relation to childhood ALL in vivo. For these drugs, there is evidence to suggest that maintenance of plasma concentrations that are biochemically optimal is necessary to maximize anti-leukaemic effects. For cytosine arabinoside in particular, optimal extracellular fluid concentrations are not likely to be achieved or maintained by bolus or short-duration i.v. infusions. A potentially important example of this may be served by the success of antimetabolite-based intrathecal chemotherapy for CNS-directed treatment of childhood ALL. Intrathecal administration of both methotrexate and cytosine arabinoside results in prolonged leukaemic cell exposure to cytotoxic concentrations of the drug. For vincristine, anthracyclines and asparaginase, the actual dose intensity received by children during consolidation therapy may be important, and there is considerable interpatient variation in the pharmacokinetics of cyclophosphamide and teniposide in the therapy of childhood cancers. The importance of this relationship to childhood ALL is not known. The pharmacological and cellular pharmacological studies performed at St Jude Children's Research Hospital (Memphis, TN, USA) have allowed investigation of the relationships between the clinical and cellular pharmacology of methotrexate and prognosis, and have supported the individualization of consolidation therapy with this drug. Cytosine arabinoside has been less well studied in relation to childhood ALL, although evidence exists to suggest that the administration of conventional-dose bolus or infusion schedules may not be optimal in terms of the antileukaemic efficacy of this antimetabolite. For L-asparaginase, ongoing studies may allow the relationship between dose and schedule of administration to be related to pharmacodynamic measures such as asparagine depletion and prognosis. Therefore, through knowledge of clinical and cellular pharmacological properties, it may be possible to optimize the consolidation phase of therapy for childhood ALL, without disrupting the fundamental principles by which the overall treatment is administered. This may be particularly important for children with disease that has inherent or acquired resistance to therapy.

Antineoplastic Agents↗