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At least 631 records · Page 35Linked to original sources
PubMed1998

The high mobility group domain protein Cmb1 of Schizosaccharomyces pombe binds to cytosines in base mismatches and opposite chemically altered guanines.

The mismatch-binding activity Cmb1 of Schizosaccharomyces pombe was enriched from wild type cells, and N-terminal sequencing enabled cloning of the respective gene. The deduced amino acid sequence of cmb1(+) contains a high mobility group domain, a motif that is common to a heterogeneous family of DNA-binding proteins. In crude protein extracts of a cmb1 gene-disruption strain, specific binding to C/T, C/A, and C/Delta was abolished. Weak binding to C/C revealed the presence of a second mismatch-binding activity, Cmb2. Cmb1, enriched from S. pombe and purified from Escherichia coli, bound specifically to C/C, C/T, C/A, T/T, and C/Delta but showed little or no affinity to other mismatches and small loops. Cmb1 recognizes 1,2 GpG intrastrand cross-links, produced by the chemotherapeutic drug cisplatin, when two cytosines are opposite the cross-linked guanines but not when other bases are present. Consistently, O6-methylguanine:C but not O6-methylguanine/T lesions were bound. Thus, cytosines in mismatches and opposite chemically modified guanines are the preferred target of Cmb1 recognition. cmb1 mutant cells are more sensitive to cisplatin than wild type cells, indicating a role of Cmb1 in repair of cisplatin-induced DNA damage.

Amino Acid Sequence↗
PubMed2002

Identification and characterization of a novel human DNA glycosylase for repair of cytosine-derived lesions.

Two candidate human orthologs of Escherichia coli MutM/Nei were recently identified in the human genome database, and one of these, NEH1, was characterized earlier (Hazra, T. K., Izumi, T., Boldogh, I., Imhoff, B., Kow, Y. W., Jaruga, P., and Dizdaroglu, M. (2002) Proc. Natl. Acad. Sci. U. S. A. 99, 3523-3528). Here we report characterization of the second protein, originally named NEH2 and now renamed NEIL2 (Nei-like). The 37-kDa wild-type NEIL2 expressed in and purified from E. coli has DNA glycosylase/AP lyase activity, primarily for excising oxidative products of cytosine, with highest activity for 5-hydroxyuracil, one of the most abundant and mutagenic lesions induced by reactive oxygen species, and with lower activity for 5,6-dihydrouracil and 5-hydroxycytosine. It has negligible or undetectable activity with 8-oxoguanine, thymine glycol, 2-hydroxyadenine, hypoxanthine, and xanthine. NEIL2 is similar to NEIL1 in having N-terminal Pro as the active site. However, unlike NEIL1, its expression was independent of the cell cycle stage in fibroblasts, and its highest expression was observed in the testes and skeletal muscle. Despite the absence of a putative nuclear localization signal, NEIL2 was predominantly localized in the nucleus. These results suggest that NEIL2 is involved in global genome repair mainly for removing oxidative products of cytosine.

Cell Cycle↗
PubMed2002

A potent cell-active allosteric inhibitor of murine DNA cytosine C5 methyltransferase.

The major DNA cytosine methyltransferase isoform in mouse erythroleukemia cells, Dnmt1, exhibits potent dead-end inhibition with a single-stranded nucleic acid by binding to an allosteric site on the enzyme. The previously reported substrate inhibition with double-stranded substrates also involves binding to an allosteric site. Thus, both forms of inhibition involve ternary enzyme-DNA-DNA complexes. The inhibition potency of the single-stranded nucleic acid is determined by the sequence, length, and most appreciably the presence of a single 5-methylcytosine residue. A single-stranded phosphorothioate derivative inhibits DNA methylation activity in nuclear extracts. Mouse erythroleukemia cells treated with the phosphorothioate inhibitor show a significant decrease in global genomic methylation levels. Inhibitor treatment of human colon cancer cells causes demethylation of the p16 tumor suppressor gene and subsequent p16 re-expression. Allosteric inhibitors of mammalian DNA cytosine methyltransferases, representing a new class of molecules with potential therapeutic applications, may be used to elucidate novel epigenetic mechanisms that control development.

Allosteric Site↗
PubMed2003

Crystal structure of yeast cytosine deaminase. Insights into enzyme mechanism and evolution.

Yeast cytosine deaminase is an attractive candidate for anticancer gene therapy because it catalyzes the deamination of the prodrug 5-fluorocytosine to form 5-fluorouracil. We report here the crystal structure of the enzyme in complex with the inhibitor 2-hydroxypyrimidine at 1.6-A resolution. The protein forms a tightly packed dimer with an extensive interface of 1450 A2 per monomer. The inhibitor was converted into a hydrated adduct as a transition-state analog. The essential zinc ion is ligated by the 4-hydroxyl group of the inhibitor together with His62, Cys91, and Cys94 from the protein. The enzyme shares similar active-site architecture to cytidine deaminases and an unusually high structural homology to 5-aminoimidazole-4-carboxamide-ribonucleotide transformylase and thereby may define a new superfamily. The unique C-terminal tail is involved in substrate specificity and also functions as a gate controlling access to the active site. The complex structure reveals a closed conformation, suggesting that substrate binding seals the active-site entrance so that the catalytic groups are sequestered from solvent. A comparison of the crystal structures of the bacterial and fungal cytosine deaminases provides an elegant example of convergent evolution, where starting from unrelated ancestral proteins, the same metal-assisted deamination is achieved through opposite chiral intermediates within distinctly different active sites.

Amino Acid Sequence↗
PubMed2006

Antisense targeting of CXXC finger protein 1 inhibits genomic cytosine methylation and primitive hematopoiesis in zebrafish.

CXXC finger protein 1 (CFP1) binds to unmethylated CpG dinucleotides and is a component of the Set1 histone methyltransferase complex. Mice lacking CFP1 suffer a peri-implantation lethal phenotype, and CFP1-deficient embryonic stem cells are viable but unable to differentiate and exhibit a 60-80% decrease in genomic cytosine methylation. A zebrafish homolog of CFP1 has been identified, is approximately 70% similar to murine CFP1, and is widely expressed during development. Zebrafish embryos treated with a zCFP1 antisense morpholino oligonucleotide had little or no circulating red blood cells and exhibited abnormal yolk sac morphology at 48 h post-fertilization. Many of the antisense-treated zebrafish also exhibited cardiac edema, and 14% were dead at 24 h post-fertilization. Morphant zebrafish also exhibited elevated levels of apoptosis, particularly in the intermediate cell mass, the site of primitive erythropoiesis, as well as aberrations in vascular development. Genomic DNA isolated from morphant embryos exhibited a 60% reduction of global genomic cytosine methylation. A similar phenotype was observed with an independent zCFP1 antisense morpholino oligonucleotide, but not following injection of an unrelated control oligonucleotide. The morphant phenotype was rescued when mRNA encoding murine CFP1 was co-injected with the antisense oligonucleotide. Genomic data base analysis reveals the presence of a second version of zebrafish CFP1 (zCFP1b). However, the morphant phenotype observed following specific depletion of zCFP1 indicates that these related genes have nonredundant functions controlling normal zebrafish hematopoiesis and epigenetic regulation. These findings establish the importance of CFP1 during postgastrulation development.

Amino Acid Motifs↗
PubMed1985

Guanine plus cytosine content of the DNA of Coccidioides immitis.

The mole per cent guanine plus cytosine was determined for DNA extracted from Coccidioides immitis to add information pertinent to the taxonomy of this zoopathogenic fungus. Four strains of C. immitis, three in the mycelial phase, one in the spherule/endospore phase yielded guanine plus cytosine in the narrow range of 49.41 to 49.61 mole percent. These values are lower than those for ascomycetes that mimic the arthroconidial form of C. immitis, higher than those for ascomycetous yeasts, but closer to those of 'transition zone' or basidiomycetous yeasts.

Coccidioides↗
PubMed1988

A systematic study of patterns of hydration in nucleic acids:(I) guanine and cytosine.

The hydration sites of guanine and cytosine are defined by examination of the crystal structures of bases, nucleosides, nucleotides, and three dinucleoside phosphate salts. The patterns of hydration for two guanine and cytosine containing oligonucleotides are then predicted. The relationship between these structural motifs and thermodynamic parameters is discussed.

Crystallography↗
PubMed1996

Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions.

An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are more stable than the neutral base pairs. Two energy contributions not present in the neutral base pairs stabilize the protonated base pairs: the molecular ion - dipole interaction, and the induction interaction. The molecular ion - dipole stabilization dominates in base pairs with highly polar neutral monomers, such as the C...CH+ base pair. The induction interaction is not included in the commonly used empirical potentials, which do not reproduce the changes in intermolecular stabilization due to protonation. We demonstrate that the base stacking of several consecutive C...CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs.

Base Composition↗
PubMed1997

Hydrated water molecules of pyrimidine/purine/pyrimidine DNA triple helices as revealed by FT-IR spectroscopy: a role of cytosine methylation.

Hydrated water molecules of pyrimidine/purine/pyrimidine DNA hairpin triplex was studied by a comparison of triplex (CC.AG6) formed by a host oligodeoxypyrimidine of 5'-d(TC)3T4(CT)3(CC) with a target hexadeoxypurine 5'-d(AG)3(AG6) strand and by triplexes (MM.AG6, MC.AG6, and CM.AG6) formed by oligonucleotides with the exact sequences as above except 5-methylcytosine replaced all (MM), 5' end half (MC), and 3' end half (CM) cytosine bases in CC via FT-IR spectroscopy in hydrated film. Results revealed that: (i) all these triplexes have a similar hydration pattern, in which water molecules probably bound in the N7 sites of adenines and guanines in the Crick-Hoogsteen groove, and to the methyl group of thymidines in the Watson-Hoogsteen groove. There are also some bound water molecules found at the O2 sites of thymines in both Watson-Crick and Crick-Hoogsteen grooves. (ii) In the CC.AG6 triplex the S-type sugars are always dominant in all hydrated states, whereas in MM.AG6 triplex the relative population of the N-type sugars is very close to that of the S-type between 86% and 66% of humidity. Furthermore, the sugar conformation in two partially modified triplexes (CM.AG6, and MC.AG6) are dominant by the N-type at lower humidity. This phenomenon might reflect that the degree of bound water varies among the binding sites of bases. (iii) The effect of introducing a methyl group on cytosine is to generate a spine of hydrophobic region in MM (MC and MC). The enlarging hydrophobic area not only increase the stability in solution, and also the stability in sodium hydrated films of the pyrimidine/purine/pyrimidine hairpin triplexes.

Cytosine↗
PubMed1975

Radical formation in salts of pyrimidines. II. Cytosine. HCl crystals.

Radicals produced by X-irradiation at 77 K and at 300 K of cytosine. HCl crystals have been analysed by electron spin resonance spectroscopy. Four radicals have been identified: the anion radical of the cytosine molecule, the radical resulting from H-addition at position C6, the radical resulting from H-addition at position O2, and finally a radical resulting from addition of a Cl- to nitrogen N3. Hückel molecular orbital calculations are presented, which support the hypothesis according to which in unsaturated pyrimidines the site of hydrogenation or protonation depends on the state of the molecule.

Cytosine↗
PubMed1991

The polymorphism of a cytosine anion studied by electron paramagnetic resonance spectroscopy.

Electron addition to the nucleic acid base cytosine and several derivatives was studied in frozen aqueous solution and in aqueous glasses containing 10 M glucose, 7 M BeF2, 10 M LiCl and 8 N NaOH. Electron paramagnetic resonance spectroscopy revealed that three major types of spectra are obtained which can be classified into a group D giving a doublet (ca. 1.6 mT) and a group of triplet patterns T and T1 (ca. 3.0 mT total spread) which differ slightly in coupling values but which are both distinct from D by showing the loss of one sizeable proton coupling (ca. 1.0 mT) in deuterated solvents. Varying the type of glasses and other parameters such as pH, together with modification of the cytosine exocyclic groups, indicated that the triplet patterns represent electron adducts protonated at the amino group, whereas the doublets D should probably involve N3-protonated species. The equilibrium between doublets and triplets was found to depend strongly on the presence of Li+ and Be2+ and less strongly on pH or the presence of Na+, the former group of ions inducing the triplets. It is suggested that the influence of the ions derives mostly from their strength in stabilizing the amino-protonated tautomer of the electron adducts.

Anions↗
PubMed1994

Thiocytosine as a radiation energy trap in a single crystal of cytosine hydrochloride.

Single crystals of cytosine hydrochloride with thiocytosine as an impurity were found suitable for the study of a possible new mechanism of long-range migration of energy deposited by ionizing radiation. In a crystal containing thiocytosine, two kinds of chlorine-containing paramagnetic centres are present that are completely absent in the pure cytosine. HCl crystals irradiated under the same condition. The thiocytosine molecules in conjunction with Cl- ions behave as hole traps. The centres have been characterized by EPR spectroscopy. One of the centres is derived from the cationic thiocytosine radical by interaction with a Cl- ion, and the other centre is formed by interaction of Cl. with a thiocytosine molecule. It is suggested that the transfer of an electron-loss site (a hole) in the Cl- network is the actual mechanism of the long-range energy transfer.

Crystallization↗
PubMed1996

Nature of the chlorine-centred paramagnetic species in irradiated crystals of cytosine hydrochloride doped with thiocytosine.

It has been demonstrated that the paramagnetic species formed in crystals of cytosine hydrochloride doped with thiocytosine are most likely the radicals formed by association of thiocytosine and chlorine. The unpaired electron is positively identified on the Cl atom and on at least one of the pyrimidine atoms, and the data are consistent with the formation of the 'three-electron' S-Cl sigma sigma * bonds. The spin density derived from the measured 35Cl and 14N coupling tensors compare reasonably well with the MO calculations for the 'in-plane' conformations of three hypothetical radicals formed by initial ionization of either thiocytosine or Cl- followed by their reaction. Two distinct and related centres, A and B, probably represent two different conformations of chemically the same radical in the crystal lattice of cytosine-HCL.

Chlorine↗
PubMedDate not supplied

Investigation of the kinetics of degradation of hexopyranosylated cytosine nucleosides using liquid chromatography.

Liquid chromatography was used to follow the degradation of hexopyranosylated cytosine nucleosides in buffers of acid, neutral and alkaline pH and of constant ionic strength. The compounds were found to degrade by hydrolysis to cytosine and/or by deamination to the corresponding uracil nucleosides. Degradation in acid is influenced by the number of sugar hydroxyl groups, presence of sugar double bonds and the type of anomer. Stability of some of the compounds was compared with that of related thymine nucleosides. Temperature studies support a unimolecular mechanism of hydrolysis at pH 1.22.

Buffers↗
PubMed1999

Enzyme/prodrug therapy for head and neck cancer using a catalytically superior cytosine deaminase.

The use of cytosine deaminase (CD) in conjunction with 5-fluorocytosine (5-FC) has been studied for cancer gene therapy as a means of achieving tumor-specific generation of the toxic metabolite 5-fluorouracil (5-FU). Since 5-FC is frequently used as an antifungal agent, and because it has little or no efficacy as an antibacterial agent, we hypothesized that yeast CD (YCD) might be more efficient at utilizing 5-FC as a substrate and hence be a better choice for a CD/5-FC gene therapy strategy than the typically utilized bacterial CD (BCD). To that end Saccharomyces cerevisiae CD was cloned from yeast genomic DNA and expressed in vitro. Functional analysis of BCD and YCD expressed in COS-1 cells indicated that BCD and YCD both utilized cytosine with equal efficacy; however, 5-FC was an extremely poor substrate for BCD, with an apparent catalytic efficiency 280-fold lower than that observed for YCD. Retroviral infection of tumor cell lines in vitro indicated that the IC50 of 5-FC was 30-fold lower in YCD-infected cultures as compared with cultures infected with BCD retrovirus. In addition, when SCCVII murine squamous cell carcinoma cells were infected in vitro at low rates of infection (< or =10%) there was no significant cytotoxicity toward BCD-expressing cells while there was potent cytotoxicity to both YCD-expressing cells and "bystander cells" even at this low level of expression. Finally, stable BCD- or YCD-expressing SCCVII clones were developed and used in an orthotopic immune-competent model of head and neck cancer. Subsequent treatment with 5-FC followed by monitoring of tumor growth by noninvasive magnetic resonance imaging (MRI) and survival of animals indicated a growth delay during the course of 5-FC treatment for BCD-expressing tumors, which quickly regrew at the end of treatment. In contrast, YCD-expressing tumors exhibited not only a growth delay, which was of longer duration, but also in some cases frank tumor regression and complete cures occurred.

Animals↗
PubMed1999

Inhibition of human immunodeficiency virus type 1 by Tat/Rev-regulated expression of cytosine deaminase, interferon alpha2, or diphtheria toxin compared with inhibition by transdominant Rev.

A retroviral vector was designed to express toxic proteins only in the presence of the HIV-1 Rev and/or Tat protein(s). The design of this vector incorporates an HIV-specific expression cassette that consists of three elements: the U3R region of the HIV-1 IIIB LTR provides the promoter and Tat-responsive element, a modified intron derived from the human c-src gene facilitates the splicing of inserted genes, and the HIV-1 RRE region enhances the transport of unspliced mRNAs. To further limit potential readthrough transcription, the expression cassette was inserted in the reverse transcriptional orientation relative to the retroviral vector LTR. Three different genes, interferon alpha2, diphtheria toxin (DT-A), and cytosine deaminase, were inserted into this vector. Tat and Rev inducibility was demonstrated directly by a >300-fold induction of interferon production and functionally by a decrease in colony-forming units when a Tat and Rev expression vector was titered on HeLa cells harboring the inducible DT-A cassette. The Tat-inducible cytosine deaminase gene was tested in the Sup-T1 T cell line and shown to inhibit HIV-1 production only when engineered cells were grown in the presence of 5-fluorocytosine. To test the ability of this system to inhibit HIV-1 infection in bulk PBL cultures, a series of transduction and challenge experiments was initiated with both the interferon and DT-A vectors. Protection against infection was documented against three HIV strains in PBLs. Last, the interferon and DT-A vectors were compared with a vector encoding a transdominant Rev protein and were shown to mediate equal or greater inhibition of HIV-1.

Blotting, Northern↗
PubMedDate not supplied

Specific cytosine demethylations within the first exons of the rat CYP2D3 and CYP2D5 genes are associated with activation of hepatic gene expression during development.

To investigate the mechanism of transcriptional activation of the CYP2D gene subfamily in rat liver during development, Northern blot analysis and DNA methylation tests using Hpa II and Hha I enzymes, which are sensitive to cytosine methylated DNA, were carried out. As the result of mRNA measurements, these genes were classified into two patterns of expression, (i) late-onset gene activation in which mRNA gradually increases until rats reach puberty and (ii) early-onset expression in which the peak of mRNA expression is reached within 1 week after birth. The CYP2D3 and CYP2D5 genes, representatives of late-onset and early-onset expression, respectively, were examined. A correlation was found between mRNA expression during development and demethylation of cytosine residues located at the same position in the first exons of both the CYP2D3 and CYP2D5 genes. These results suggest that specific demethylation events are associated with developmentally programmed hepatic gene activation.

Animals↗
PubMed1998

High-resolution analysis of cytosine methylation in the 5ĺong terminal repeat of retroviral vectors.

Retroviral vectors based on the Moloney murine leukemia virus (Mo-MuLV) are among the most commonly used vectors for stable gene transfer into mammalian cells. However, expression from the transcription unit of the Mo-MuLV long terminal repeat (LTR) has often been unsatisfactory. Transcriptional suppression of retroviral vectors in vitro in embryonal carcinoma (EC) cells and in vivo in hematopoietic stem cells (HSCs) has been associated with increased levels of cytosine methylation in the vector 5' LTR. To obtain a comprehensive picture of the methylation pattern in the 5' LTR of retroviral vectors, we employed the bisulfite genomic sequencing technique, which allows detection of the methylation pattern of every CpG dinucleotide in a target sequence. We studied the 5' LTR within the Mo-MuLV-based vector, LN, and a series of multiply modified vectors, which show improved expression in vitro and in vivo. Methylation patterns of the vectors were compared in PA317 (3T3-derived) fibroblasts, which are permissive for expression from all of the vectors, and in F9 embryonal carcinoma (EC) cells, which are restrictive for expression from the parental Mo-MuLV LTR but show improved expression from the modified vectors. These analyses revealed that the levels of methylation of CpG dinucleotides were globally consistent throughout the entire LTR, including the region of transcriptional factor binding. All vectors showed no measurable methylation of CpG dinucleotides throughout the 5' LTR in the PA317 fibroblasts. The CpG dinucleotides of the standard Mo-MuLV-based vector (LN) were highly methylated in F9 EC cells (49.1%). The doubly modified vector, MD-neo, which did not show improved expression, exhibited a relatively high level of methylation (45%), similar to that found in the LN vector. In contrast, the CpG dinucleotides of the triply modified vectors, which showed improved expression in EC cells (MND-neo and MTD-neo), were much less methylated (26.2 and 23.4%, respectively). The results extend our previous findings of an inverse correlation between gene expression and methylation of cytosine residues of the LTR of retroviral vectors.

Animals↗