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PubMed1986

500-MHz 1H NMR study of poly(dG).poly(dC) in solution using one-dimensional nuclear Overhauser effect.

Secondary structures of poly(dG).poly(dC) and poly(dG).poly(dm5C) in solution are determined by nuclear Overhauser effect (NOE) measurements on GH8-deuterated and -nondeuterated DNAs with low presaturation pulse lengths (10-25 ms) and low-power and prolonged accumulations in the range of 50,000-72,000 scans. Under these conditions, the NOE difference spectra were free from diffusion. Primary NOEs between base protons GH8/CH6 and sugar protons H1', H2'/H2'', and H3' suggest that in poly(dG).poly(dC) both guanine and cytosine nucleotides adopt a C3'-endo, low anti X = 200-220 degrees conformation. Computer modeling of the NOE data enable identification for the first time, in terms of the geometry of the nucleotide repeat, handedness, and helix geometry, of the structure of poly(dG).poly(dC) to be the A form, and the derived structure for the polymer duplex is very close to the single crystal structure of the double-helical d-GGGGCCCC [McCall, M., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 183, 385-396]. Similar nuclear Overhauser effect data on poly(dG).poly(dm5C) revealed that G and m5C adopt a C2'endo, anti X = 240-260 degrees conformation, which indicates that this DNA exhibits the B form in solution. In summary, the results presented in this paper demonstrate that methylation of cytosines in poly(dG).poly(dC) causes A----B transition in the molecule.

Hydrogen↗
PubMed2002

Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase.

Gene silencing in eukaryotes is associated with the formation of heterochromatin, a complex of proteins and DNA that block transcription. Heterochromatin is characterized by the methylation of cytosine nucleotides of the DNA, the methylation of histone H3 at lysine 9 (H3 Lys 9), and the specific binding of heterochromatin protein 1 (HP1) to methylated H3 Lys 9 (refs 1-7). Although the relationship between these chromatin modifications is generally unknown, in the fungus Neurospora crassa, DNA methylation acts genetically downstream of H3 Lys 9 methylation. Here we report the isolation of KRYPTONITE, a methyltransferase gene specific to H3 Lys 9, identified in a mutant screen for suppressors of gene silencing at the Arabidopsis thaliana SUPERMAN (SUP) locus. Loss-of-function kryptonite alleles resemble mutants in the DNA methyltransferase gene CHROMOMETHYLASE3 (CMT3), showing loss of cytosine methylation at sites of CpNpG trinucleotides (where N is A, C, G or T) and reactivation of endogenous retrotransposon sequences. We show that CMT3 interacts with an Arabidopsis homologue of HP1, which in turn interacts with methylated histones. These data suggest that CpNpG DNA methylation is controlled by histone H3 Lys 9 methylation, through interaction of CMT3 with methylated chromatin.

Amino Acid Sequence↗
PubMed1986

Periodate-oxidized adenosine induction of murine thymidine kinase: role of DNA methylation in the generation of tumor cell heterogeneity.

We previously reported that thymidine kinase (TK) activity in a spontaneously TK-deficient (TK-) murine tumor cell line (called L61-M) could be partially restored following brief treatment of the cells in vitro with the potent DNA-hypomethylating agent 5-azacytidine. We now show here that similar results may be obtained by exposing cells in vitro to periodate-oxidized adenosine, a potent inactivator of the S-adenosylhomocysteine hydrolase enzyme. The ability of periodate-oxidized adenosine to induce TK activity within the L61-M cell line was dependent upon the concentration of drug used and the treatment period. Inhibiting DNA synthesis completely prevented the effects of periodate-oxidized adenosine from being observed. Periodate-oxidized adenosine had no obvious mutagenic effect upon the L61-M cell line and had a slight but significant inhibitory effect upon the methylation of the cytosine nucleotides which were incorporated into DNA during the treatment period. These results suggest that during tumor development, alterations in the relative levels of S-adenosylhomocysteine and S-adenosylmethionine may lead to the inhibition of DNA methylation, resulting in the activation of previously quiescent genes, thereby promoting the phenotypic diversification of tumor cell populations as well as their progression from a relatively benign to a highly malignant state.

5-Methylcytosine↗
PubMed1971

Inhibitory effects and metabolism of 5-fluoropyrimidine derivatives in pneumococcus.

5-Fluorouracil (FU), 5-fluorocytosine, and the riboside and deoxyriboside derivatives of these fluoropyrimidines each exhibit a different spectrum of inhibitory effects in pneumococci. The biochemical basis of this finding seems to be the extremely low level of nucleoside phosphorylase (hydrolase) and N-trans-deoxyribosylase activity in pneumococcus and the consequent, relatively limited metabolic interconversion of the different fluoropyrimidines, which can therefore selectively affect one or the other of the several drug-sensitive biochemical reactions in this bacterium. Special attention was paid to the effect of fluoropyrimidines on the metabolism of cytosine and thymidine. In spite of the fact that FU is converted to both fluorouridine triphosphate and fluorocytidine triphosphate, only fluorouridylate but no fluorocytidylate can be detected in the ribonucleic acid Exogenous FU and fluorouridine also inhibit the synthesis of cytosine nucleotides from supplied uridine in a pyrimidine auxotroph. Thymidine was found to be a poor reversing agent for any of the fluoropyrimidine inhibitions. In both the wild type and in a thymidine-requiring (thymidylate-synthetase deficient) mutant, growing with supplied thymidine in the medium, fluorodeoxyuridine (FUdR) treatment caused cell death and inhibition of the incorporation of radioactive thymidine, adenosine, or uracil into deoxyribonucleic acid. It is suggested that FUdR (or a metabolic derivative) inhibits the transport of phosphorylation of thymidine in this microorganism.

Aluminum↗
PubMed2004

Genetic variety of bovine viral diarrhea virus 2 strains isolated from sheep.

Bovine viral diarrhea virus 2 (BVDV-2) strains, isolated from sheep showing clinical symptoms of border disease, have been evaluated by the palindromic nucleotide substitution (PNS) method at the three variable loci (V1, V2 and V3) in the 5'-untranslated region (UTR) of genomic RNA. The characteristic two base-pairings common to the BVDV-2 species, a C-G pairing which was common to the V1 locus, and a G*U pairing common to the V2 locus, were observed in all tested strains. Strains BD-78 and C413 were identified by a unique C-G pairing at position 4 from the bottom of the V2 stem region, which is characteristic to BVDV-2b. BVDV-2d characteristic U-A pairing at position 18 of the V1 stem region was observed in five strains, Lees, 167 237, 168 149, 173 157 and 175 375. No strains have been assigned to the genotypes BVDV-2a or BVDV-2c. Furthermore, the investigation at the level of the 5'-UTR excluded the application in sheep of the proposed BVDV-2 genetic virulence markers described in cattle. The two specific positions of uracil and cytosine nucleotides related to low or high virulence where indifferently present in the ovine BVDV-2 strains responsible of border disease.

Animals↗
PubMed1995

Formation of 1,N6-ethenoadenine and 3,N4-ethenocytosine by lipid peroxidation products and nucleic acid bases.

Lipid peroxidation (LPO) products are known to interact with DNA, yielding several types of adduct with nucleobases. In this study, we demonstrate the formation of two ethenobase adducts, 1,N6-ethenoadenine and 3,N4-ethenocytosine, by reaction of LPO products with nucleic acid bases. Rat liver microsomes were incubated at 37 degrees C for 30 min in the presence of inducers of LPO [Fe(II) or cumene hydroperoxide] and adenine or cytosine nucleotides or nucleosides, followed by further heating at 80 degrees C for 30 min to complete the reactions. The etheno adducts detected after immunoaffinity chromatography were 1,N6-etheno-cAMP and 1,N6-etheno-2'-deoxyadenosine (HPLC/fluorimetry), 3,N4-etheno-2'-deoxycytidine (competitive radioimmunoassay), and 1,N6-etheno-2'-deoxyadenosine 3'-monophosphate and 3,N4-etheno-2'-deoxycytidine 3'-monophosphate (32P-postlabeling). Incubation of arachidonic acid supplemented with Fe(II) also led to the formation of the 1,N6-etheno adduct from cAMP. LPO intermediates that may be involved are discussed. These data suggest that etheno adducts may be markers of DNA damage associated with LPO.

Adenine↗
PubMed2005

Case of progressive dysplasia concomitant with intralesional cidofovir administration for recurrent respiratory papillomatosis.

Recurrent respiratory papillomatosis (RRP) is characterized by benign wartlike growths in the larynx with occasional spread to the lungs. A broad range of therapeutic measures have been used to treat RRP; the primary treatment is laser vaporization of the lesions. Recurrences of the disease are common, and alternate methods of treatment are being used to prevent recurrence, including cidofovir. Cidofovir is a cytosine nucleotide analog with antiviral properties that is approved by the US Food and Drug Administration for treatment of cytomegalovirus retinitis and is currently being used off-label for RRP. Cidofovir has gained initial success in slowing the rate of disease recurrence when used at the time of surgery. However, the use of cidofovir lends concern to several adverse side effects, including the potential for carcinogenesis. We report here a 28-year-old woman who was treated with intralesional cidofovir at the time of surgery over the span of 27 months. The initial pathology results demonstrated benign disease with progression to severe dysplasia during the treatment time. Cidofovir's potential for carcinogenicity remains largely undefined, and thus, we are currently undertaking a project involving the evaluation of sequential paraffin-embedded samples of resections from a large cohort of patients with RRP treated at the University of Iowa Hospitals and Clinics.

Adult↗
PubMed2006

Down-regulation of radioresistance by LexA2 in Deinococcus radiodurans.

The extremely radioresistant bacterium Deinococcus radiodurans contains two LexA homologues (LexA1 and LexA2) that are possible transcriptional regulators associated with the DNA damage response. In this study, resequencing revealed that there was an additional cytosine nucleotide (nucleotide position 612) in the D. radiodurans lexA2 gene. Purified LexA2 possessed proteolytic activity that could be stimulated by RecA. In an effort to gain an insight into the role of LexA2 in the radiation response mechanism, recA, lexA1 and lexA2 disruptant strains were generated and investigated. The intracellular level of RecA increased in lexA1 and lexA2 disruptant strains following gamma-irradiation as in the wild-type strain. These results indicated that the two LexA homologues did not possess functional overlap regarding the induction of RecA. The lexA2 disruptant strains exhibited a much higher resistance to gamma-rays than the wild-type strain. Furthermore, a luciferase assay showed that pprA promoter activation was enhanced in the lexA2 disruptant strain following gamma-irradiation. The pprA gene encoding the novel radiation-inducible protein PprA plays a critical role in the radioresistance of D. radiodurans. The increase in radioresistance of the lexA2 disruptant strain is explained in part by the enhancement of pprA promoter activation.

Amino Acid Sequence↗
PubMed2001

Electrophoretic behaviour of oligonucleotides and mono-, di- and triphosphate nucleotides by capillary zone electrophoresis.

A systematic investigation has been made into the mechanisms of the capillary zone electrophoresis (CZE) separation of 12 common nucleotides (mono-, di- and triphosphorylated) and polydeoxythymidylic acid oligonucleotides (pd(T)5-18) using electrophoretic mobility values calculated from migration time data. Relationships between electrophoretic mobility and the physicochemical characteristics of the analytes (charge, dissociation constants, charge-to-mass ratio) and the background electrolyte conditions (buffer strength, percentage organic modifier and buffer pH) were characterised. Nucleotide migration was dominated by the negatively charged phosphate groups. Additionally, there were important contributions to migration behaviour from the ionised amide groups of the nucleobases guanine and uracil at higher buffer pH values or with the presence of methanol in the electrolyte. Calculated electrophoretic mobility values for the nucleotides showed a substantially improved (5-fold) inter-run repeatability compared with migration time data. These studies show the value of representing nucleotide migration data as electrophoretic mobility in CZE for obtaining a more thorough analysis of separation mechanisms and to compensate for variation in migration time data caused by small changes in electrosmotic flow. Oligonucleotides pd(T)5-11 could be adequately resolved from their nearest neighbour, but the limit of single-base separation was pd(T)10 from pd(T)11 under the conditions used. It was calculated that a difference in charge-to-mass ratio of 2.64 x 10(-5) was required for resolution under the CZE conditions used.

Adenine Nucleotides↗
PubMed2002

No evidence for hypermethylation of the hSNF5/INI1 promoter in pediatric rhabdoid tumors.

The hSNF5/INI1 gene on chromosome 22 has been implicated as a tumor suppressor gene in pediatric rhabdoid tumor, an aggressive malignancy that generally occurs in the first two years of life. The most common sites for tumor development are the brain and kidney. We and other investigators have identified deletions and mutations of the INI1 gene in the majority of rhabdoid tumors of the central nervous system, kidney, and extrarenal tissues. At least 20% of cases do not have genomic alterations of INI1, although expression at the RNA or protein level may be decreased. The aim of this study was to determine whether hypermethylation or mutation of the 5' promoter region of INI1, or hypermethylation of CpG dinucleotides in a GC-rich repeat region within the first intron, could account for the decreased expression of INI1 observed in these tumors. We employed bisulfite modification, polymerase chain reaction, and sequence analysis to determine the methylation status of the cytosine nucleotides in the predicted promoter region of the INI1 gene, and two GC repeat regions in intron 1. DNA from 24 tumors with or without coding-sequence mutations was analyzed. None of the tumors demonstrated methylation of the promoter or intron 1 regions. This mechanism is unlikely to account for the inactivation of INI1 in rhabdoid tumors without coding-sequence mutations. One tumor demonstrated a potential mutation in the promoter region, but further studies are required for determining its functional significance.

5' Untranslated Regions↗
PubMed1998

Genomic organization and chromosomal localization of the human sepiapterin reductase gene.

Sepiapterin reductase (SPR) catalyzes the final step of the biosynthetic pathway of tetrahydrobiopterin, which is an essential cofactor for aromatic amino acid hydroxylases and nitric oxide synthases. To aid the analysis of any possible human diseases caused by mutations in SPR, we have cloned and characterized the human SPR gene. The gene is composed of three exons spanning approximately 4 kilobases. The transcriptional starting point was determined around the cytosine nucleotide at position -81 by primer extension and RT-PCR analyses. There was no typical TATA-box within 300 bp from the transcriptional starting point. We found the Sp1-binding consensus sequence in the 5'-flanking region. The human SPR gene was mapped to chromosome band 2p13 by fluorescence in situ hybridization.

Alcohol Oxidoreductases↗
PubMed2001

Typing of IS 1311 polymorphisms confirms that bison (Bison bison) with paratuberculosis in Montana are infected with a strain of Mycobacterium avium subsp. paratuberculosis distinct from that occurring in cattle and other domesticated livestock.

Isolates of Mycobacterium avium subsp. paratuberculosis from nine bison (Bison bison) from Montana, United States of America, were compared with those from other species from the United States of America. All 16 isolates had a novel IS 1311 genotype in which all copies of the element possessed a thymidine-cytosine nucleotide variation at base position 223. Isolates from bison were termed B strain. Thirteen isolates from cattle and goats were polymorphic at this locus, a status previously recognised in isolates from cattle which are termed C strains. Differences in cultural phenotype between B and C strains which were noted upon primary isolation did not manifest upon subculture to Herrold's egg yolk medium or modified Middlebrook 7H10 agar. Rapid differentiation of these strains from each other and from S strains from sheep is possible using polymerase chain reaction and restriction endonuclease analysis. The epidemiology of paratuberculosis in bison in Montana appears to be distinct from that in cattle and other farmed livestock investigated thus far.

Animals↗
PubMed1994

Myotonic dystrophy and limb girdle muscular dystrophy in one family.

A family is reported in which a 29-year-old woman showed the clinical features of myotonic dystrophy while her 26-year-old brother presented with the clinical picture of limb girdle syndrome. In the affected female, direct genetic testing for the specific myotonic dystrophy mutation on chromosome 19 revealed abnormal expansion of a repeat unit containing the three nucleotides cytosine, thymine, and guanine (CTG)-typical for myotonic dystrophy-while her diseased brother displayed two normal alleles. This supports the hypothesis of the extremely rare occurrence of two clinically and genetically different myopathies in one family. Genetic analysis of six other family members showed that the father of the diseased siblings as well as all of his three brothers and sisters had a pathological CTG repeat expansion, and that the other two family members tested had a normal allelic pattern. The number of CTG repeats in the diseased women was approximately tenfold higher than in her asymptomatic relatives who revealed an abnormal allelic pattern. The increase in CTG repeats with transmission to a subsequent generation in this family was paralleled by a dramatic increase in the severity of myotonic dystrophy.

Adult↗
PubMed2006

Functional inference of the methylenetetrahydrofolate reductase 677C > T and 1298A > C polymorphisms from a large-scale epidemiological study.

Two functional single nucleotide polymorphisms, 677C > T and 1298A > C have been described for the methylenetetrahydrofolate (MTHFR) gene. Both are associated with reduced enzyme activity in vitro. For the 677T, but not the 1298C allele, significantly lower serum folate and higher plasma total homocysteine (tHcy) have been reported. We genotyped 10,034 middle-aged (50-64 years old) subjects and measured serum folate and tHcy. Within strata of 677 genotypes, 1,298 genotypes had significantly different serum folate and tHcy (P < or = 0.03 for all comparisons). Each additional 1298C allele reduced mean serum folate and increased mean tHcy, by (on average) 4.5 and 3.0%, respectively. In comparison, within strata of 1,298 genotypes, the increase from no, to one 677T-allele reduced serum folate and increased tHcy by, 7.1 and 6.3%, respectively. Lowest serum folate and highest tHcy level was found for the 677TT/1298AA genotype. The difference in tHcy was significantly larger at low folate than at high folate when genotypes 677TT/1298AA and 677CT/1298AA, 677CT/1298AC and 677CC/1298AC, and genotypes 677CT/1298AC and 677CT/1298AA were compared. We interpreted these data in the context of a model of the MTHFR enzyme that describes the enzyme as a dimer that mainly exist in six different configurations. The model reconciled the observed phenotypic effects of the 677/1,298 combination genotypes with previous in vitro measurements, and identified enzyme configurations that are sensitive to low folate levels. In conclusion, this report demonstrates functional inference of the MTHFR 677 C > T and 1,298 A > C polymorphisms from a large-scale epidemiological study.

Adenine Nucleotides↗