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J Jiricny

Publications and source records attributed to J Jiricny.

99 records · Page 6Linked to original sources

Guanine and adenine analogues as tools in the investigation of the mechanisms of mismatch repair in E. coli.

The efficiency of in vivo correction of five "mismatch analogues", incorporated into M13mp9 DNA, was studied in an attempt to elucidate the structural determinants required for mismatch recognition by the repair machinery of E. coli. Inosine was efficiently removed from an I/T mismatch, presumably by the action of hypoxanthine glycosylase. The mismatch analogues DI/T (DI = 7-deazainosine), Tu/C (Tu = tubercidin), N/C (N = nebularine) and DN/C (DN = 7-deazanebularine) were left largely unrepaired, giving rise to high yields of mutant phenotype. The efficiency of correction of these mismatch analogues could be correlated with their structure within the base-pair.

Adenine↗

Restriction endonucleases HindII and TaqI cleave DNA with mismatched nucleotides within their recognition sequences.

Restriction endonucleases HindII and TaqI, but not SalI, were found to efficiently cleave synthetic hexadecanucleotide duplexes which contained either an A/C or a G/T mismatch within their respective restriction sites. Double-stranded M13 DNAs with identical mismatches were also cleaved under the assay conditions. These results suggest that the distortion of the DNA duplex, caused by these purine/pyrimidine mismatches is not sufficiently large so as to interfere with the recognition and the subsequent cleavage of the DNA by these two enzymes. HindII and SalI, but not TaqI, were furthermore shown to hydrolyze the two strands of the duplex with different rates. The differences between the mode of recognition of their respective restriction sites by these three enzymes are discussed.

Base Sequence↗

Oligonucleotide directed mutagenesis of cauliflower mosaic virus DNA using a repair-resistant nucleoside analogue: identification of an agnogene initiation codon.

Mutation of the initiation codon of the dispensible open reading frame, ORF VII, of cauliflower mosaic virus (CaMV) delayed the appearance of disease symptoms, but the mutants reverted with high frequency. This suggests a role of this start codon in viral expression. Oligonucleotide-directed mutagenesis, utilizing a novel, repair-resistant deoxyguanosine analogue, 2'-deoxy-7-deazainosine (dDI), highly improved the yield of mutants.

Base Sequence↗

In vitro secondary activation (memory effect) of avian vitellogenin II gene in isolated liver nuclei.

The vitellogenin II gene is specifically reactivated in vitro (secondary stimulation, memory effect) in purified liver nuclei that had ceased to express the gene in vivo a month after the roosters had received a single injection of estradiol (primary stimulation). The in vitro reactivation depends on the addition to the nuclei of nuclear and cytoplasmic extracts from estradiol-stimulated livers, polyamines (0.1-1.0 mM), and calmodulin (0.1 mM). Under identical incubation conditions the vitellogenin gene could not be reactivated in oviduct, embryonic, and immature chicken liver nuclei. Two other genes, those for ovalbumin and lysozyme, which are regulated by estradiol in the oviduct, could not be activated in the liver nuclei. The correct initiation of vitellogenin gene transcription in the liver nuclei was tested by primer extension studies. Addition of the antiestrogen tamoxifen (0.1 microM) to the system decreased vitellogenin mRNA synthesis by about 45% without affecting total RNA synthesis. Addition of quercetin (0.1 mM) and trans-flupenthixol (0.2 mM), inhibitors of nuclear protein kinase II and calmodulin-dependent kinase, respectively, inhibited the synthesis of vitellogenin mRNA by about 55% without affecting total RNA synthesis. The inhibitory effects of the antiestrogen and the kinase inhibitors were not additive, suggesting that both classes of inhibitor act on the same target or related targets. Depleting the estradiol receptors from the cell and nuclear extracts by means of estradiol-receptor antibodies covalently bound to Matrex beads reduced the stimulation of the vitellogenin gene by 40%. We conclude that in addition to the estradiol receptor and phosphorylation of nuclear protein(s) there are additional factors responsible for the in vitro secondary activation of the avian vitellogenin II gene.

Animals↗

Genomic sequencing reveals a positive correlation between the kinetics of strand-specific DNA demethylation of the overlapping estradiol/glucocorticoid-receptor binding sites and the rate of avian vitellogenin mRNA synthesis.

Genomic sequencing was used to study the extent of cytosine methylation of four CpG sites within the regulatory region of the estradiol-inducible avian vitellogenin II gene. Three of these sites, two of which lie within the estradiol-receptor binding site and one in a short stretch of alternating purines and pyrimidines, were initially fully methylated. Analysis of DNA isolated from liver nuclei revealed that hormone treatment of immature White Leghorn roosters resulted in a demethylation of these sites, which occurred initially in only one DNA strand. This demethylation correlated well with the induction of vitellogenin mRNA synthesis. The demethylation of the complementary DNA strand lagged approximately equal to 24 hr behind. The fourth CpG, located within an overlapping glucocorticoid-receptor binding site, was already hemimethylated at the onset of the experiment. The demethylation of this site also occurred with kinetics similar to the rate of vitellogenin mRNA synthesis. All four CpGs remained demethylated even after cessation of gene transcription. A comparison of the methylation state of these four sites in DNA from different tissues demonstrated a clear dependence of the demethylation on estradiol. Our results suggest that this hormone-dependent event occurs via an active pathway through excision repair and/or enzymatic demethylation.

5-Methylcytosine↗

A nuclear Overhauser enhancement study on the imino proton resonances of a DNA pentadecamer comprising the specific target site of the cyclic AMP receptor protein in the ara BAD operon.

A 500 MHz 1H-NMR study on a synthetic DNA pentadecamer comprising the specific target site of the cAMP receptor protein in the ara BAD operon is presented. Using pre-steady state NOE measurements, unambiguous assignments of all the imino proton resonances and associated adenine (H2) resonances are obtained. From the NOE data interbase pair interproton distances involving the imino and adenine (H2) protons are determined. It is shown that these distances are very similar to those expected for classical B DNA (RMS difference of 0.5 A), but are significantly different from those expected for classical A DNA (RMS difference of 1.1 A).

Adenine↗

Modified SV40 for analysis of mismatch repair in simian and human cells.

We have developed a way of introducing specific mispairs into the genome of simian virus 40 and of determining the fate of the mispaired bases in simian and human cells. Mispairs are introduced into viral DNA within the intron of the gene coding for the large T antigen. Each DNA molecule harbors a single mispair in a defined orientation. Transfection of mismatch-containing SV40 DNA into host cells yields plaques, each corresponding to a productive infection initiated by a single viral DNA molecule. Isolation of DNA derived from individual plaques and determination of the DNA sequence at the site of the mispair reveals whether correction occurred and what the repair products are. Here we describe repair patterns for G/T and A/C mispairs in CV-1 African green monkey kidney cells, and for G/T mispairs in human fibroblasts derived from 3 normal individuals, 1 patient with xeroderma pigmentosum (complementation group A), and 3 patients with Bloom's syndrome. G/T mispairs, which arise in resting DNA through the deamination of 5-methylcytosine (mC) to form thymine, are corrected in all cases with extremely high efficiency and nearly always in favor of guanine. In contrast, A/C mispairs are corrected randomly and relatively inefficiently in simian cells.

Animals↗

An enhancer-like sequence within the Xenopus U2 gene promoter facilitates the formation of stable transcription complexes.

Enhancers are eukaryotic promoter elements that increase transcriptional efficiency in a manner relatively independent of their position and orientation with respect to a nearby gene. There is growing evidence that enhancer action is mediated by transacting factors, but the mode of action of these factors is not yet known. We report here on the Xenopus U2 gene promoter, which contains two sequence elements. The distal sequence element increases promoter activity 20-fold by facilitating the formation of stable transcription complexes. A synthetic 14-base-pair (bp) oligonucleotide corresponding to part of the distal sequence element, which shows homology to an immunoglobulin gene promoter element and to both the simian virus 40 (SV40) and the immunoglobulin heavy-chain gene enhancers, stimulates transcription in an orientation-independent manner.

Animals↗