Formal Methods for Designing Clean Processes

Johns, W.R.

doi:10.1007/978-3-642-79940-2_5

Cited by 5 publications

(5 citation statements)

References 3 publications

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“…After precipitation with 20% TCA on ice, cells were washed twice with 5% TCA, twice with ethanol, and once with diethyl ether. The entire H1 histone fraction was isolated by overnight extraction in 0.2 M H 2 SO 4 followed by a second extraction in 10% (w/v) PCA (Johns, 1977).…”

Section: Methodsmentioning

confidence: 99%

“…Isolation of H1 Histone in Its Poly(ADP-ribose)-Free Isoform. To obtain the poly(ADP-ribose)-free isoform of H1 histone, mouse fibroblasts (at a cell density of 20 × 10 6 cells/175 cm 2 flask) were preincubated for 24 h with 3ABA, and the H1 histone was isolated by overnight extraction of cells in 0.2 M H 2 SO 4 followed by a second extraction in 10% (w/v) PCA (Johns, 1977).…”

Section: Methodsmentioning

confidence: 99%

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Does Poly(ADP-ribosyl)ation Regulate the DNA Methylation Pattern?

et al. 1997

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The existence of a possible correlation between poly(ADP-ribosyl)ation and DNA methylation processes was investigated. In vivo and in vitro experiments were carried out on L929 mouse fibroblasts preincubated for 24 h with or without 3-aminobenzamide, a well-known inhibitor of poly(ADP-ribose) polymerase. Both experimental approaches evidenced a close relationship between these two important nuclear enzymatic mechanisms, suggesting that the poly(ADP-ribosyl)ated isoform of H1 histone and/or long and branched protein-free ADP-ribose polymers could act as protecting agents against full methylation of the CpG dinucleotides in genomic DNA.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Does Poly(ADP-ribosyl)ation Regulate the DNA Methylation Pattern?

et al. 1997

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“…H1) are very lysine rich, whereas others are slightly arginine rich (e.g. H3 and H4) (16,17). Other examples include nucleases (18) and antiterminators (19).…”

Section: Introductionmentioning

confidence: 99%

Synthesis and hybridization analysis of a small library of peptide- oligonucleotide conjugates

Harrison

1998

Nucleic Acids Research

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A small library of 49 peptide-oligonucleotide conjugates were synthesized to explore the influence of various peptide side chains on the hybridization properties of the DNA. An invariant 8mer oligonucleotide was coupled to a peptide portion that contained a five residue variable region composed of the cationic amino acids lysine, ornithine, histidine and arginine, the hydrophobic amino acid tryptophan, and alanine as a spacer. Melting temperature analysis indicated that T m depended principally on the number of cationic residues. The free energies of binding for polycationic peptide-oligonucleotides were enhanced compared with the unmodified 8mer. The origin of this stabilizing effect was found to be derived from a more exothermic enthalpic term. Improvement in Delta G vH was found to depend on the presence of positive charge and also the exact identity of the cationic amino acid, with the polyarginine peptide giving the most favourable Delta G vH value and the most exothermic Delta H vH. Further exploration suggested that the cationic peptide fragments interacted mainly with single-stranded rather than duplex DNA. A study of pH dependence showed that the polyhistidine conjugate was particularly sensitive to pH changes near neutrality, as indicated by a significant rise in T m from 19.5 degrees C at pH 8.0 to 28.5 degrees C at pH 6.0.

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“…The supernatant was pelleted with 6 vol of acetone. The pellet, resuspended in water, was reextracted in 10% perchloric acid (w/v), according to Johns (19).…”

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confidence: 99%

In Vitro Induction of H1−H1 Histone Cross-Linking by Adenosine Diphosphate−Ribose Polymers

et al. 2000

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It is well-known that H1-H1 interactions are very important for the induction of 30 nm chromatin fiber and that, among all posttranslational modifications, poly(ADP-ribosyl)ation is one of those capable of modifying chromatin structure, mainly through H1 histone. As this protein can undergo both covalent and noncovalent modifications by poly(ADP-ribosyl)ation, our aim was to investigate whether and how ADP-ribose polymers, by themselves, are able to affect the formation of H1-H1 oligomers, which are normally present in a condensed chromatin structure. The results obtained in our in vitro experimental system indicate that ADP-ribose polymers are involved in chromatin decondensation. This conclusion was reached as the result of two different observations: (a) H1 histone molecules can be hosted in clusters on ADP-ribose polymers, as shown by their ability to be chemically cross-linked, and (b) H1 histone has a higher affinity for ADP-ribose polymers than for DNA; ADP-ribose polymers compete, in fact, with DNA for H1 histone binding.

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Formal Methods for Designing Clean Processes

Cited by 5 publications

References 3 publications

Does Poly(ADP-ribosyl)ation Regulate the DNA Methylation Pattern?

Does Poly(ADP-ribosyl)ation Regulate the DNA Methylation Pattern?

Synthesis and hybridization analysis of a small library of peptide- oligonucleotide conjugates

In Vitro Induction of H1−H1 Histone Cross-Linking by Adenosine Diphosphate−Ribose Polymers

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