Nuclease sensitivity

Except for histone H4, each of the other histone types are found in different isoforms and are called histone variants. The chapter by Pehrson (Chapter 8) will provide a more in-depth discussion of these forms. It is worth pointing out that with regard to transcription through nucleosomes, some of these variants are expressed in a replication-independent process and are found in active gene fractions that have been prepared using the nuclease-sensitive solubilization procedures described above. Of particular note are two minor histone variants, H2A.Z and H3.3. Both are expressed throughout the cell cycle and incorporated into the nucleosomes of active genes ([38,39], see reviews [46,47]). For example, both Tetrahymena, H2A.Z (termed Tetrahymena hvl) and an H3.3-like histone (hv2) are preferentially present in the active macronucleus and are expressed in the micronucleus just prior to the time when this nucleus becomes transcriptionally active [48,49]. Suto et al. [50] have determined the crystal structure of a nucleosome... 

The mechanisms involved in gene aclivatinn and inactivation are major problems in biology, so that transient, or permanent structures associated with such phenomena will continue to attract much attention. There is now evidence for changes in chromatin structure at chromosome sites prior to their becoming transcriptionally active nuclease sensitive sites, enhancers, and promolerx have also been identified at various loci. 

Martin-Bertram 1981,1982 Martin-Bertram et al. 1983 for DNA isolated from y-irradiated yeast cells see Andrews et al. 1984). While such lesions, detected by SI nuclease ( Sl-nuclease-sensitive sites ), are not observed with A phage DNA y-irradiated in aqueous solutions (Martin-Bertram et al. 1984), they become prominent when the solutions is highly scavenged (Junker et al. 1984). Under such conditions, the damage caused by the direct effect plays a role because the indirect effect is largely suppressed (Ward 1981). 

Andrews J, Martin-Bertram El, Elagen U (1984) SI nuclease-sensitive sites in yeast DNA an assay for radiation-induced base damage. Int J Radiat Biol 45 497-504 Antoku S (1983) Radiosensitization and radioprotection of E. coli by thiourea in nitrous oxide saturated suspensions. Int J Radiat Biol 43 451-458... 

Junker B, Martin-Bertram H, Hagen U (1984) Distribution of Si-nuclease sensitive sites and doublestrand breaks iny-irradiated A-DNA. Int J Radiat Biol 46 675-679 Kan Y, Schuster GB (1999a) Radical cation transport and reaction in triplex DNA long-range guanine damage. J Am Chem Soc 121 11608-11614... 

Bielinska, A.U., Kukowska-Latallo, J.F. and Baker, Jr., J.R. (1997) The interaction of plasmid DNA with polyamidoamine dendrimers mechanism of complex formation and analysis of alterations induced in nuclease sensitivity and transcriptional activity of the complexed DNA. Biochim. Biophys. Acta., 1353,180-190. 

Both probes used to monitor structural changes in DDP-modified DNA - (1) the mobility of c s DNA in gel electrophoresis and (2) SI nuclease sensitivity - clearly cuid consistently indicate differences in the mode of binding for the cis- and trans-DDP isomers ... 

Many techniques besides NMR and crystallography may be used to study G-quadruplex formation, for example circular dichroism, Raman spectroscopy, electrophoresis, nuclease sensitivity, chemical probing and calorimetry. However, tetra, bi- and intramolecular quadruplexes behave quite differently, and their folding kinetics require specific experimental constraints. To summarize ... 

Chromatin remodeling, nucleosome remodeling, and nucleosome disruption are general terms that have been used to summarize a number of changes in chromatin structure. Often, these terms are used to define any event that alters the nuclease sensitivity of a region of chromatin, as nuclease sensitivity is a frequendy used marker of changes in chromatin structure. However, there have been other in vitro assays devised to... 

Hache, R.J.G. Deeley, R.G. (1988). Organization, sequence and nuclease sensitivity of repetitive elements flanking the chicken apoVLDUI gene extended Similarity to elements flanking the chicken vitellogenin gene. Nucl. Acids Res., 16, 97-113. 

To assess whether the results obtained with Ho33342 related to some innate feature of cellular chromatin, namely accessibility, permeabilised cells were exposed to a low level of DNase II (under conditions which produced a linear relationship between enzyme concentration and break frequency) and accessibility monitored as the frequency of enzyme-induced DNA strand-breaks. The results (Table 1) show that nuclease sensitivity correlated with the frequency of ligand-induced breaks. 

We emphasize that the distinction between nuclease sensitivity and hype sensitivity is not merely a semantic one. During the activation of gene expression in vivo, it is quite likely that as a first step, a large stretch of chromatin undergoes some stmctural transition to a more accessible conformation (it is possible that such a transi-... 

R. H. Heflich, D. J. Dorney, V. M. Maher, and J. J. McCormick, Reactive derivatives of benzo(a)pyrene and 7,12-dimethylbenz(a)anthracene cause Si nuclease sensitive sites in DNA and UV-like repair, Biochem. Biophys. Res. Commun. 77, 634-641 (1977). 

Latimer, L. J. P, Hampel, K, and Lee, J S (1989) Synthetic repeating sequence DNAs containing phosphorothioates nuclease sensitivity and triplex formation. Vmc/ Acids Res 17, 1549-1561. 

Single base pair mismatches, particularly dA dG or dG - dG, are inefficiently cleaved by nuclease SI (13,14). The nuclease sensitivity increases gradually as the mismatching length increases from 1 to 6 nt. Yet the cleavage at 4-bp mismatches occurs incompletely, and the efficiency varies depending on mismatching sequences (4). 

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