Site-Specific Chemical Modification of B-Z Junctions in Supercoiled DNA as Detected by Nuclease SI Digestion, Inhibition of Restriction Cleavage and Nucleotide Sequencing

Nejedlý, Karel; Matyášek, Roman; Paleček, Emil

doi:10.1080/07391102.1988.10507712

Cited by 15 publications

(3 citation statements)

References 30 publications

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“…There are several possible mechanisms for the formation of stable alkaline-sensitive sites in nuclear DNA that involve base modification (12,14). However, Si-hypersensitive sites have been associated with changes in DNA conformation most clearly marked by B-Z transition segments (15,16). These transition segments are linked with the appearance of abrupt changes in helical arrangement introduced by repeating structures such as homopurine or homopyrimidine segments.…”

mentioning

confidence: 99%

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Tomei

Shapiro

Cope

1993

Proc. Natl. Acad. Sci. U.S.A.

153

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Apoptosis in embryonic C3H/10T/2 (done 8) cells is marked by specific changes in morphology and DNA fragmentation that differ from those found in apoptotic thymocytes. These results demonstrate that ultrastructural changes within the nucleus associated with endonucleolytic degradation are linked with structural degradation at higher levels of chromatin organization. Strand modifications within the internucdeosomal linker region are shown to involve alkaline-sensitive sites that appear to be sensitive to Si endonudease. Our results suggest that apoptosis is not dependent upon internucleosomal cleavage and may reveal the penultimate step and the nature of the metabolic cascade that leads to cell death.Apoptosis is a term originally proposed by Kerr, Wyllie, and Currie (1) to describe a process of controlled cell deletion in tissues following either physiological or pathological stimuli. The concept of apoptosis implies that a common metabolic pathway leading to cell death may be initiated by a wide variety of signals, including hormones, serum growth factor deprivation, chemotherapeutic agents, and ionizing radiation (2)(3)(4)(5)(6). Understanding this process of apoptosis is critical to understanding the mechanisms of cell death common to embryonic development, cellular immunology, and protection against the expression of heritable genotypic changes in cells linked with mutagenesis and carcinogenesis (see ref. 7).Much of the basic research on apoptosis has focused upon the phenomenon as it occurs in thymocytes and lymphocytederived cell lines. Perhaps the most widely accepted markers of apoptotic cell death are morphological changes observed by electron microscopy (EM) and the nonrandom nature of the fragmentation of nuclear DNA. We have focused our research on the study of regulation of cell proliferation and death as it is expressed in the pluripotent, untransformed mouse embryonic cell, C3H/1OTY2 clone 8 (10T1/2). Previ-ously published evidence has shown that this cell exhibits the ability to modulate proliferation, differentiation, and death. Its phenotype is subject to transformation by various physical and chemical agents and it has been used to study the process of multistage carcinogenesis in vitro (see ref. 8).There has been considerable debate over the precise role of DNA fragmentation in apoptosis and the mechanism by which the integrity of the genome is irreversibly damaged.This report demonstrates that apoptosis does not require double-strand DNA cleavage in the internucleosomal linker region and that apoptosis in the 1OTY2 cell is marked by specific changes in morphology and DNA fragmentation unlike that in thymocytes. Our results suggest that ultrastructural changes previously associated with apoptosis are actually linked with DNA structural degradation at levels ofDNA organization above that of the nucleosome. Furthermore, although it is generally assumed that DNA degradation in apoptotic cells progresses through a series of steps or metabolic cascade, the evidence presented here demonstr...

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mentioning

confidence: 99%

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Tomei

Shapiro

Cope

1993

Proc. Natl. Acad. Sci. U.S.A.

153

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“…The pAT32 plasmid (a pUC19 derivative containing a (dAdTh6 insert cloned into the SmaI site; [3]) was isolated from chloramphenicol amplified cells as described previously [16].…”

Section: Plasmid Dnamentioning

confidence: 99%

Supercoil‐stabilized left‐handed DNA in the plasmid (dA‐dT)₁₆ insert formed in the presence of Ni²⁺

1989

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The (dA-dT)~o insert of the plasmid pAT32 was probed with diethyl pyrocarbonate (DEPC) and nuclease Bal31 in the presence of Ni 2+ known to be able to induce transition to left-handed conformation in the synthetic poly(dA-dT).poly (dA-T). It has been shown that this insert in a supercoiled plasmid displays a DEPC modification pattern characteristic of left-handed DNA under conditions not sufficient to induce a left-handed structure in the linear plasmid and poly(dA-dT) • poly(dA-T).

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“…[1][2][3][4][5]). The results of these studies contribute to a further understanding of how DNA can be protected from the enzyme-catalyzed hydrolysis.…”

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confidence: 99%

Restriction‐enzyme cleavage of DNA modified by platinum(II) complexes

Brabec

Balcarová

1993

European Journal of Biochemistry

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The effect of binding of cis-diamminedichloroplatinum(II), its trans isomer and diethylenetriaminechloroplatinum(I1) chloride to DNA on the splicing effectiveness of BamHI, EcoRI and SalI restriction endonucleases has been determined by means of gel electrophoresis. All three platinum complexes inhibit the cleavage of linearized plasmid DNA. In addition, the three platinum complexes bound to DNA constitute a barrier across which the linear diffusion of EcoRI on DNA is difficult. We interprete these findings to mean that the splicing effectiveness of restriction enzymes is influenced by bifunctional and monofunctional DNA adducts of platinum via both steric interference and DNA conformational distortions. Whereas the platinum adducts in the restriction sites or in their very close proximity inhibit the cleavage, the lesions occurring a greater distance from the restriction site can slow down the process of the localization of recognition sequences.

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Site-Specific Chemical Modification of B-Z Junctions in Supercoiled DNA as Detected by Nuclease SI Digestion, Inhibition of Restriction Cleavage and Nucleotide Sequencing

Cited by 15 publications

References 30 publications

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Supercoil‐stabilized left‐handed DNA in the plasmid (dA‐dT)₁₆ insert formed in the presence of Ni²⁺

Restriction‐enzyme cleavage of DNA modified by platinum(II) complexes

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Site-Specific Chemical Modification of B-Z Junctions in Supercoiled DNA as Detected by Nuclease SI Digestion, Inhibition of Restriction Cleavage and Nucleotide Sequencing

Cited by 15 publications

References 30 publications

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Apoptosis in C3H/10T1/2 mouse embryonic cells: evidence for internucleosomal DNA modification in the absence of double-strand cleavage.

Supercoil‐stabilized left‐handed DNA in the plasmid (dA‐dT)16 insert formed in the presence of Ni2+

Restriction‐enzyme cleavage of DNA modified by platinum(II) complexes

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Supercoil‐stabilized left‐handed DNA in the plasmid (dA‐dT)₁₆ insert formed in the presence of Ni²⁺