Efficiency of formation of pyrimidine dimers in SV40 chromatin in vitro

Snapka, Robert M.; Linn, Stuart

doi:10.1021/bi00504a012

Cited by 14 publications

(7 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Indeed, Hanawalt and coworkers have shown that the yield of PD in a DNA of African green monkey cells and amplified DNA in Chinese hamster cells (containing the transcriptionally active dihydrofolate reductase gene) is very similar to the yield determined for the bulk of the DNA in chromatin (8,9). Studies have also been performed at the nucleosome level of chromatin, focusing on the distribution of PD between nucleosome core DNA and linker DNA (11)(12)(13). The results ofthese studies indicate that the distribution of PD is essentially uniform between these two regions of the nucleosome unit at low to moderate UV doses.…”

mentioning

confidence: 96%

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Gale

Nissen²,

Smerdon³

1987

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

196

150

View full text Add to dashboard Cite

a DNase I cut site was incorrectly given as a 3' phosphate. The liberation of fragments with 3' hydroxyls by this enzyme makes the charge of these fragments the same as that of those liberated by T4 polymerase-exonuclease. The latter fragments differ only by the presence of a PD (cyclobutane pyrimidine dimer) at the 3' end.Proc. Natl. Acad. Sci. USA Vol. 84, pp. 6644-6648, October 1987 Biochemistry UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases (UV photoproduct ABSTRACTWe have determined the distribution of the major UV-induced photoproducts in nucleosome core DNA using the 3'-*5' exonuclease activity of T4 DNA polymerase, which has been shown to stop digestion immediately 3' to UV-induced pyrimidine dimers. This assay is extremely sensitive since all DNA fragments without photoproducts (background) are reduced to small oligonucleotides, which can be separated from those fragments containing photoproducts. The results show that the distribution of UV-induced photoproducts (primarily cyclobutane dipyrimidines) is not uniform throughout core DNA but displays a striking 10.3 (± 0.1) base periodicity. Furthermore, this characteristic distribution of photoproducts was obtained regardless of whether nucleosome core DNA was isolated from UV-irradiated intact chromatin fibers, histone H1-depleted chromatin fibers, isolated mononucleosomes, or cells in culture. The yield of pyrimidine dimers along the DNA seems to be modulated in a manner that reflects structural features of the nucleosome unit, possibly core histone-DNA interactions, since this pattern was not obtained for UV-irradiated core DNA either free in solution or bound tightly to calcium phosphate crystals. Based on their location relative to DNase I cutting sites, the sites of maximum pyrimidine dimer formation in core DNA mapped to positions where the phosphate backbone is farthest from the core histone surface. These results indicate that within the core region of nucleosomes, histone-DNA interactions significantly alter the quantum yield of cyclobutane dipyrimidines, possibly by restraining conformational changes in the DNA helix required for formation of these photoproducts.Irradiation by UV light produces a variety of lesions in cellular DNA, which, if unrepaired, may have lethal, mutagenic, or carcinogenic effects (1). The major lesion produced is the cyclobutane pyrimidine dimer (PD) formed between adjacent pyrimidines (2, 3), and the photochemistry of the formation of this lesion has been studied in detail (3). Several other photoproducts are also formed to a lesser extent. Among these are the pyrimidine-pyrimidone(6-4) adducts, which may play an important biological role since they have been shown to correlate with some mutational "hot spots" in specific DNA sequences (4).Since the "target" for PD formation in intact cells is DNA folded into the compact structure of chromatin (for reviews on chromatin structure, see refs. 5 and 6), it is important to understand the influence of...

show abstract

mentioning

confidence: 96%

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Gale

Nissen²,

Smerdon³

1987

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

196

150

View full text Add to dashboard Cite

show abstract

“…Unlike furococoumarin adducts, the pyrimidine dimers produced by UV,,, are located both in cores and linkers. At biologically relevant doses, the pyrimidine dimer frequency per unit DNA may even be higher in the nucleosome cores than in linker DNA [56].…”

Section: Role Of Chromatin Structure In Dna Repairmentioning

confidence: 99%

Repair Responses to DNA Damage: Enzymatic Pathways in E coli and Human Cells

Hanawalt

Cooper

Ganesan

et al. 1982

J of Cellular Biochemistry

View full text Add to dashboard Cite

Bacteria and eukaryotic cells employ a variety of enzymatic pathways to remove damage from DNA or to lessen its impact upon cellular functions. Most of these processes were discovered in Escherichia coli and have been most extensively analyzed in this organism because suitable mutants have been isolated and characterized. Analogous pathways have been inferred to exist in mammalian cells from the presence of enzyme activities similar to those known to be involved in repair in bacteria, from the analysis of events in cells treated with DNA damaging agents, and from the analysis of the few naturally occurring mutant cell types.Excision repair of pyrimidine dimers produced by UV in E coli is initiated by an incision event catalyzed by a complex composed of uvrA, uvrB, and uvrC gene products. Multiple exonuclease and polymerase activities are available for the subsequent excision and resynthesis steps. In addition to the constitutive pathway, which produces short patches of 20-30 nucleotides, an inducible excision repair process exists that produces much longer patches. This long patch pathway is controlled by the recA-lexA regulatory circuit and also requires the recF gene. It is apparently not responsible for UV-induced mutagenesis. However, the ability to perform inducible long patch repair correlates with enhanced bacterial survival and with a major component of the Weigle reactivation of bacteriophage with double-strand DNA genomes. stitutive pathway in E coli. Although not as well understood, the incision event is at least as complex, and repair resynthesis produces patches of about the same size as the constitutive short patches. In mammalian cells, no patches comparable in size to those produced by the inducible pathway of E coli are observed.Repair in mammalian cells may be more complicated than in bacteria because of the structure of chromatin, which can affect both the distribution of DNA damage and its accessibility to repair enzymes. A coordinated alteration and reassembly of chromatin at sites of repair may be required. We have observed that the sensitivity of digestion by staphylococcal nuclease (SN) of Mammalian cells possess an excision repair pathway similar to the con-

show abstract

“…Williams and Friedberg (1979) irradiated human cells and found no difference between total DNA and the nucleosomal core particles in the yield of thymine-containing dimers, measured by thin layer chromatography. Snapka and Linn (1981) irradiated in vitro mixtures of SV40 chromatin and DNA [in the presence of 10 mM Tris-C1 (pH 7.5). 0.13 M NaCI, 0.2 mM EDTA.…”

Section: Discussionmentioning

confidence: 99%

“…After a further 10 min, the lysed cells were scraped into centrifuge tubes, held on ice 30 min, and pelleted (10000 rpm, 5 min, Sorvall RC2B); the supernatant contains SV40 chromosomes. Snapka and Linn, 1981). Dishes were rinsed twice with PBSd.…”

Section: Triton Extraction (Green and Brooks 1976) Dishesmentioning

confidence: 99%

“…Several groups have examined the distribution of UV-induced pyrimidine dimers between micrococcal nuclease-sensitive (linker) DNA and resistant (core) DNA. Williams and Friedberg (1979) and Niggli and Cerutti (1982) report a random distribution of dimers, whereas Snapka and Linn (1981) report that at fluences below 380 J/m2 core DNA is 1.8-fold more susceptible to dimer introduction than is free DNA or linker DNA. Niggli and Cerutti suggest that the discrepancy might be related to the fact that Snapka and Linn used SV40 chromosomes and irradiated them in vitro.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

FORMATION OF PYRIMIDINE DIMERS IN SIMIAN VIRUS 40 CHROMOSOMES AND DNA in vitro: EFFECTS OF SALT

Edenberg

1984

Photochem & Photobiology

View full text Add to dashboard Cite

Simian virus 40 chromosomes were used to determine whether packaging of DNA into chromatin affected the yield of cyclobutane pyrimidine dimers introduced by ultraviolet light (254 nm). SV40 chromatin and purified SV40 DNA (radioactively labeled with different isotopes) were mixed and irradiated in vitro. The proteins were extracted and pyrimidine dimers detected as sites sensitive to the UV-endonuclease encoded by bacteriophage T4. When irradiation was carried out in the presence of at least 0.05 M NaCl the same number of dimers were formed in chromatin as in free DNA. Irradiation in the absence of NaCI. however, reduced the relative yield of dimers in chromatin to 89% of that in free DNA. Different methods of chromatin preparation did not influence these results.

show abstract

Efficiency of formation of pyrimidine dimers in SV40 chromatin in vitro

Cited by 14 publications

References 30 publications

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

UV-induced formation of pyrimidine dimers in nucleosome core DNA is strongly modulated with a period of 10.3 bases.

Repair Responses to DNA Damage: Enzymatic Pathways in E coli and Human Cells

FORMATION OF PYRIMIDINE DIMERS IN SIMIAN VIRUS 40 CHROMOSOMES AND DNA in vitro: EFFECTS OF SALT

Contact Info

Product

Resources

About