Internucleotide protein linkers in Ehrlich ascites cell DNA

Ribonucleoprotein-masked nicks at 50-kbp intervals in the eukaryotic genomic DNA

By using a microscopic approach, field inversion single-cell gel electrophoresis, we show that preformed single-strand discontinuities are present in the chromatin of resting and proliferating mammalian and yeast cells. These single-strand breaks are primarily nicks positioned at approximately 50-kbp intervals throughout the entire genome that could be efficiently labeled in situ by DNA polymerase I holoenzyme but not by Klenow fragment and terminal transferase unless after ribonucleolytic treatments. The RNA molecules involved appear to comprise R-loops, recognized by the S9.6 RNA/DNA hybrid-specific antibody. By using the breakpoint cluster region of the Mixed Lineage Leukemia (MLL) gene as a model, we have found that the number of manifest nicks detected by FISH performed after field inversion single-cell gel electrophoresis depends on epigenetic context, but the difference between germ-line and translocated MLL alleles is abolished by protease treatment. Our data imply that the double-stranded genomic DNA is composed of contiguous rather than continuous single strands and reveal an aspect of higher-order chromatin organization with ribonucleoprotein-associated persistent nicks defining approximately 50-kbp domains.

Protein oxidation and DNA-protein crosslink induced by sulfur dioxide in lungs, livers, and hearts from mice

In this article, protein oxidative damage and DNA-protein crosslinks (DPC) induced by sulfur dioxide (SO(2)) in lungs, livers, and hearts of mice were studied. The protein carbonyl (PCO) content was measured using spectrophotometric DNPH assay to reflect the degree of protein oxidative damage, and the DPC coefficient was measured by using a KCl-sodium dodecyl sulfate (SDS) assay to show the degree of DNA damage in lungs, livers, and hearts from mice exposed to SO(2) at various concentrations (0, 14, 28, and 56 mg-m(- 3)) for 6 h per day for 7 days. The results indicate that SO(2) caused an increase of PCO and DPC level in all organs tested from mice in a concentration-dependent manner. The concentration-response relationships in all organs tested of both female and male mice could be fitted well with monolinear regression equations. The adjusted coefficient R squared of all equations is more than 0.9. These results lead to a conclusion that SO(2) may cause an increase of protein oxidation damage and DNA-protein crosslinking in lungs, livers, and hearts from mice. The rank order of absolute increase in PCO contents and DPC coefficient in three organs from mice compared with controls was lung > liver > heart. Our results also indicated the regulation of PCO and that of DPC induced by SO(2) were conformed to each other; this implies that the protein oxidative damage may be associated with the emergence of DPC.

Assessment of DNA-protein crosslinks in the course of aging in two mouse strains by use of a modified alkaline filter elution applied to whole tissue samples

Two different mouse strains have been used for determination of age dependence of DNA-protein crosslinks by alkaline filter elution: a long lived laboratory strain, NMRI and an accelerated senescence-prone, short lived strain, SAMP1. Five organs were selected: Brain, kidney, lung, heart and liver. Remarkably in all five organs of short lived SAMPI mice crosslinks increased significantly with age. In NMRI however only in brain and heart a significant rise in old age has been observed, while in the other organs there was no increase in DNA-protein crosslinking. Appreciable mitotic activity which is lacking in brain and heart could be the reason for this difference. Poor repair in all five organs could be an important component for the multiple ailments and shortened life span in SAMP1 mice.

Microgel electrophoresis: sensitivity, mechanisms, and DNA electrostretching

Based on the treatment of microgels to remove proteins, we speculate that proteins may be bound to DNA in the microgels even after electrophoresis. We speculate that some DNA single-strand breaks may be a reflection of these protein-DNA complexes. We suggest methods to limit such artifacts, and present data demonstrating a lymphocyte DNA double-strand break sensitivity of 12.5 rads and day-to-day reproducibility of microgel electrophoresis using these principles. Extending these principles, we describe DNA behavior during alkaline and neutral microgel electrophoresis based on observations of the stained DNA and its migration patterns. During microgel electrophoresis, individual DNA molecules behave as if anchored at one end while the other end is free to migrate in response to the electric field. We capitalize on this behavior by developing a neutral microgel method to stretch chromosomes.

DNA status in brain and heart as prominent co-determinant for life span? Assessing the different degrees of DNA damage, damage susceptibility, and repair capability in different organs of young and old mice

Alkaline filter elution has been modified by a freeze-grinding step that allows the evaluation of the DNA status of whole tissue, including mouse tail cross-sections, with only small additional artefacts. Four to seven different organs from individually coordinated female NMRI mice, rated as young when 2-3 months, and as old when 24-27 months, of age, have been used. Tissues of individual mice differ significantly in their DNA status. Alkali-labile sites are relatively rare and differ in amount in the different organs in the young. They show significant increases in the old, reaching the highest values in the brain and the heart. Proteinase K dependent DNA-protein cross-links are not prominent nor are they increased with age in some organs, except in the brain and the heart. DNA damage susceptibility was measured after application of 3.5 microM nitoquinolin-N-oxide to 15 mg fresh. tissue pieces for 90 min. The susceptibility is large and varying in wide ranges in the different organs. Upon 3 h post-exposure incubation in full medium all samples showed DNA repair, the young reach nearly complete repair in the lung, while repair, generally, in the old is significantly decreased. In old brain and heart it is even near zero. This together with high values in alkali-labile sites and protein-DNA cross-linking suggests that these two organs may act as pacemakers and play a role as prominent co-determinants for the life span of the species.

Stably DNA-bound chromosomal proteins

DNA accomplishes its biological function in a complex with nuclear proteins. A minor protein fraction has been found in chromatin which could not be dissociated from DNA by reagents abolishing non-covalent type of interactions. The controversy surrounding the nature of the protein moiety and the nature of the bond linking the two components on the one hand, and the fact pointing to its evolutionary conservatism and metabolic stability on the other, make it necessary to critically evaluate the data in view of the possible biological function for such proteins.

Chemical and enzymatic analysis of covalent bonds between peptides and chromosomal DNA

DNA from Ehrlich ascites tumor (EAT) cells and from human placenta was examined for covalent bonds between hydroxy amino acid residues in peptides and nucleotide phosphate groups. The residual proteinaceous material in highly purified DNA was radiolabelled with 125Iodine and the linking-groups between peptides and nucleotides released by combined protease and nuclease treatment were investigated with respect to their chemical and enzymatic stabilities. The residual nucleotide(s)-peptide(s) fraction from DNA isolated after prolonged alkaline cell lysis and phenol extraction contains mainly alkali and acid-stable but phosphodiesterase-sensitive peptide-nucleotide complexes which indicates phosphodiesters between tyrosyl residues in peptides and nucleotide phosphates. In contrast, the linking-group fraction from DNA isolated under native conditions contains additional peptide components. (a) Phospho-peptides that co-purify with DNA but that are not covalently bound to nucleotides. (b) A fraction of peptides that is released from nucleotides by alkali in a time and concentration-dependent reaction. Evidence is presented indicating that the latter fraction involves phospho-triesters between hydroxy amino acid residues in peptides and internucleotide phosphates. The phosphodiesters between hydroxy amino acids and nucleotide phosphates representing the predominant class of peptide-nucleotide complexes in alkali-denatured DNA are most likely side products of peptide-nucleotide phospho-triester hydrolysis.

Age-correlated DNA damage in human muscle tissue

This investigation represents the largest study so far published on human DNA damage and aging. The subject of this investigation is damage, determined as DNA alterations which give rise to complete molecular breaks in the course of treatment of purified DNA solutions with single-strand-specific nucleases. The DNA is derived from milligram samples of human muscle of individuals mostly undergoing surgical treatment. Care has been taken to bring the muscle samples, once shut off from blood circulation to liquid nitrogen temperatures within few seconds. The DNA is prepared by a procedure keeping breaks by handling and by DNAase attack as low as possible, however pushing DNA purity, especially with respect to protein as high as possible. Highly purified DNA treated in this way has some sites which are susceptible to single-strand (ss) specific DNAase splitting (ss-events). Three different deoxyribonucleases have been used: Nuclease S1, Nuclease BAL31 and Pea Endo-Nuclease. They give very similar results, i.e. splitting of the DNA so as to yield DNA pieces of given distribution. The lengths of these double-strand (ds) pieces have been determined from their electron microscopical pictures, either by following the image contours with a magnetostrictive stylo of the projected photo on a pad, by following the contours with a mileage ruler, or by integrating the silver grains on the photo. The molecular weight averages of the ds DNA threads between two ss-events for each individual have been determined from 20 to 200 molecules. The 470 individuals contributing their data were from age groups from 1 to 91 years. The molecular weights show a considerable scatter with an average molecular weight of the DNA ds pieces between two ss-events of 43.93 MDa and a standard deviation of 17.99 MDa. Among the single-strand breaks (ssb) that split the DNA into such pieces is a fraction, the number of which increases in a highly significant fashion with the age of the donor. From this derives the fact that the average molecular weight of the DNA strand pieces between two ssb decreases with age. It is remarkable that the standard deviation of the molecular weights of such pieces increases with age significantly, too. On the basis of additional information mainly supplied by the DNA donor himself or by his parents the 470 members of the main group M where grouped according to their life-style, into: (1) abstinent people, essentially non-smokers and refraining from use of licit or illicit drugs, sub-group N.(ABSTRACT TRUNCATED AT 400 WORDS)

Screening of isolated DNA for sequences released from anchorage sites in nuclear matrix

Isolated chromosomal DNA is associated with polypeptides that are not released from DNA by several methods designed to purify DNA, e.g. treatment with sodium dodecyl sulphate. DNA fragments associated with these very tight DNA/protein complexes show high affinity to nitrocellulose filters in the presence of salt concentrations of 500 mM or greater. Consequently, a fraction of AluI-fragmented native DNA comprising the complexes and 0.2 to 0.3 micron of vicinal DNA can be isolated by one filtration step. This fraction of DNA shows characteristics of residual DNA sequences retained in nuclei after extraction with nucleases and high salt (nuclear matrix). The DNA fragments retained on filters are highly enriched in replicative DNA; and their degree of hybridization with poly(A)+ RNA points to enrichment in actively transcribed sequences. The results support previous work indicating that the very tight DNA/polypeptide complexes co-isolating with DNA under conditions that release other peptide materials from DNA may be anchorage sites of DNA in the nuclear matrix. Moreover, the method described here allows isolation of replicating and actively transcribed DNA sequences directly from isolated total genomic DNA by skipping artefact-prone isolations of the nuclear matrix.

Antibodies to the most tightly bound proteins in eukaryotic DNA. Formation of immuno-complexes with 'nuclear matrix' components

Chromosomal DNA is associated with polypeptides covalently bound to internal DNA ends. Since these polypeptides can only be released from chromosomal DNA by enzymes or other agents hydrolysing phosphodiester bonds they were termed 'the most tightly bound' (MTB) polypeptides in DNA. Antibodies developed against the MTB polypeptides are shown to form immunocomplexes with major 'nuclear matrix' polypeptides as well as with polypeptides which are still associated with 'nuclear matrix' DNA isolated by means of SDS/proteinase K and phenol. Immuno-complex formation is revealed by immunoblotting and by indirect immunofluorescence. Thus, since MTB polypeptides, major 'nuclear matrix' polypeptides and 'nuclear matrix' DNA-associated polypeptides share common antigenic sites they can be considered to be identical or at least closely related. This suggests that a fraction of distinct 'nuclear matrix' polypeptides is either transiently or permanently linked to DNA by covalent bonds. Consistently, isolated eukaryotic 'bulk' DNA is inevitably associated with residual 'nuclear matrix' polypeptides.

Effect of alkali on the size dispersity of mammalian DNA measured by filter elution

DNA from unirradiated and irradiated cultured 9L rat brain tumor cells was held for varying times in low ionic strength solutions at pH 11.0, 12.3, or 12.9. The effect of this exposure to alkali on the DNA size distribution was determined by comparing the DNA filter elution profiles obtained experimentally with those theoretically predicted for monodispersed and random distributions. At pH 12.3 or 12.9, DNA from cells irradiated with 300 rad eluted with first-order kinetics corresponding to a random DNA size distribution. The median size of the distribution decreased if the irradiated DNA was exposed to pH 12.3 for 24 h. At pH 12.3 or 12.9, DNA from unirradiated cells eluted initially with complex kinetics that later became linear (18-21 h for pH 12.3 or 13-15 h for pH 12.9), characteristic of a monodispersed DNA size distribution. Holding either unirradiated or irradiated DNA at pH 11.0, below the critical unwinding pH, produced no effect on the elution profiles. Analysis of these filter elution data indicated that after sufficient exposure to pH 12.3 or 12.9, undamaged DNA molecules from mammalian cells elute as a single-stranded monodispersed size distribution of approximately 1 X 10(10) daltons. While the possibility cannot be completely eliminated that this monodispersed size represents an upper limit determined by physical forces, these results, in conjunction with those obtained using other techniques, lend credence to the existence of a nonrandom higher-order structure in mammalian chromosomal DNA.

DNA polymerases in isolated 'nuclear matrix' of Ehrlich ascites cells

Isolated nuclei from Ehrlich ascites tumor cells continue a replicative-like in vitro DNA synthesis. Polymerase alpha is the major dNTP polymerizing enzyme in nuclei. Following complete achromatinization dNTP polymerizing activities are still associated with the residual structure termed 'nuclear matrix'. In contrast to DNA synthesis in native nuclei, 'nuclear matrix' DNA synthesis is mainly due to polymerase beta-like activity.

Proteins tightly bound to HeLa cell DNA at nuclear matrix attachment sites

DNA-protein complexes have been isolated from HeLa cell nuclei and nuclear matrix preparations. Two proteins, 55 and 66 kilodaltons in size, remain bound to HeLa DNA after treatment at 80 degrees C in 2% sodium dodecyl sulfate and purification by exclusion chromatography on Sepharose 2B-CL in the presence of 0.3% sodium dodecyl sulfate. These proteins appear to be tightly bound but not covalently linked to the DNA, and they are distributed over the DNA with an average spacing of 40 kilobase pairs. This spacing distribution remains essentially constant throughout the cell cycle. The proteins are bound to the residual 2% of HeLa cell DNA which remains attached to the nuclear matrix after extensive nuclease digestion, a condition which reduces the average size of the DNA to approximately 150 base pairs. Our results suggest that these tightly bound proteins are involved in anchoring cellular DNA to the nuclear matrix. These tightly bound proteins are identical by partial peptide mapping to proteins found tightly bound to the DNA of mammalian, plant, and bacterial cells (D. Werner and C. Petzelt, J. Mol. Biol. 150:297-302, 1981), implying that these proteins are involved in the organization of chromosomal domains and are highly conserved in both procaryotic and eucaryotic cells.

Proteins tightly bound to HeLa cell DNA at nuclear matrix attachment sites

DNA-protein complexes have been isolated from HeLa cell nuclei and nuclear matrix preparations. Two proteins, 55 and 66 kilodaltons in size, remain bound to HeLa DNA after treatment at 80 degrees C in 2% sodium dodecyl sulfate and purification by exclusion chromatography on Sepharose 2B-CL in the presence of 0.3% sodium dodecyl sulfate. These proteins appear to be tightly bound but not covalently linked to the DNA, and they are distributed over the DNA with an average spacing of 40 kilobase pairs. This spacing distribution remains essentially constant throughout the cell cycle. The proteins are bound to the residual 2% of HeLa cell DNA which remains attached to the nuclear matrix after extensive nuclease digestion, a condition which reduces the average size of the DNA to approximately 150 base pairs. Our results suggest that these tightly bound proteins are involved in anchoring cellular DNA to the nuclear matrix. These tightly bound proteins are identical by partial peptide mapping to proteins found tightly bound to the DNA of mammalian, plant, and bacterial cells (D. Werner and C. Petzelt, J. Mol. Biol. 150:297-302, 1981), implying that these proteins are involved in the organization of chromosomal domains and are highly conserved in both procaryotic and eucaryotic cells.

Measurement of the molecular weight distributions in human muscular deoxyribonucleic acid

Highly purified DNA has been prepared from human muscle tissue and treated with three different single-strand specific desoxyribonucleases. The molecular weight of treated individual DNA molecules was determined by length measurements. Average DNA molecular weights and their standard deviations were correlated to the age of donors. No significant correlation could be established using seven different mathematical functions. Factor analytical considerations suggested grouping according to extreme smoking habits. Two populations with significant double linear correlations of age versus molecular weight and standard deviation then emerge. From the data it may be speculated that in heavy smokers with increasing age (or time of smoking) high molecular weight DNA integrity is lost to an increasing extent in post-mitotic tissue.

Phosphodiester bonds between polypeptides and chromosomal DNA

Polypeptides co-purifying with DNA in alkali are covalently bound to DNA. DNA purified by treatment with alkali, sodium dodecyl sulphate and phenol absorbed 125I under conditions designed to radioiodinate exclusively tyrosine and histidine in peptides. A significant amount of the absorbed 125I remained associated with DNA during treatment with phenol as well as during precipitation with ethanol from neutral and alkaline solutions. However, after prolonged digestion with proteinase K, most of the radiolabelled material could be removed from 125I-treated DNA. Further treatment with a second protease (Pronase) released no larger fraction of the 125I label. The residual radiolabelled material could be precipitated together with DNA by ethanol and it remained associated with DNA also in the presence of alkali (95 degrees C), acid (37 degrees C) and hydroxylamine (37 degrees C). In contrast, radiolabelled peptides were released from DNA by treatment with hot piperidine (10% at 95 degrees C) and by agents that hydrolyse peptides and modify DNA, e.g. strong acid (95 degrees C) and formic acid/diphenylamine. The radiolabelled peptides, once released from DNA by these chemical methods, could be further cleaved by Pronase. This shows that the residual DNA/peptide complex isolated after prolonged protease digestion is protease-resistant unless it is cleaved or otherwise modified by harsh chemical treatment. The linking groups between deoxynucleotides and the radiolabelled residual peptides could be isolated by digestion of DNA in the DNA/peptide complex. Radiolabelled peptides could be released from this linking group material by phosphodiesterases, indicating the involvement of phosphodiesters in the linking groups.

Artifacts in sodium dodecyl sulfate-polyacrylamide gel electrophoresis due to 2-mercaptoethanol

Mercaptoethanol, when present in the sample buffer during sodium dodecyl sulfate-polyacrylamide gel electrophoresis, is responsible for the appearance of two nonprotein bands (electrophoretic mobilities corresponding to 68 and 54 kdalton) stainable with silver and with Coomassie blue. After iodination in vitro of DNA preparations isolated by alkaline phenol extraction using chloramine-T procedure, part of the radioactive label is found in these bands, provided the reaction is terminated by mercaptoethanol, whereas only a diffuse background is present in this area if the reaction is stopped by sodium metabisulfite. Similar results are obtained with highly purified total cytoplasmic RNA. The results indicate that the appearance of the 68- and 54-kdalton bands is in artifact. The relevance of these results to the proteins tightly bound to DNA is discussed.

Ellipticine-induced protein-associated DNA breaks in isolated L1210 nuclei

DNA intercalating agents have been found to produce protein-associated DNA strand breaks in mammalian cells. At a first step towards a subcellular system for the study of this reaction, we demonstrate that the reaction can take place in isolated cell nuclei. Ellipticine induces in these nuclei DNA strand breaks and stable DNA-protein complexes. Complexes and breaks are present in equivalent amounts. DNA breaks are revealed only if protein-mediated DNA adsorption to filters is abolished. These findings make it unlikely that similar effects observed in cells in culture after treatment with intercalating agents are caused by metabolically activated drugs.

DNA double strand breaks in Ehrlich ascites tumour cells at low doses of x-rays. I. Determination of induced breaks by centrifugation at reduced speed

DNA double strand breaks (dsb) were determined in Ehrlich ascites tumour cells at doses down to 5 Gy. The method is based on the separation of DNA from other components by heating in a solution of pronase and detergents held in wide-mouth syringes, which were also used to facilitate the application of the released high molecular weight DNA to sucrose gradients. Purified DNA was sedimented in neutral sucrose gradients at low speed to reduce speed artifacts. The sedimentation profiles were analysed using a computer program and the number of dsb was determined by simulation of random breaks in the mass distribution of the control sample and by comparison of this simulated profile with that of the irradiated one. The number of dsb formed was proportional to X-ray dose in the range of 5 to 2000 Gy. The induction per dose was found to be nmr-1 D-1 = (11.7 +/- 2) x 10(-12) Gy-1.

Non-random distribution of N-methyl-N-nitrosourea sensitive sites in a eukaryotic genome

DNA released from Ehrlich ascites cells by lysis in the presence of 50 microgram X ml-1 of proteinase K contains long alkali-stable strands in the order of 50-100 X 10(6) daltons. In contrast, DNA released in the presence of 6 mg X ml-1 of autodigested pronase is significantly nicked. According to sedimentation rates the number of internal ends liberated during this procedure is 24/200 X 10(6) daltons. The number of alkali-labile sites introduced into DNA by incubation of Ehrlich ascites cells with 1 nM of N-methyl-N-nitrosourea (MNU) followed by cell lysis in the presence of 50 microgram X ml-1 of proteinase K and alkali-denaturation is 16.6/200 X 10(6) daltons. From this one should expect that denatured DNA released from cells pretreated with 1 mM of MNU which are subsequently lysed with 6 mg X ml-1 of pronase would have about 40 single-strand breaks/200 X 10(6) daltons. However, denatured DNA strands released by 6 mg X ml-1 of pronase either from MNU-treated or untreated cells cannot be separated by centrifugation through alkaline sucrose gradients. This phenomenon could be explained by a non-random distribution of MNU-inducible alkali-labile sites of DNA in vivo.

Organization of highly purified calf thymus DNA. I. Cleavage into subunits and release of phosphopeptides

DNA (N-DNA) prepared under conditions eliminating the exposure of chromatin to cytoplasmic components exhibits some special properties not observed for DNA prepared by standard methods (S-DNA).N-DNA, having a sedimentation coefficient of 24.7 S and a firmly bound protein content of 0.7%, can be cleaved (in contrast to S-DNA) by treatment with chelating agents, into stable subunits having a mean molecular weight of about 500 000. This cleavage was shown to be an ordered process which involved no enzymatic or shear degradation. It was accompanied by the release of phosphopeptides. The analyses of these phosphopeptides revealed the presence of two main fractions. One contained phosphoserine and glycine (Mr about 1400), and the other contained phosphoserine, glycine, alanine, glutamic and aspartic acids (Mr about 900). The amount of released phosphopeptides could be correlated to the extent of cleavage.