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At least 19 recordsLinked to original sources
PubMed1978

Periodic organisation of foldback sequences in Physarum polycephalum nuclear DNA.

Nuclear DNA from the slime mould Physarum polycephalum is shown to contain interspersed inverted repeat sequences, such that denatured fragments of DNA containing pairs of these sequences form intra-chain duplexes under appropriate conditions. The organisation and distribution of the nucleotide sequences responsible for the formation of foldback structures in Physarum DNA have been investigated using the electron microscope. The majority of foldback duplexes have sizes ranging up to 800 base pairs, and about 60-80% of DNA molecules 2.2 X 10(4) bases in length contain interspersed foldback elements. The size of individual foldback duplexes, and also the length of the intervening sequences which separate them, are non-random. The results can best be explained by a model in which separate foldback foci in Physarum DNA are spaced periodically at regular intervals. The regions containing foldback foci are thought to contain smaller, tandemly-arranged sequences of discrete sizes, in some cases related to other nucleotide sequences of a similar nature in the same locality in Physarum DNA.

Base Sequence↗
PubMed1976

[Isolation of mitochondrial DNA, purified of nuclear DNA, from animal tissues (degree of methylation and level of pyrimidine nucleotide clustering--criteria of purity)].

A method of preparation of mitochondria free of nuclear DNA and its fragments by treatment of mitochondria with DEAE-cellulose has been developed. This method is based on binding nuclear nucleic acids and nucleoproteins to DEAE-cellulose particles in the media used for isolation of mitochondria. Treatment with DEAE-cellulose under the conditions described does not induce any visible degradation of mitochondria and mitochondrial DNA. The mitochondrial DNA preparations obtained from beef and rat liver are represented with closed circular molecules of contour length about 5.5 mu. The 5-methylcytosine content in beef and rat mitochondrial DNA (3.03 and 2.0 mole %, respectively) is twice as much as in corresponding nuclear DNA. Besides, mitochondrial DNA strongly differs from nuclear ones by a lower degree of pyrimidine clustering: the amount of mono- and dipyrimidine fragments (about 32 mole %) in mitochondrial DNA is 1.5 times as large and the content of long pyrimidine clusters (hexa- and others) is 2--4 times as low as those in nuclear DNA. The methylation level and the pyrimidine clustering degree may be used as criteria for the purity of mitochondrial DNA from nuclear DNA.

Animals↗
PubMed1978

Evidence that the amount of chloroplast DNA exceeds that of nuclear DNA in mature leaves.

Cell-free homogenates containing intact chloroplasts and nuclei were allowed to settle for up to 1 h before the top 2 ml of the 5-ml homogenate was withdrawn. Whereas less than 18% of the chloroplasts moved from the top to the bottom portions, the ratio of nuclei to chloroplasts in the top portion changed from approximately 1/200 to 1/900. The total numbers of chloroplasts and nuclei were counted in the homogenate before settling and in the top 2 ml and bottom 3 m1 after settling. The total DNA content of the homogenate and the top and bottom portions after settling was determined by the diphenylamine colorimetric assay. By simultaneous equations, the absolute amount of DNA in chloroplasts and nuclei was determined. The results are consistent with previous observations of chloroplast DNA by fluorescence microscopy which indicated that the amount of chloroplast DNA per chloroplast is a function of chloroplast size. In addition, the results show that the amount of chloroplast DNA per average chloroplast in large leaves is 0.14 times 10(-12) g, a magnitude higher than previous reports in the literature, and that large leaves contain about twice as much chloroplast DNA as nuclear DNA.

Cell Fractionation↗
PubMed1979

Organisation of inverted repeat sequences in hamster cell nuclear DNA.

Hamster cell nuclear DNA is shown to contain inverted repeat (foldback) sequences, in some respects similar to the foldback fraction in DNA from other animal cell types. Using electron microscopy the majority of foldback duplexes are shown to be located in simple hairpin-like DNA structures, formed from individual pairs of complementary inverted repeated sequences 50--1000 nucleotides in length, in some cases arranged in tandem, and in other cases separated by intervening sequences, up to 16000 nucleotide residues long. In addition, a novel class of foldback structure, referred to as 'bubbled hairpins' is reported, which appear to be formed from clusters of inverted repeat sequences that are separated from adjacent clusters of complementary inverted repeats by large intervening sequences which vary in length from 5000 to over 20000 nucleotide residues. Due to the special pattern of distribution of these latter inverted repeat sequences, 'bubbled hairpins' are observed only in long foldback DNA. Evidence is presented that the distribution of foldback sequences in hamster cell DNA is highly ordered. The lengths of the intervening single chains in foldback structures appear to vary non-randomly. This gives rise to a localised periodic pattern of organisation that is believed to be a consequence of regular alternating arrangements of foldback and non-foldback sequences in the segments of DNA from which foldback structures are derived.

Animals↗
PubMed1977

Mitochondrial DNA synthesis in mouse L cells temperature sensitive in nuclear DNA replication.

Temperature-sensitive (ts) A 1S9 mouse L cells continue to synthesize double-stranded covalently closed mitochondrial (mt) DNA at a temperature (38.5 degrees C) which is nonpermissive for chromosomal DNA replication. The amount of mt DNA made appears to be quantitatively linked to nuclear DNA synthesis. Nuclear DNA replication proceeds normally for 6-8 h after the cells are shifted to 38.5 degrees C, and then declines to reach a minimum at 20-24 h. The level of mt DNA synthesis remains high during this period and decreases once the ts lesion has been established.

Animals↗
PubMed1976

Nuclear dna amounts in angiosperms.

The number of angiosperm species for which nuclear DNA amount estimates have been made has nearly trebled since the last collected lists of such values were published, and therefore, publication of a more comprehensive list is over due. This paper lists absolute nuclear DNA amounts for 753 angiosperm species. The dats were assembled primarily for reference purposes, and so the species are listed in alphabetical order, as this was felt to be more helpful to cyto- and biochemists whom, it is anticipated, will be among its major users. The paper also reviews aspects of the history, nomenclature, methods, accuracy and problems of nuclear DNA estimation in angiosperms. No attempt is made to reconsider those aspects of nuclear DNA estimation which have been fully revised previously, although the bibliography of such aspects is given. Instead, the paper is intended as a source of basic information regarding the terminology, practice and limitations of nuclear DNA estimation, especially by Feulgen microdensitometry, as currently practiced.

Cell Nucleus↗
PubMed1977

Isolation of single stranded transcription sites from human nuclear DNA.

Single stranded DNA (ss-DNA) isolated from nuclear DNA of human rhabdomyosarcoma (RD line) cells amounts to 2% of total DNA. As compared with native double-stranded DNA (ds-DNA), ss-DNA has a lower mean sedimentation coefficient, higher buoyant density, contains fewer repeated DNA sequences and a greater proportion of it can be hybridized to human RNAs (up to 35% and less than 8% for ds-DNA). The hybridization kinetics determined by S1 nuclease digestion and verified by other methods (hydroxylapatite chromatography, density gradient centrifugation and thermal melting) indicate that ss-DNA corresponds to a great number and variety of transcripts. These data are discussed as evidence for DNA strand dissociation in the course of gene activity.

Cell Line↗
PubMed2025

Nondestructive Larval Genotyping of Danio rerio for Mitochondrial and Nuclear DNA Genetics.

The rapid advancement of nuclear and mitochondrial genomic editing tools has created an urgent need for efficient, nonlethal larval genotyping methods in zebrafish (Danio rerio) research. This study optimizes and validates a nondestructive proteinase K digestion method for mitochondrial and nuclear DNA genotyping while characterizing its impact on larval survival and gene expression. Using optimized protocol parameters, we demonstrate successful amplification of different mitochondrial and nuclear genetic loci with consistently high sensitivity. Molecular validation through PCR, restriction fragment length polymorphism analysis, and Sanger sequencing confirmed the specificity and reliability of the extracted DNA. The method successfully detected C-to-T base edits in the mt-tl1 gene introduced using the FusX TALE Base editor system, demonstrating its applicability to gene editing studies. Both 48-well and optimized 96-well formats were used, enabling this approach to be deployed at scale. This optimized method enables researchers to correlate genotypes with phenotypes in longitudinal studies while maintaining specimen viability, particularly valuable for investigating early-onset mitochondrial diseases, and utilizes standard laboratory equipment and reagents, facilitating widespread adoption in zebrafish research while adhering to ethical principles in reducing animal mortality.

Animals↗
PubMedDate not supplied

Nuclear DNA content of trophoblastic tumors.

The nuclear DNA content of trophoblasts was measured in 25 cases of normal pregnancy, 46 cases with hydatidiform mole, ten cases with destructive mole and six cases of chorionepithelioma (choriocarcinoma). In normal pregnancy, DNA distribution in syncytiotrophoblasts and cytotrophoblasts showed a sharp peak at the diploid region, although a few cytotrophoblasts with increased DNA content were observed in the first trimester. In chorionepithelioma the DNA content of the trophoblastic cells showed extremely wide distribution without any special peak. In destructive mole, although a wide distribution was observed, the sharp peak was usually noted at the diploid range. Cases with hydatidiform mole were divided into two categories according to the DNA distribution patterns. Type I showed the patterns similar to the first trimester of normal pregnancy and type II resembled the patterns of destructive mole. In hydatidiform mole of type II, subsequent progress towards destructive mole was frequently encountered.

Cell Nucleus↗
PubMed1978

[Nuclear DNA synthesis rate and labelling index: effects of carcinogenic and non-carcinogenic chemicals on its behaviour in the organism of growing CBA-mice. The thymidine-incorporation-screening-system (TSS) (author's transl)].

During the last few decades there has been an extraordinary accumulation of man-made chemicals in the human environment. There is a growing consensus in oncology that a large proportion of human cancers are environmental in origin by exposure of man to such carcinogenic chemicals. These chemicals in the majority of all cases have not been tested to prove their carcinogenicity. Testing of new chemical compounds is needful prior to their introduction into commerce, foods, agriculture or the working places to prevent human cancer. To test such a large number of possibly carcinogenic chemicals, economical and rapidly practicable bioassays are necessary. In the following we compare some well known bioassays with our autoradiographic thymidine-incorporation-screening-system and other assays based on biochemical quantification of DNA synthesis as parameter for identification of carcinogenic substances. The partial inhibition of the whole DNA synthesis in a proliferating cell population after treatment with toxic and carcinogenic chemicals is an early common response especially in hepatectomized animal, livers caused by the effects of those substances. However, by quantitative evaluation of the nuclear DNA synthesis rate as a basic parameter using autoradiographs of kidney and liver of juvenile growing CBA-mice, it is possible to differentiate carcinogenic from non-carcinogenic chemicals by means of silver grain counting after 3H-TdR incorporation. Contrarily the "whole DNA synthesis" expressed by the percentual 3H-labelling index of kidney and liver did not permit such a differentiation in our experimental arrangement. We could demonstrate that carcinogenic compounds of different chemical classes partially inhibit the nuclear DNA synthesis rate significantly over a time period longer than 24 hours. The tested non-carcinogenic compounds did not show this suppressive effect on the nuclear DNA synthesis rate.

Animals↗
PubMed1978

Organization, replication and modification of the human genome: differential methylation of two classes of HeLa nuclear DNA separated on Ag+--Cs2SO4 gradients.

HeLa nuclear DNA sediments as a single peak, in neutral CsCl, while it is separated in a heavier and a lighter components, in alkaline Ag+--Cs2SO4. The heavy fraction, on the average, represents about 20% of the total DNA. CsCl analytical ultracentrifugation shows that heavy DNA bands at 1.715 g/cm3 and contains 53% GC (10% of the total GC), whereas light DNA bands at 1.703 g/cm3 and contains 40% GC (32% of the total GC). Coherently, Tm values in 0.1 x SSC are 82.5 degrees C, for heavy DNA, and 72.5 degrees C, for light DNA. After treatment with [3H-methyl-S-adenosyl-L-methionine in isolated nuclei, the concentration of labelled 5-methylcytosine was found to be highest in the more dense regions of the heavy peak and in the less dense regions of the light peak. Exposure to ultrasound modifies the quantitative relationship of the two peaks and improves the separation of supermethylated AT- and GC-rich DNAs. Four possible triplets as sites for DNA-methylase recognition are discussed.

Cell Nucleus↗
PubMed2026

Somatic Mitochondrial-Nuclear DNA Transfer in Lymphoproliferative Disorders.

INTRODUCTION: Somatic mitochondrial-nuclear DNA transfer (SMNT) is a process by which mitochondrial DNA (mtDNA), of varying sizes, integrate into the nuclear genome and has been previously reported in solid tumours. METHODS: EuroClonality-NGS DNA Capture sequencing data from 755 lymphoid malignancies and 59 lymphoid cell lines were analysed for SMNT-associated structural variants. RESULTS: Five malignancies (0.66%) harboured SMNTs, predominantly involving IGH genes, with one PTEN gene disruption identified. Breakpoint features supported non-homologous end joining-mediated integration. CONCLUSION: SMNTs are rare but recurrent events in lymphoid malignancies and may represent stable clonal markers for minimal residual disease monitoring. TRIAL REGISTRATION: The authors have confirmed clinical trial registration is not needed for this submission.

Journal Article↗
PubMed1979

[Dynamics of the nuclear DNA content in the liver, skeletal muscles and myocardium of the rat in the postmortem period (a microspectrophotometric study)].

A comparative microspectrophotometric analysis of changes in nuclear DNA in the liver, skeletal muscle and myocardium of noninbred male albino rats which had died of cerebrocranial injury was conducted during three days following death. A decrease in the content of nuclear DNA within an interval of 30-72 h can be depicted mathematically by regression curves of the type M(t) = e-at+b. The data obtained allowed one to mathematically show the postmortem changes in DNA of the test material.

Animals↗
PubMed1979

Low level incorporation of tritiated thymidine into the nuclear DNA of Purkinje neurons of adult mice.

Adult mice were pulse labeled with tritiated thymidine [3H]TdR and killed 9 hr later. A low level incorporation of [3H]TdT into the nuclear DNA of Purkinje neurons was found in autoradiographs. Enzymatic digestions with DNase and with RNase in combination with autoradiographic grain counts indicate that a portion of nuclear DNA is not stable in the Purkinje nucleus. These results are discussed in light of reports of the stable nature of DNA in Purkinje neurons of adult mice.

Animals↗
PubMed1978

Characterization of inverted repeated sequences in wheat nuclear DNA.

The properties of inverted repeated sequences in wheat nuclear DNA have been studied by HAP(1) chromatography, nuclease S1 digestion and electron microscopy. Inverted repeated sequences comprise 1.7% of wheat genome. The HAP studies show that the amount of "foldback HAP bound DNA" depends on DNA length. Inverted repeats appear to be clustered with an average intercluster distance of 25 kb. It is estimated that there are approximately 3 x 10(6) inverted repeats per haploid wheat genome. The sequences around inverted repeats involve all families of repetition frequencies. Inverted repeats are observed as hairpins in electron microscopy. 20% of hairpins are terminated by a single-stranded spacer ranging from 0.3 to 1.5 kb in length. Duplex regions of the inverted repeats range from 0.1 to 0.45 kb with number average values of 0.24 kb and 0.18 kb for unlooped and looped hairpin respectively. Thermal denaturations and nuclease S1 digestions have revealed a length of about 100 bases for duplex regions. The methods used to study inverted repeated sequences are compared and discussed.

Base Sequence↗
PubMed1979

Electron-microscopy of intact nuclear DNA from human cells.

Structures retaining many of the morphological features of nuclei may be released by lysing human cells in a non-ionic detergent and 2 M NaCl. Such nucleoids contain all the nuclear DNA packaged within a flexible cage of RNA and protein. HeLa nucleoids have been spread at an air-water interface and viewed in the electron microscope. A tangled network of superhelical fibres surrounds the collapsed cage. Irradiation with gamma-rays abolishes supercoiling and treatment with the untwisting enzyme or a low concentration of ethidium reduces it. A high concentration of ethidium induces supertwisting. The nuclear DNA of higher cells can be isolated naked, supercoiled and intact.

Cell Nucleus↗
PubMed1978

The diagnostic significance of nuclear DNA measurement in cytologic smears of benign and malignant gastric lesions.

Gastric mucosa was obtained from 126 patients by endoscopic biopsy and subsequent cell brushing for histological, cytological and DNA cytophotometric studies. 23 cases were carcinomatous. DNA histogram evaluation for each case was carried out with special consideration of the position of the DNA stem line and the scatter of the measured DNA values. Additionally, DNA distribution characteristics were established for clinical or cytological diagnostic groups. By ascertaining relative mean ploidy values (U values) and relative frequency of euploid and polyploid values (Z values) in the sample populations, cell nuclear DNA determination was used as a criteria for differentiating between benign and malignant alterations of the stomach. The results allow optimistic prognosis concerning the use of cell nuclear DNA content as a significant, though not as the only measuring factor in automated diagnostic procedures.

Biopsy↗