Triplet anisotropy decay measurements of DNA internal motion

Triplet anisotropy decay techniques have been used to measure the internal flexibility and overall rotational motions of DNA over a time range of 15 ns to 200 microseconds. Nearly monodisperse DNA fragments with lengths varying from 65 to 600 base pairs were studied using the intercalating dye methylene blue as a triplet probe. The slow end-over-end tumbling of short DNA fragments (less than 165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motions of its helix axis. At the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when it is bound, methylene blue monitors fast internal motions of the helix. Since the rod-like end-over-end tumbling rules out fast bending motions (for short DNA fragments), the fast components of DNA anisotropy decay must be due to twisting motions of the helix, occurring with a time constant near 50 ns. The same techniques were used to measure the conformational flexibility of DNA in the nucleosome. It is concluded that, when the DNA helix is wrapped to form a nucleosome, it experiences substantial internal flexibility, occurring with a time constant near 30 ns. The amplitude and time-scale of this motion appear to be similar to that seen in the uncomplexed DNA helix.

Use of urinary hydroxyproline excretion as a tumor marker in diagnosis and follow-up of prostatic carcinoma

Urinary hydroxyproline/creatinine ratio was measured in 49 patients of prostatic carcinoma and 13 patients with benign prostatic hypertrophy, the latter group serving as controls. The results show that it is a very sensitive indicator of osseous metastases in prostatic carcinoma. The ratio was also measured in 18 patients of prostatic carcinoma with bony metastases before commencement of treatment and during treatment. The results show that the elevated pretreatment values were significantly reduced in those who responded to therapy whereas in nonresponders, the values remained high. Changes in urinary hydroxyproline appeared to reflect the nature of response to treatment better than other parameters.

Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding

Negative superhelical coiling of covalently closed DNA plasmids facilitates the formation of left-handed Z-DNA segments. This was demonstrated by binding of antibodies specific for Z-DNA. Plasmid pBR322 and two derivatives from it, pLP32 and pLP014, carrying inserts of alternating CG sequences of 32 bp and 14 bp, respectively, were used. Longer inserts required less negative superhelical density to induce the B-Z transitions. Antibody binding to supercoiled plasmids was also visualized by electron microscopy. Cross-linking of the antibody to the negatively supercoiled plasmid and restriction of the DNA with restriction endonucleases demonstrated that the antibodies combine with the CG insert in pLP32. For pBR322, however, evidence suggests that the antibody combines with a section of DNA containing 14 bases with alternating purine and pyrimidine residues with one residue out of alternation: CACGGGTGCGCATG. These cross-linking studies provide evidence for the binding specificity of the anti-Z-DNA antibodies. On the basis of experimental findings, we have calculated the changes in free energy associated with B-Z transitions in superhelical plasmids.

DNA motions in the nucleosome core particle

We have used time-resolved triplet state anisotropy decay techniques to measure the conformational flexibility of DNA in the nucleosome. From these measurements we conclude that, in a nucleosome, the DNA helix experiences substantial internal flexibility, which occurs with a time constant near 30 nsec. We find that our data can be fit well by a modified version of the Barkley-Zimm model for DNA motion, allowing only DNA twisting motions and the overall tumbling of the nucleosome. That fit yields a calculated torsional rigidity equal to 1.8 X 10(-19) erg X cm, a value equal to that measured for uncomplexed DNA. We conclude from such similarity that large, fast twisting motions of the DNA helix persist, nearly unaltered, when DNA is wrapped to form a nucleosome.

Isolation and properties of L-amino acid oxidase from Ophiophagus hannah venom

This paper reports the isolation and some properties of L-amino acid oxidase from Ophiophagus hannah venom. The differences between L-amino acid oxidase from Ophiophagus hannah and that from other sources in specific activity, properties and the spectrum of isozymes are noticeable. The result of electrophoresis on polyacrylamide gel shows that this purified enzyme is homogenous. The molecular weight determined by gradient polyacrylamide gel slab (4--30%) is around 15 X 10(4) dalton. The molecular weight of the subunit determined by SDS gradient gel electrophoresis (4--30%) is around 7.3 X 10(4) dalton. Therefore, this enzyme is composed of two subunits. The absorption spectrum reveals that there are two FADs in each molecule. The optimum pH of enzymic reaction is around 8.7--9.0 when L-leucine is used as substrate. The inhibition of the products is noticeable when substrate concentration goes beyond 3mM. This enzyme is heat stable and its activity would not decrease obviously after heating at 55 degrees C for 40 min. A linear relationship between enzyme concentration and reaction rate was noticed when enzyme concentration was below 5.7 micrograms/ml.

Cytofluorometric determination of nuclear DNA in living and preserved algae

Three DNA-localizing fluorochromes used in conjunction with epi (incident) UV illumination were examined for sensitivity and selectivity for the cytofluorometric determination of nuclear DNA in ten species of six algal genera: Mougeotia, Oedogonium, Sirogonium, Spirogyra and Zygnema among the green algae, and the marine red alga Polysiphonia boldii. In comparison with absorption photometry for the determination of nuclear DNA, the cytofluorometric procedure proved to be simpler and considerably more sensitive. Following staining with 4',6-diamidino-2-phenylindole (DAPI), nuclei fluoresce blue-white, the fluorescence intensity of the DNA-DAPI complex being considerably greater than that of the unbound dye molecule. Algal strains stained with 2,5-bis[4'-aminophenyl(1')]-1,3,4-oxadiazole (BAO) also showed brilliant blue-white nuclear fluorescence. Although the BAO schedule requires the use of freshly prepared dye and sulfite water, and careful control of hydrolysis, nuclear fluorescence of the stained specimens does not fade under irradiation of the UV beam as rapidly as it does with certain other fluorochrome procedures. A more useful fluorochrome was the fungal antibiotic mithramycin. Its staining schedule is simple and the bright orange-yellow fluorescence of the nuclei is associated with an exceptional degree of sensitivity and specificity for DNA. Forty-eight-year-old preserved filaments of Spirogyra jatobae, stained with either BAO or mithramycin, exhibited a fluorescence brilliance of nuclear and chloroplast DNA equal to that of fresh specimens of this species. The three schedules, but particularly the one with mithramycin, have proven useful in providing indirect evidence for variation in ploidy level in several of the above algal genera, and in verifying the assumed ploidy level of the gametophyte (haploid) and tetrasporophyte (diploid) of Polysiphonia boldii.

Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling

Negative supercoiling of plasmid DNAs containing 24--42 base pairs of alternating d(pCpG) inserts is shown to cause the flipping of the helical hand of the inserts from right to left under physiological conditions. For a negatively supercoiled DNA with a fixed linking number, this flipping reduces its superhelicity and, therefore, is accompanied by a shift of its electrophoretic mobility in agarose gel. Quantitation of the mobility shifts indicates that essentially the whole stretch of contiguous alternating d(pCpG) flips to the left-handed helical form when the negative superhelical density (specific linking difference) is greatest than or equal to 0.03.

Expression of the marker (X) (q28) in lymphoblastoid cell lines

The marker(X)(q28) chromosome associated with one type of X-linked mental retardation has been demonstrated in lymphoblastoid cell lines established from affected individuals. The mar(x) can reliably and repeatedly be seen by the addition of FUdR to the cultures for 24 hrs prior to harvest. This simple technique provides an excellent in vitro experimental test system for investigation of the mar(X).

Mechanism of extramedullary haematopoiesis in rabbits with saponin-induced myelofibrosis and myeloid metaplasia

The saponin-induced myelofibrosis and myeloid metaplasia model in the rabbit was used to study mechanisms of extramedullary haematopoiesis. Haematopoietic progenitor cells, erythroid colony forming units (CFU-E) and burst forming units (BFU-E) were assayed serially in the peripheral blood, spleen and bone marrow after saponin administration, employing the in vitro methylcellulose culture technique. Animals that had undergone splenectomy prior to saponin administration were also studied. The results demonstrated increases of progenitor cells in the blood and spleen and a simultaneous depletion of such cells in marrow after saponin treatment. The results in splenectomized animals were similar to those observed in non-splenectomized animals after saponin administration. The findings indicate that following saponin administration there is a release of CFU-E and BFU-E from bone marrow into periphery and probably deposition in the spleen, and suggest that myeloid metaplasia in myelofibrosis may result from colonization of extramedullary sites originating from the bone marrow.

Molecular motion of DNA as measured by triplet anisotropy decay

We have used triplet anisotropy decay techniques to measure the internal flexibility and overall rotational motion of DNA, covering a time range from 15 ns to 200 mus. Nearly monodisperse DNA fragments 65--600 base pairs long were studied by using the intercalating dye methylene blue as a triplet probe. We found that the slow end-over-end tumbling of short DNA fragments (less than or equal to 165 base pairs) is as predicted for a rigid rod. As expected, a longer DNA fragment (600 base pairs) experiences slow segmental motion of its helix axis. We found that, at the earliest times, anisotropy decays more rapidly than expected for a rigid rod, suggesting that, when bound, methylene blue monitors fast internal motion of the helix. Since the rod-like end-over-end tumbling of short fragments rules out fast bending motions, we conclude that the fast components of DNA anisotropy decay are due to twisting motion of the helix, occurring with a time constant near 50 ns.

Yeast DNA topoisomerase II. An ATP-dependent type II topoisomerase that catalyzes the catenation, decatenation, unknotting, and relaxation of double-stranded DNA rings

An activity from the yeast Saccharomyces cerevisiae, initially noted for its catalysis of aggregation of covalently closed double-stranded DNA rings in the presence of ATP, has been identified as a type II DNA topoisomerase and is designated yeast DNA topoisomerase II. The formation of the DNA aggregate, which has been shown to be a network of DNA rings that are topologically interlocked, requires the presence of a yeast DNA-binding protein in addition to the topoisomerase. In the absence of the binding protein, yeast DNA topoisomerase II catalyzes decatenation and unknotting of duplex DNA rings and the relaxation of negatively or positively supercoiled DNA. All reactions are ATP-dependent and require Mg(II). Similar to other eukaryotic and phage T4-type II DNA topoisomerases, the yeast enzyme does not catalyze DNA supercoiling under the assay conditions employed. The activity is not sensitive to the gyrase inhibitor nalidixic acid, oxolinic acid, or novobiocin. Coumermycin inhibits the activity, however, at a concentration as low as 5 microgram/ml.

Body composition in affective disorder before, during, and after lithium carbonate therapy

The body composition of three unipolar and 17 bipolar patients, studied during the depressive state, was compared with that of 48 controls. The ratio of extracellular to intracellular water content was significantly less in male patients than in male controls: the difference between female patients and female controls was not statistically significant. In patients of both sexes, residual sodium concentration was greater in patients than in controls. The intracellular content of potassium was the same in patients as in controls. In six patients, body composition was studied prior to lithium carbonate therapy, after 17 days of treatment, and 17 days after discontinuing administration of the drug. The significant changes were a decrease in body weight during therapy, and a decrease in body water content and an increase in residual sodium concentration after drug treatment was discontinued.

Body composition measurements in normal man: the potassium, sodium, sulfate and tritium spaces in 58 adults

The aqueous phase of total body composition varies with sex, and changes with age, necessitating age, sex and method-specific normal values. Consensus has developed for the methods most suited to clinical studies. 3H20 for water, 35SO4 for ECW, 24Na for NAc, and 40K for body potassium were used in 58 normal volunteers aged 19-80, 30 men and 28 women. This report shows significant age regressions in both sexes for total body water and intracellular water, and for both Na and K when referenced to body water. Combination of these findings with the highly age related decrease in total body potassium confirms previous studies that body cell mass decreases with age. Intracellular K+ and Na+ at the zero age intercept are 130 and 14.5 for males, and 124 and 24mEq/1 for females respectively. Secular decrease in K+ and increase in Na+ concentrations in the average cell are suggested although not established. Values for normal body composition, in subjects healthy by all available criteria are in some instances age and sex dependent, but in all parameters except fat show wide normal range (SD = 7% of mean) which derive more from biological variation than from limitations of measurement precision. However, use of body water rather than weight succeeds in narrowing this wide range, and is a more logical denominator which is readily subject to accurate measurement. In serial studies of the same subject, significant changes can be measured which are well within the normal range.