DNA supercoiling and its effects on the structure of DNA

In prokaryotic organisms, there is strong evidence that the DNA is underwound or negatively supercoiled. The degree of supercoiling of intracellular DNA is less certain, and various estimates that can be made from existing data place the specific linking difference (superhelical density) of intracellular DNA in prokaryotes around -0.04. The effects of negative supercoiling on DNA structure are illustrated by the flipping of alternating C-G or T-G sequences from right-handed B-helical form to the left-handed Z-helical form. For a plasmid containing a 42 base-pair alternating C-G insert, the B-to-Z transition occurs at a specific linking difference of 0.031 in a dilute aqueous buffer; the same transition occurs at a specific linking difference of -0.041 for a plasmid containing a 42 base-pair alternating T-G insert. The probing of the structure of a particular sequence of intracellular DNA is discussed.

Folate metabolism in cells from fragile X syndrome patients and carriers

The in vitro folate sensitivity of the fragile site at Xq27 and the claims of a beneficial response of patients given folic acid prompted us to examine the folate metabolism in cells cultured from fragile X syndrome patients and carriers. Using Epstein-Barr virus we established permanent lymphoblastoid lines from 4 fragile X syndrome males and 3 carriers from 7 families. All these lines expressed the fragile site when 0.1 microM 5-fluorodeoxyuridine (FUdR) was added to the cultures 24 hr prior to harvest; thus, the lines seemed suitable for seeking an intrinsic defect. Fragile X syndrome patient and carrier lines and normal control cell lines did not differ in regard to folate requirement for growth, the ability to use homocysteine in place of methionine, the ability to utilize reduced folates as the sole folate source, or methotrexate sensitivity. These results suggest that no intrinsic defect in folate metabolism is present in fragile X syndrome cells.

Characterization of human hybridomas secreting antibody to tetanus toxoid

We have selected a thioguanine-resistant lymphoblastoid cell line (LTR228) that forms human-human hybrids with high efficiency. Fusions with peripheral B cells consistently yield one colony per 10(5) cells plated. To produce antitetanus monoclonal antibodies, we withdrew blood from persons who had recently received booster injections of tetanus toxoid. T cells were separated from peripheral mononuclear cells by 2-aminoethylisothiouronium bromide-induced rosette formation, given 1,500 rads (1 rad = 0.01 gray), and cultured in a 1:1 ratio with nonrosetting cells. After 3 days of pokeweed mitogen stimulation, heterokaryons were produced by a plate-fusion technique and cultured in Iscove's Dulbecco's minimal essential medium for 24 hr prior to hybrid selection. Colonies appeared after 10-14 days in hypoxanthine/azaserine supplemented medium. A direct binding enzyme-linked immunosorbent assay with specific tetanus toxoid inhibition identified positive wells. The hybridomas were cloned twice in soft agarose and by limiting dilution. The subcloned hybridomas double every 26 hr (vs. every 16 hr for LTR228) and produce 1-5 micrograms of specific IgG, kappa antibody per 10(6) cells per ml per 24 hr. All subclones (almost 200) continue to secrete antibody after 11 months of continuous culture. Twelve representative subclones have near tetraploid amounts of DNA. From hybridomas grown in 5-liter spinner flasks, milligram quantities of the IgG, kappa antibody were purified by staphylococcus protein A affinity chromatography. Specific antibody from hybridoma cultures protected mice injected with 1,000 times the LD50 of tetanus toxin. Our cell line and associated techniques should permit the production of therapeutically important human monoclonal antibodies.

Energetics of B-to-Z transition in DNA

Analysis by two-dimensional gel electrophoresis of topoisomers of plasmids containing d(pCpG)n . d(pCpG)n inserts, in which n ranges between 8 and 21, shows that the B-to-Z transition within the alternating C-G is readily induced by negative supercoiling and is highly cooperative. The free energy parameters for the transition in dilute aqueous buffers have been evaluated from a statistical mechanical analysis of the data, and these parameters allow prediction of the superhelicities of plasmids at which the transition occurs in alternating C-G inserts over a wide range of lengths. In agreement with the crystal structures, the helical handedness of the B structure in solution and that of the Z structure are shown to be opposite to each other. Furthermore, it is found that the B form of the alternating C-G sequence in solution has a helical periodicity of 10.5 +/- 0.1 base pairs per turn, and the Z form has a helical periodicity of 11.6 +/- 0.3 base pairs per turn. There also appears to be a significant unwinding of the right-handed DNA duplex at each of the B/Z junctions.

Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions

Cruciform formation in a pBR322 derivative containing a 68 base pair perfect palindromic sequence has been studied. In relaxed DNA the cruciform is unstable by about 17 kcal mole-1 in free energy. In a supercoiled DNA with a negative specific linking difference (superhelical density) of 0.03 or higher, however, the cruciform becomes the stable species. Nevertheless, even at native superhelical densities (typically around -0.06), cruciform formation is extremely slow, unless the DNA is subjected to conditions that destabilize base pairing. When precautions are taken to avoid artificial triggering of cruciform formation, the 68 bp perfect palindrome-containing plasmid isolated from cells is devoid of the cruciform. The rate of disappearance of the cruciform in linear DNA and the deletion of the palindromic sequence in vivo have also been examined.

Circulating granulocyte and macrophage progenitor cells in primary and secondary myelofibrosis

Patients with primary myelofibrosis (PMF) and myelofibrosis secondary to carcinoma (SMF) were compared with regard to circulating granulocyte macrophage progenitor cells (CFU-GM) using in vitro tissue culture techniques. Although increased numbers of CFU-GM had previously been well documented in PMF, few patients with the secondary variety had been studied. Our data indicate that there is an increase in circulating CFU-GM in patients with SMF but it is significantly lower than in those with PMF. It is suggested that in both conditions disruption of the marrow microvascular system results in a release of CFU-GM to the circulation. In PMF stem cell colonization of the spleen with its consequent myeloid metaplasia may be responsible for the additional increase in CFU-GM. The determination of CFU-GM numbers may provide additional data to help to distinguish PMF and SMF in atypical cases where the distinction is unclear.

Mapping of single-stranded regions in duplex DNA at the sequence level: single-strand-specific cytosine methylation in RNA polymerase-promoter complexes

A method based on the differential rate of cytosine methylation in single- and double-stranded nucleic acids by dimethyl sulfate [Peattie, D.A. & Gilbert, W. (1980) Proc. Natl. Acad. Sci. USA 77, 4679-4682] has been developed for probing unpaired cytosines in DNA and DNA-protein complexes at the sequence level. Application of the method to the complexes between Escherichia coli RNA polymerase (EC 2.7.7.6) and three related promoters, lac UV5, trp, and a hybrid promoter tac resulting from the fusion of the two, reveals distinct differences in the way RNA polymerase unpairs DNA in these promoters. No single-stranded region is detectable in the complex with the trp promoter. For the lac UV5 promoter, the cytosines at positions -6, -4, -2, and -1 are in an unpaired region. The same cytosines in the tac promoter, which is homologous in sequence to lac UV5 in this region, are also found to be single stranded. For the pair of promoters lac UV5 and tac, the cytosine methylation reaction has also been used to demonstrate the steep temperature dependence of opening of base pairs by RNA polymerase. One striking feature is that the midpoint of this transition for the tac promoter is 3 degrees C lower than the corresponding value for lac UV5, even though the sequence of the unpaired region in the two promoters is identical.

Gyrase . DNA complexes visualized as looped structures by electron microscopy

Gyrase bound to duplex DNA in the absence of ATP is seen by electron microscopy as a nearly spherical particle frequently located at the intersection of two duplex DNA strands. Such looped structures with gyrase situated at the base of the loops are observed with both linear and circular DNA substrates, and two or three individual DNA molecules bound to the same protein are also seen at high DNA concentrations. Addition of the nonhydrolyzable beta,gamma-imido analog of ATP to the gyrase . DNA reaction mixture prior to sample fixation for microscopy reduces the frequency of gyrase molecules found at DNA intersections. Looped structures similar to those of the gyrase . DNA complex are also seen with the complex of DNA and the A subunit of gyrase. When negatively supercoiled DNA which has been partially relaxed by gyrase in the absence of ATP is fixed for electron microscopic examination, intermediate forms are observed that contain both supercoiled and relaxed loops in a single DNA molecule, with the enzyme located at the common base of the loops. These results suggest that gyrase possesses multiple DNA-binding sites, a feature which allows the enzyme to hold DNA in constrained loops. The relation of these observations to the mechanism of gyrase action is discussed.

Cloning of the gene topA encoding for DNA topoisomerase I and the physical mapping of the cysB-topA-trp region of Escherichia coli

The gene topA of Escherichia coli that encodes for DNA topoisomerase I has been cloned by a combination of genetic and radioimmunal screening. The gene has been mapped to be within a 3.4 Kb segment of the bacterial genome. The intracellular level of the enzyme in strains harboring extrachromosomal copies of topA gene increases with increasing copy number of the gene and the introduction of extrachromosomal copies of the topA gene truncated at its 3' side into a topA strain of E. coli does not significantly influence the expression of the chromosomal copy of topA. These results suggest that the expression of topA is not tightly regulated. Strains in which DNA topoisomerase I is overproduced grow significantly slower in broth and give smaller size colonies on agar plates. Physical mapping of a 20 Kb region containing cysB; topA and trp has also been carried out with a number of restriction enzymes; topA is found to be immediately adjacent to cysB and is separated from trp by a 7 Kb segment where no known gene resides.

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.

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.

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.

Knotted DNA from bacteriophage capsids

The majority of the DNA prepared from tailless capsids of bacteriophage P2 by the phenol extraction procedure consists of monomeric rings that have their cohesive ends joined. Electron microscopic and ultracentrifugal studies indicate that these molecules have a complex structure that is topologically knotted; they have a more compact appearance and a higher sedimentation coefficient when compared with regular nicked P2 DNA rings. Linearization of these rings by thermal dissociation or repair of the cohesive ends by DNA polymerase I in the presence of all four deoxynucleoside triphosphates gives molecules that are indistinguishable from normal P2 DNA that has been similarly treated. The knotted nature of the majority of P2 head DNA is further supported by analyzing the products when these molecules are treated with ligase and the ligase-treated molecules are subsequently nicked randomly with DNase I. The data are consistent with the notion that, if such a molecule is first converted to a form that contains only one single-chain scission per molecule, strand separation gives a linear strand and a highly knotted single-stranded ring. The results suggest that the DNA packaged in tailless P2 capsids is arranged in a way that leads to the formation of a complex knot when the ends join. In an intact phage particle, the anchoring of one terminus of the DNA to the head-proximal end of the tail [Chattoraj, D. K. & Inman, R. B. (1974) J. Mol. Biol. 87, 11-22] presumably diminishes or prevents this kind of joining. The novel knotted DNA can be used to assay type II DNA topoisomerases that break and rejoin DNA in a double-stranded fashion.

Mutations in the gene coding for Escherichia coli DNA topoisomerase I affect transcription and transposition

Mutations in top, the structural gene for Escherichia coli DNA topoisomerase I, have been identified and mapped at 28 min on the chromosome, near cysB. Strains carrying deletions of the top gene are viable. The top mutations, however, do exert pleiotropic effects on transcription and transposition. Mutants lacking DNA topoisomerase I have a more rapid rate of induction and a higher level of catabolite-sensitive enzymes including tryptophanase and beta-galactosidase. This general activation of transcription by top mutations can be attributed to an increase in the negative superhelicity of the DNA in vivo when the topoisomerase activity is abolished. The frequency of transposition of Tn5, a transposon carrying kanamycin resistance, is decreased by a factor of 40 or more in top mutants. A direct or indirect role of the topoisomerase in transposition is discussed. The transposition frequency of Tn3, however, is not dependent on top. Based on the studies of the E. coli top mutants, it appears that the supX gene, which was originally studied in Salmonella typhimurium [Dubnau, E. & Margolin, P. (1972) Mol. Gen. Genet. 117, 91-112] is likely to be the structural gene for DNA topoisomerase I.

Particle size measurements using an optical variable-frequency-grid technique

A fringe visibility method for sizing particles 10 microm and larger has been developed. As the image of a particle scans across a variable frequency grid, the transmitted light signal oscillates with varying visibility. The visibility goes through a null at a well-defined point where the particle diameter approximates the local grid spacing. Several optical arrangements implementing the variable frequency grid technique have been tested. Using classified alumina and pulverized coal particles we obtained good agreement between size distributions measured by this technique and those from a commercial off-line analyzer. However, our optical arrangement and signal processing techniques require further development to reduce them to practice.

Mapping the topography of DNA wrapped around gyrase by nucleolytic and chemical probing of complexes of unique DNA sequences

Complexes between DNA gyrase and DNA fragments of unique sequences were used to probe the topography of the DNA with nucleases and dimethyl sulfate. The results indicate that the flanking regions, each 50 bp in size, of a 145--155 bp DNA segment resistant to staphylococcal nuclease contain groups of pancreatic DNAase I-susceptible sites that are spaced 10--11 nucleotides apart. Pairs of adjacent DNAase I-sensitive sites on complementary strands are typically staggered by 2--4 bp. The binding of DNA to gyrase confers no protection against alkylation of the DNA by dimethyl sulfate. These properties of the gyrase-DNA complex are reminiscent of those of the nucleosome, and the common underlying structural feature appears to be wrapping of the DNA around a protein core. The gyrase-DNA complex differs from the nucleosome, however, in that it must possess features necessary for the catalysis of DNA chain breakage and the modulation of the DNA-enzyme interaction by ATP. We present evidence that the breakage and rejoining of the DNA by gyrase occur within a central region of the staphylococcal nuclease-resistant DNA segment. The relation of this observation to the mechanism of DNA supercoiling by gyrase is discussed. Addition of ATP or its beta, gamma-imido analog has essentially no effect on the patterns of susceptibilities to DNAase I, implying that the DNA-enzyme contacts mapped by the nuclease ae little affected by ATP-induced conformational changes.

Deoxyribonucleic acid gyrase-deoxyribonucleic acid complex containing 140 base pairs of deoxyribonucleic acid and an alpha 2 beta 2 protein core

Staphylococcal nuclease digestion of the complex between DNA and DNA gyrase yields a gyrase-DNA core particle composed of a 140 base pair DNA segment and an active gyrase enzyme. The partial specific volume and S20,w of this purified core complex are measured to be 0.70 cm3/g and 14.5 S, respectively, by sedimentation measurements in H2O and D2O media. The molecular weight of the core complex estimated from equilibrium centrifugation is 470 000; the ratio of the translational frictional coefficient to that of the unsolvated equivalent sphere is calculated to be 1.9. Treatment of free gyrase in solution with dimethyl suberimidate gives three cross-linked species of roughly equal amounts that can be identified as alpha 2, alpha 2 beta, and alpha 2 beta 2. When the gyrase core complex is treated with the same cross-linking agent, 70-80% of the protein is converted to the alpha 2 beta 2 species. These results establish that the gyrase-DNA core complex contains a 140 base pair DNA segment and a tetrameric alpha 2 beta 2 protein.

E. coli and M. luteus DNA topoisomerase I can catalyze catenation of decatenation of double-stranded DNA rings

Escherichia coli and Micrococcus luteus DNA topoisomerase I are found to promote catenation of double-stranded DNA rings. At low DNA concentration dimeric catenanes are the major catenated products; at high DNA concentration or when spermidine is present, catenanes containing more than two rings are formed. There is no requirement of extensive sequence homology between the conponent rings forming a catenane; dimeric catenanes between Pseudomonas phage PM2 DNA and E. coli plasmid pBR322 are readily formed. The formation of a dimeric catenane by these type I topoisomerases, however, requires the presence of at least one preexisting single-chain scission in one of the two component rings. This is in contrast to the cases with the type II DNA topoisomerases which can form catenanes made of covalently closed rings only. The catenanes formed by the type I enzymes can be unlinked by the same enzymes, or by DNA gyrase, a type II enzyme, upon dilution of the isolated catenanes. The catenation and decatenation of duplex DNA rings adds a fourth type of reaction promoted by these type I DNA topoisomerases to the three reported previously: relaxation of superhelical DNA, interconversion between single-stranded DNA rings with and without knots and the intertwining of single-stranded DNA rings of complementary sequences into a covalently closed duplex ring with a high linking number. All four topoisomerization reactions involve the crossing of one DNA strand through a transient break of another DNA strand. The new reaction reported here suggests that such a crossover event might not require pairing of complementary nucleotide sequences.

Urinary hydroxyproline excretion as a marker of osseous metastasis in carcinoma of the prostate

Urinary hydroxyproline was elevated significantly in patients with untreated stage D prostatic carcinoma when compared to values in patients with benign prostatic hypertrophy and prostatic carcinoma without bony metastasis. Our results indicate that hydroxyproline may be a valuable marker in early staging, followup and evaluating treatment in prostatic cancer.

Urinary hydroxyproline excretion in myelofibrosis

Urinary hydroxyproline measurements were performed in a group of health volunteers as well as patients with cancer and myelofibrosis. Patients in whom there was no metastatic involvement of bone marrow excreted an amount of hydroxyproline not different from that of the control group. Those who had marrow metastasis produced elevated levels of hydroxyproline; the highest excretions were observed when marrow fibrosis was associated with metastasis. These results contrasted with those observed in agnogenic myeloid metaplasia patients whose excretions were equivalent to the control group. The result suggests differences in the pathogenesis of myelofibrosis and a technique potentially useful for distinguishing between patients who may otherwise be diagnostic problems.

Structural alterations of the liver induced by N,N'-diacetylbenzidine. A new model of cirrhosis

Little is known about hepatic structural alterations induced by administration of the aromatic amine, N,N'-diacetylbenzidine. Therefore, we injected adult rats with this chemical at a dose of approximately 1 g/kg of body weight. Light and electron microscopy of liver specimens revealed hepatocellular degeneration and prominent changes in bile canaliculi, including dilation, disappearance of microvilli, and an apparent loss of structural integrity of the cell membrane. These findings were seen in the peripheral part of the hepatic lobules. Cirrhotic changes eventually developed. We concluded that N,N'-diacetylbenzidine injected intraperitoneally is capable of inflicting structural damage to the liver in rats.

Helical repeat of DNA in solution

The helical repeat of DNA in solution has been measured directly by analyzing the gel electrophoretic patterns of pairs of covalently closed DNAs with length differences between 1 and 58 base pairs, out of a total length of about 4350 base pairs per DNA molecule. The method is based on the observation that for a covalently closed DNA of a fixed size of n base pairs (n of the order of several thousand), under appropriate conditions, two topological isomers (topoisomers) differing by 1 in their linking numbers are well resolved by gel electrophoresis. If the size of the DNA is increased to n + x base pairs, unless x is an integral multiple of the helical repeat h, the bands of the topoisomers with n + x base pairs per molecule are all shifted relative to the bands of the topoisomers with n base pairs per molecule. The magnitude of the shift is directly related to the nonintegral residual of x/n. Analysis of the set with x ranging from 1 to 58 gives the DNA helix repeat in solution as 10.4 base pairs per turn under physiological conditions, with an estimated probable error of +/- 0.1. This result strongly supports the double helix structure of DNA and rejects the side-by-side model of Rodley et al. [Rodley, G.A., Scobie, R.S., Bates, R.H. T & Lewitt, R.M. (1976) Proc. Natl. Acad. Sci. USA 73, 2959-2963]. The helical repeat of DNA measured in solution is significantly different from the value 10.0 base pairs per turn for the B form fiber structure.

Primary hyperparathyroidism and chronic lymphocytic leukemia

Although hypercalcemia is a frequent event during the course of many malignancies it has only rarely been described with patients with chronic lymphocytic leukemia. Review of the literature revealed only eleven such case reports. The mechanism of the hypercalcemia in these patients was generally unclear although one patient was found to have a parathyroid adenoma and in another patient tested the level of osteoclast activating factor was high. Two additional chronic lymphocytic leukemia patients with hypercalcemia are described in this report and in each a parathyroid adenoma was found. The patient in whom the diagnosis was made ante mortem had an excellent response to parathyroidectomy. Osteoclast activating factor level was measured in one patient and found to be within normal limits. Since three of the thirteen reported cases of chronic lymphocytic leukemia with hypercalcemia have demonstrated parathyroid adenomas, it is suggested that consideration be given to that possibility in such patients so that appropriate surgery may be done.

Escherichia coli DNA topoisomerase I catalyzed linking of single-stranded rings of complementary base sequences

Eco DNA topoisomerase I (E. coli omega protein) has been observed to catalyze the formation of double-stranded, covalently closed DNA from complementary single-stranded DNA rings, a novel reaction which is topologically forbidden without the enzyme-catalyzed breakage and rejoining of DNA backbone bonds. Incubation of a mixture of single-stranded PM2 DNA rings of complementary base sequences with omega yields a species with a sedimentation coefficient in an alkaline medium characteristic of a covalently closed circular double-stranded DNA. Buoyant density measurements in CsCl at alkaline pH also identify the product as a covalently closed duplex ring. If the omega-catalyzed reaction is stopped short of completion, highly negatively supercoiled molecules are formed which sediment more slowly in an alkaline medium than the final duplex product. As the reaction proceeds the mean sedimentation rate of the intermediates increases. This is in agreement with the expectation that the linking number between the two complementary rings increases gradually during the course of the reaction from zero to that of a relaxed covalently closed circular DNA duplex. The possible role of DNA topoisomerases in genetic recombination is discussed.

Physiochemical studies on interactions between DNA and RNA polymerase. Ultraviolet absorption measurements

The interaction between Escherichia coli RNA polymerase and a restriction fragment of coliphage T7 DNA containing four promoter sites for the coli enzyme has been studied by difference uv absorption spectroscopy in a low ionic strength buffer containing 10 mm MgCl2 and 50 mM KCl. The binding of the enzyme to the DNA is accompanied by a hyperchromic shift which shows a maximum around 260 nm, and increases with increasing temperature in the temperature range studied (4-40 degrees C). Measurements were also carried out with whole T7 DNA and a restriction fragment containing no promoter site. A comparison of the results obtained with the various DNAs suggests that the binding of an RNA polymerase to a promoter site in the low ionic strength medium causes the disruption of a short segment of the DNA helix, of the order of ten pairs; the binding of an enzyme molecule to a promotor site appears to have a cooperative effect on the binding of the enzyme molecules to adjacent non-promoter sites with concomitant disruption of DNA base pairs.

Micrococcus luteus DNA gyrase: active components and a model for its supercoiling of DNA

Two active components alpha and beta of micrococcus luteus DNA gyrase, of peptide weights of 115,000 and 97,000, respectively, have been purified. Each individual component exhibits little DNA gyrase activity; the ATP-dependent negative supercoiling of a covalently closed circular DNA duplex is catalyzed by a combination of the two. Covalent closure by Escherichia coli ligase of a circular DNA containing single-chain scissions, when carried out in the presence of a combination of the DNA gyrase components alpha and beta, gives a positively supercoiled DNA upon removal of the bound protein molecules. ATP was not present during the ligase treatment; therefore the positive supercoiling of DNA observed is a result of the binding of gyrase molecules, presumably as multi-subunit oligomers, during the ligation step. This is in contrast to the negative supercoiling of DNA catalyzed by gyrase in the presence of ATP. A model in which negative supercoiling of DNA is achieved by ATP-modulated repetitive wrapping of the DNA around gyrase is described. The model also suggests a plausible mode of action by which translocation of a DNA along its helix axis can be actively driven by an ATPase.

Nonhistone proteins HMG1 and HMG2 change the DNA helical structure

Two chromatin nonhistone proteins (from calf thymus) of the high mobility group, HMG1 and HMG2, reduce the linking number (topological winding number) of a circular DNA if the covalent closure of the DNA is carried out in their presence. This indicates that these proteins can either unwind the double helix, or induce a supercoiling of the DNA.

Interaction between DNA and Escherichia coli protein omega. Formation of a complex between single-stranded DNA and omega protein

Escherichia coli omega protein is found to form a complex with single-stranded DNA. The complex is stable in buoyant CsCl or Cs2SO4 density gradients. Addition of Mg(II) to the concentrated salt solutions, however, leads to the dissociation of the complex, even in the presence of EDTA in molar excess over Mg(II). The dissociated omega retains its enzymatic activity; the DNA recovered from the dissociated complex is indistinguishable from the original DNA. Exposure of the complex to alkali results in the cleavage of the DNA. This cleavage generates a 3'-hydroxyl DNA terminus, and the omega protein is found linked to the 5'-terminus, presumably covalently. Pronase digestion of the complex results initially in the removal of approximately 30% of the protein. A significant fraction of the residual complex is still stable in concentrated salt solutions, and can be dissociated by Mg(II). Extensive digestion with pronase results in the removal of the protein and the cleavage of the DNA chain.