Modeling DNA supercoils and knots with B-spline functions

A method is offered to model the complex trajectories of closed circular DNA supercoils and knots. The trajectories are approximated by polygons and analytical expressions of the curves are generated from the polygons with B-spline functions. The resulting curves are used to evaluate the writhe and elastic energy of a series of interrelated supercoils, and to generate detailed atomic models of the deformed double helix.     

Binding of heparin to human high molecular weight kininogen

The binding of heparin to high molecular weight kininogen (H-kininogen) was analyzed by the effect of kininogen in decreasing the heparin-induced enhancement of the rate of inactivation of thrombin by antithrombin. The conditions were arranged so that the heparin-catalyzed antithrombin-thrombin reaction, monitored in the presence of the reversible thrombin inhibitor p-aminobenzamidine, followed pseudo-first-order kinetics and the observed rate constant (kappa obsd) varied linearly with the heparin concentration. In the absence of metal ions, H-kininogen minimally affected kappa obsd, measured at a constant concentration of heparin with high affinity for antithrombin (30 nM), at I = 0.15, pH 7.4 and 25 degrees C. However, at a saturating concentration of Zn2+ (10 microM), kappa obsd was reduced to 50% at approximately 20 nM H-kininogen and to that of the uncatalyzed reaction at greater than or equal to approximately 0.2 microM H-kininogen. Conversely, at a saturating concentration of H-kininogen (0.5 microM), kappa obsd was decreased to 50% at approximately 0.6 microM Zn2+ and to the kappa obsd of the uncatalyzed reaction at greater than or equal to 10 microM Zn2+. Other metal ions were effective in the order Zn2+ approximately Ni2+ greater than Cu2+ approximately Co2+ approximately Cd2+. The single-chain and two-chain forms of H-kininogen and the H-kininogen light chain reduced the heparin enhancement in the presence of Zn2+ to the same extent, whereas low molecular weight kininogen had no influence.(ABSTRACT TRUNCATED AT 250 WORDS)     

Melting behavior of a covalently closed, single-stranded, circular DNA

We synthesized the 26-residue deoxynucleotide sequence d(TTCCT5GGAATTCCT5GGAA) which folds intramolecularly to form a dumbbell-shaped, double-hairpin structure with a gap between the 3' and the 5' ends. We used T4 polynucleotide kinase to phosphorylate the 5' end followed by T4 DNA ligase to close the 3' and 5' ends. Melting of the dumbbell structure formed by this ligated sequence produces a covalently closed, single-stranded, circular final state. We employed calorimetric and spectroscopic techniques to characterize thermodynamically the melting behavior of the ligated molecule and compared it with the corresponding melting behavior of its unligated precursor. This comparison allowed us to characterize uniquely the influence of single-stranded ring closure on intramolecular duplex melting. The data reveal that ring closure produces a thermally more stable structure which exhibits significantly altered melting thermodynamics. We rationalize these thermodynamic differences in terms of differential solvation and differential counterion association between the ligated and unligated molecules. We also note the importance of such constrained dumbbell structures as models for hairpins, cruciforms, and locally melted domains within naturally occurring DNA polymers.     

Phototoxic liposomes coupled to an antibody that alone cannot modulate its cell-surface antigen kill selected target cells

Summary Molecules such as antibodies that bind to cell surfaces can be used to deliver cytotoxic drugs to selected cells. To be effective the drug must usually be taken into the cells by endocytosis. In this study a T-cell line (CCRFCEM) was effectively killed by liposomes carrying a photosensitizer and bearing the antibody OKT4 (anti-CD4). The unconjugated antibody does not induce antigenic modulation in the target cells, an indication of the absence of endocytosis, and would therefore not normally have been selected as an agent for drug delivery. It cannot, however, be concluded with certainty that the conjugates act at the cell surface and several alternative explanations of their efficacy are offered.     

The use of metronidazole, tinidazole and dimetridazole in eliminating trichomonads from laboratory mice

Metronidazole, tinidazole and dimetridazole were administered in the drinking water for 5 days to mice experimentally infected with Tritrichomonas muris and Tetratrichomonas microta. Mice were successfully infected with T. muris and T. microta recovered from infected gerbils. The trichomonas infection was successfully eliminated in mice given a 1% sucrose solution containing 2.5 mg/ml metronidazole or tinidazole. Mice receiving 1.0 mg/ml metronidazole, 1.0 mg/ml tinidazole and 1.2, 5.0 and 10.0 mg/ml dimetridazole failed to eliminate the trichomonas organism. A reduction in water intake was only noted with mice receiving 10 mg/ml dimetridazole. In mice receiving only 1% sucrose the infection was not eliminated.     

Spatial arrangement of tiller replacement in Agropyron desertorum following grazing

Summary The spatial arrangement of tiller replacement was assessed on grazed and ungrazed tussocks of Agropyron desertorum (Fisch. ex Link) Schult. for three annual cycles. Frequency distributions of the number of replacement tillers per single progenitor were also determined. Tiller replacement was usually greater on the perimeter of tussocks than within the core, with or without grazing. Replacement was inversely related to grazing intensity, both on the perimeter and within the core of tussocks. Heights of replacement tillers on the perimeter or within the core seldom differed. Furthermore, grazing seldom affected the number of replacement tillers per progenitor. Greater tillering on the perimeter than within the core indicates that the tussocks were expanding. Apparently, grazing neither enhances tussock expansion and subsequent disintegration, nor does it necessarily lead to patches of tillers (multiple tillering per progenitor) within tussocks of A. desertorum.     

Evidence Against the Involvement of Ionically Bound Cell Wall Proteins in Pea Epicotyl Growth

Ionically bound cell wall proteins were extracted from 7 day old etiolated pea (Pisum sativum L. cv Alaska) epicotyls with 3 molar LiCl. Polyclonal antiserum was raised in rabbits against the cell wall proteins. Growth assays showed that treatment of growing region segments (5-7 millimeters) of peas with either dialyzed serum, serum globulin fraction, affinity purified immunoglobulin, or papain-cleaved antibody fragments had no effect on growth. Immunofluorescence microscopy confirmed antibody binding to cell walls and penetration of the antibodies into the tissues. Western blot analysis, immunoassay results, and affinity chromatography utilizing Sepharose-bound antibodies confirmed recognition of the protein preparation by the antibodies. Experiments employing in vitro extension as a screening measure indicated no effect upon extension by antibodies, by 50 millimolar LiCl perfusion of the apoplast or by 3 molar LiCl extraction. Addition of cell wall protein to protease pretreated segments did not restore extension nor did addition of cell wall protein to untreated segments increase extension. It is concluded that, although evidence suggests that protein is responsible for the process of extension, the class(es) of proteins which are extracted from pea cell walls with 3 molar LiCl are probably not involved in this process.     

cDNA and deduced primary structure of rat protein B23, a nucleolar protein containing highly conserved sequences

Protein B23 (Mr/pI = 38,000/5.1) is a major RNA-associated nucleolar phosphoprotein which contains highly acidic segments and has a high affinity for silver ions. Using synthetic oligonucleotides as probes cloned cDNAs encoding protein B23 were isolated and characterized. One of the cDNAs, obtained from a rat brain library, contained an insert of 1232 base pairs of DNA encoding a polypeptide of 292 amino acid residues. Segments of the protein sequence were confirmed by partial sequencing of CNBr fragments from rat hepatoma protein B23. The protein contains a methionine-rich amino-terminal sequence and two highly acidic segments in the center of the sequence. The first acidic segment, in which 11 of the 13 residues are acidic, begins at residue 120 and contains a major phosphorylation site. In the second segment (residues 159-187) there are four copies of the sequence Asp-Asp-Glu, and all but two of the 29 residues have acidic side chains. When the sequence of the rat protein was compared with available sequences from other species a high degree of conservation was found; the 77-residue carboxyl-terminal sequence is identical with that of human protein B23 (Chan, P. K., Chan, W.-Y., Yung, B. Y. M., Cook, R. G., Aldrich, M. B., Ku, D., Goldknopf, I. L., and Busch, H. (1986) J. Biol. Chem. 261, 14335-24341), and about 63% of the residues are identical when the rat B23 sequence is compared with protein N038 from Xenopus laevis (Schmidt-Zachmann, M. S., Hügle-D?rr, B., and Franke, W. (1987) EMBO J. 6, 1881-1890). Except for the presence of highly acidic regions no significant similarities were found with protein C23 (nucleolin), the other major nucleolar protein.     

Dexamethasone blocks increased leukotriene B4 production during endotoxin-induced lung injury

We hypothesized that leukotriene B4 (LTB4) might be produced during endotoxemia in pigs and, if so, might play a role in the pathophysiology of acute respiratory failure. Escherichia coli endotoxin (055-B5) was infused intravenously into anesthetized pigs at 5 micrograms/kg the 1st h, followed by 2 micrograms.kg-1.h-1 for 3 h. Endotoxemic pigs were treated with dexamethasone (DEX, iv) 18 h (5 mg/kg) and 1 h (5 mg/kg) before onset of endotoxemia. During phases I (i.e., 0-2 h) and II (i.e., 2-4 h), endotoxin decreased cardiac index, caused granulocytopenia, and increased mean pulmonary arterial pressure, pulmonary vascular resistance, alveolar-arterial O2 gradient, and hematocrit. During phase II, plasma LTB4 levels were increased (as determined by radioimmunoassay, reverse-phase high-performance liquid chromatography, and ultraviolet spectroscopy). Endotoxin increased the levels of LTB4 and albumin in bronchoalveolar lavage fluid (BALF). DEX blocked or greatly attenuated the endotoxin-induced hemodynamic abnormalities and blocked the increases in plasma and BALF LTB4 levels. We conclude that LTB4 is produced during porcine endotoxemia and could possibly play a role in the pathophysiology of endotoxin-induced lung injury in anesthetized pigs.