A computer graphics study of sequence-directed bending in DNA

We present theoretical results to account for the unusual physical properties of a 423 bp DNA restriction fragment isolated from the kinetoplast of the trypanosomatid Leishmania tarentolae. This fragment has an anomalously low electrophoretic mobility in polyacrylamide gels and a rotational relaxation time smaller than that of normally-behaved control fragments of the same molecular weight. Our earlier work (Proc. Natl. Acad. Sci. USA 79, 7664, 1982) has attributed these anomalies to the highly periodic distribution of the dinucleotide ApA in the DNA sequence. As originally proposed by Trifonov and Sussman (Proc. Natl. Acad. Sci. USA 77, 3816, 1980) local features of the DNA structure such as a small bend at ApA, if repeated with the periodicity of the helix, will cause systematic bending of the molecule. Computer graphics representations of DNA chain trajectories are presented for different structural models. It is shown that the structural model of Calladine (J. Mol. Biol. 161, 343, 1982) which is based on crystallographic data, is unsuccessful in predicting the systematic bending of DNA in solution.     

Phased psoralen cross-links do not bend the DNA double helix

Although the chemical reaction of psoralens with nucleic acids is well understood, the structure of psoralen-DNA cross-linked products is still not clear. Model building studies base on the crystal structure of the psoralen-thymine monoadduct suggest that each cross-link bends the DNA double helix by 46.5 degrees [Pearlman, D. A., Holbrook, S. R., Pirkle, D. H., & Kim, S.-H. (1985) Science (Washington, D.C.) 227, 1304-1308]. On the other hand, Sinden and Hagerman [Sinden, R. R., & Hagerman, P. J. (1984) Biochemistry 23, 6299-6303] find that, in solution, psoralen cross-linked DNA is not bent. Here we use gel electrophoresis to test the validity of the current models. We have synthesized a series of DNA fragments (21-24 base pairs in length), each containing one unique T-A site for 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) cross-linking. Because of an estimated 28 degrees unwinding of the helix by HMT [Wiesehahn, G., & Hearst, J. E. (1978) Proc. Natl. Acad. Sci. U.S.A. 75, 2703-2707], one expects that the 22-bp cross-linked fragment will be repeated nearly in phase with the average helical screw when multimerized. In that sequence ligation will maximally amplify any deformation to the double helix. We find that the ligated multimers of cross-linked DNA migrate close to the multimers of non-cross-linked DNA on polyacrylamide gels. Our observations place an upper limit of 10 degrees on DNA bending induced by psoralen cross-linking and indicate unwinding by about 1 bp, as well as stiffening of the double helix. These properties are not unexpected for classical intercalators.     

Fechner-Benham subjective colors do not induce McCollough after-effects

Fechner-Benham subjective color is widely believed to be governed by local interactions in early (probably retinal) mechanisms. Here we report three lines of phenomenological evidence that suggest otherwise: subjective colors seen in spatially extended stimuli (a) are dependent on global aspects of the stimuli; (b) can become multistable in position; and (c) even after being stabilized do not support the creation of McCollough's colored after-effects--a cortically based phenomenon generally thought to be more central than Fechner-Benham color. These phenomena suggest a central locus that controls perception of subjective color, characterized by pattern dependent interactions among cortical mechanisms that draw their inputs from peripheral units.     

Sulphate-reducing bacteria which do not induce accelerated corrosion

The corrosive activity of the recently isolated SRB genera has not previously been reported in the literature. In this investigation, three genera of sulphate-reducing bacteria (SRB). Desulfovibrio vulgaris, Desulfobacter postgatei and Desulfobulbus propionicus were tested for their ability to induce accelerated corrosion of mild steel in laboratory growth media. Desulfovibrio vulgaris, well-recognised for its corrosive activity, caused a 78·2% increase in weight loss compared to the control, uninoculated medium (95% confidence limits +37·0% to +130·6%). Desulfobacter postgatei and Desulfobulbus propionicus had no significant effect on corrosion. For Desulfobacter postgatei the mean rate of corrosion was 10·6% more than the control (95% confidence limits −12·0% to +39·0%). For Desulfobulbus propionicus the mean corrosion rate was increased by 5·8% over control (95% confidence limits −9·8% to +24·2%).     

Perfluorocarbons do not induce cytochrome P-448 in the rat liver

Cytochrome P-450 forms appearing in the liver after injection of methylcholanthrene, polychlorinated biphenyls and perfluorochemical emulsion to rats were studied. Activities of marker enzymes, benzpyrenehydroxylase and 7-ethoxyresorufin-O-deethylase, as well as the interaction of liver microsomal membranes with antibodies against different cytochrome forms were investigated. It was shown that fluorocarbon emulsion containing perfluorodecalin did not induce cytochrome P-448 in the rat liver.     

Restriction endonucleases do not induce sister-chromatid exchanges in Chinese hamster ovary cells

Bacterial restriction enzymes offer the unique opportunity to determine the biological and cytogenetic consequences of DNA double-strand breakage. To examine the role of various types of breaks in sister-chromatid exchange (SCE) formation, we used restriction enzymes with different recognition sequences and different cutting frequencies to generate DNA double-strand breaks in Chinese hamster ovary (CHO) cells. The restriction enzymes were introduced by electroporation into exponentially growing cells during the second replication cycle in bromodeoxyuridine, and SCEs were analyzed at mitosis. Contrary to results reported by others, we found no increase in SCE frequency in cells exposed to restriction enzymes despite the presence of numerous cells with chromatid aberrations. These data suggest that DNA double-strand breaks do not lead to SCE formation.     

Phenothiazines: equal concentrations in lipid bilayers do not induce equal response

Perturbation of the order-disorder transition in dipalmitoyl-lecithin bilayer by a series of phenothiazines is measured by differential scanning calorimetry. The membrane concentrations of the various phenothiazines required to induce equal response (i.e., broadening of the phase transition profile) vary over a one hundred-fold concentration range, and correlate well (r = 0.97 for 38 compounds) with the total drug concentration that induces equal response.     

Cytotoxic lymphocyte-derived lytic granules do not induce DNA fragmentation in target cells

When target cells are exposed to CTL, they very quickly sustain nuclear damage, including DNA cleavage, and then they lyse. Nuclear damage of this type is not seen when cells are killed by antibody and C. The role of nuclear damage in the T cell-mediated killing process as well as the mechanism by which the killer cell induces this damage are unknown; however, accumulating evidence suggests that cytolysis may depend on induction of nuclear damage. The exocytosed contents of CTL granules are thought by many workers to mediate target cell lysis. We have now determined whether lytic granules also induce nuclear damage (DNA fragmentation) in cells which they lyse. They do not. In addition, no DNA fragmentation was detected in nuclei incubated with lytic granules or activated CTL. In summary, our results suggest that target cell DNA fragmentation induced by CTL is mediated neither by lytic granules nor by a CTL-derived endonuclease and support the view that the target cell is itself responsible for the internal damage it sustains.     

IL 3 and IL 6 do not induce bone resorption in vitro

Bone resorption in vitro and in vivo can be induced by interleukin 1 (IL 1) and tumor necrosis factor (TNF), both of which are potent inflammatory cytokines. Additionally, there are other factors produced by cells which can active osteoclasts. Because diverse factors are involved in bone resorption, we examined the role of two other inflammatory cytokines, IL 3 and IL 6. IL 3 has been shown to induce the formation of osteoclast-like cells from precursors, while IL 6 is a potent mediator of inflammatory responses. Osteoclast activity in neonatal mouse calvaria was measured as 45Ca released into the supernatant fluid following a 48 hr incubation period with cytokine. Our results show that while parathyroid hormone (PTH) and IL 1 are potent inducers of bone resorption, neither IL 3 nor IL 6 displayed such activity.     

Dissolved solids do not induce diapause in the calanoid copepod Aglaodiaptomus leptopus

The effect of different total dissolved solid levels (TDS) was investigated as a predictor of diapause induction in the calanoid copepod Aglaodiaptomus leptopus. We collected adult copepods in the field and monitored seasonal changes in diapause egg production. We determined total dissolved solid levels, conductivity and temperature values from five ponds. In experimental work, females bearing clutches, collected from the field, were monitored under laboratory conditions to determine the extent of diapause induced. Females without clutches were placed with males and then subjected to low, medium and high TDS levels. After six days, females bearing clutches were isolated to determine the proportion of clutches that were diapausing. The relationship between TDS and food levels was calculated using Williamson and Butlers food limitation index (f). We concluded that neither TDS nor temperature are predictors of the induction of diapause in this study. The obtained results suggest, however, that density possibly plays a role in predicting diapause induction.     

Three regions in the DNA of plasmid pLS1 show sequence-directed static bending.

Three regions showing abnormal electrophoretic mobility, which is an indication of the existence of bends in DNA, have been observed in the DNA of plasmid pLS1. These loci have been characterized by assays designed to detect sequence-directed bending in DNA (temperature-dependence migration and two dimensional electrophoresis). The first region (locus B-1) was located within a fragment that contains a proposed inhibitor countertranscribed RNA (RNAII). The second locus (B-2) contains the plasmid plus origin of replication and the third region (locus B-3) was located in the vicinity of a putative antisense RNA (RNAI) of unknown function. The centres of the first two bent DNA regions were located by circular permutation assays at nucleotides 882 (locus B-1) and 634 (locus B-2). The bend centre of locus B-1 was found to be upstream of the promoter for the putative antisense RNAII. The centre of curvature in locus B-2 was located in the vicinity of the putative promoter of the replication proteins RepA and RepB and of a sequence that has three 11-bp direct repeats. The DNA sequence at this region showed the existence of A.T tracts, with an internal repeat of 10 to 11 base pairs, for five helix turns. A complex curvature in the DNA of pLS1 at locus B-2 that may have a regulatory role in plasmid replication is postulated.     

Molecular dynamics studies of sequence-directed curvature in bending locus of trypanosome kinetoplast DNA.

The macroscopic curvature induced in the double helical B-DNA by regularly repeated adenine tracts (A-tracts) plays an exceptional role in structural studies of DNA because this effect presents the most well documented example of sequence specific conformational modulations. Recently, a new hypothesis of its physical origin has been put forward. According to it, the intrinsic bends in B-DNA may represent one of the consequences of the compressed frustrated state of its backbone. The compressed backbone hypothesis agrees with many data and explains some controversial experimental observations. The original arguments of this theory came out from MD simulations of a DNA fragment with a strong bending propensity. Its sequence, however, was not experimental. It was constructed empirically so as to maximize the magnitude of bending in calculations. To make sure that our computations reproduce the experimental effect we carried out similar simulations with an A-tract repeat of a natural base pair sequence found in a bent locus of a minicircle DNA. We demonstrate spontaneous development of static curvature in the course of MD simulations excluding any initial bias except the base pair sequence. Its direction and magnitude agree with experimental estimates. The results confirm earlier qualitative conclusions and agree with the hypothesis of a compressed backbone as the origin of static bending in B-DNA.     

Toxic levels of amyloid beta peptide do not induce VEGF synthesis

Alzheimer's disease is a neurodegenerative disorder associated with progressive loss of cognitive function and memory. Amyloid beta peptide (Abeta) is the major component of senile plaques and is known to exert its cytotoxic effect mainly by producing H2O2. Vascular endothelial growth factor (VEGF) is elevated in the cerebrospinal fluid (CSF) and brain of AD patients, and H2O2 is one of the factors that induce VEGF. Therefore, we tested whether Abeta might be responsible for the increased VEGF synthesis. We found that Abeta induced the production of H2O2 in vitro. Comparison of the amount of H2O2 required to induce VEGF synthesis in HN33 cells and the amount of H2O2 produced by 10 muM Abeta1-42 in vitro suggested that a toxic concentration of Abeta might induce VEGF synthesis in these cells. However, toxic concentrations of Abeta failed to induce VEGF synthesis in several cell systems. They also had no effect on antioxidant enzymes such as glutathione peroxidase, catalase, and peroxiredoxin in HN33 cells. Cu2+, Zn2+ and Fe3+ are known to accumulate in the brains of AD patients and promote aggregation of Abeta, and Cu2+ by itself induces synthesis of VEGF. However, there was no synergistic effect between Cu2+ and Abeta1-42 in the induction of VEGF synthesis and Zn2+ and Fe3+ also had no effect on the synthesis of VEGF, alone or in combination with Abeta.     

Cellular double-stranded RNA in Phaseolus vulgaris

Summary High molecular weight double-stranded (ds) RNAs have been detected in apparently virus-free French (common) bean Phaseolus vulgaris cv. Black Turtle Soup (BTS). Several other bean cultivars were free of detectable high molecular weight dsRNAs. The dsRNAs have been partially characterized and have homology to the BTS genome as well as to the genomes of other bean cultivars. The T_m of hybrids formed between BTS DNA and denatured dsRNA have been estimated.