Hydrodynamic properties of DNA and DNA-lipid complex in an elongational flow field

The aim of this study was to determine the difference between hydrodynamic properties of DNA-cetyltrimethylammonium (CTA) complex and those of DNA, which may be related to the difference in fibre-forming ability of DNA-CTA from that of DNA. Responses of DNA and DNA-CTA complex to an elongational flow field were investigated. In both solution systems, results suggesting a coil-stretch transition were obtained. From a critical strain rate value, the radius of gyration of DNA-CTA molecules in ethanol-glycerol solution was revealed to be 0.3-0.5 times of that of DNA in aqueous NaCl solution. Shear viscosity of DNA-CTA solution was much smaller than that of DNA solution, also suggesting a smaller size of DNA-CTA in ethanol-glycerol solution than that of DNA in aqueous NaCl solution. The plateau birefringence value of the DNA-CTA system, a parameter that indicates the local molecular conformation and the molecular arrangement, was only about 1/10 of that of the DNA system. There is an empirically determined molecular model of DNA-CTA complex in which a DNA molecule is sheathed by a cylindrical crust made of CTA chains. This structure reduces the DNA molecular density in a pure elongational flow field region but cannot explain the observed reduction of birefringence intensity. The small plateau birefringence value of DNA-CTA compared with that of DNA was attributed to the reduced molecular polarizability by the particular conformation of DNA molecules and CTA chains in the DNA-CTA system such as that expected by the conformational models.     

Elongational flow studies on DNA in aqueous solution and stress-induced scission of the double helix.

Elongational flow techniques are used to investigate the birefringent response and flow-induced molecular scission of monodisperse phage-DNA samples in aqueous solution. A 4-roll mill apparatus was used to characterize the solutions at low stain rates, epsilon less than or equal to 300 s-1, and the opposed jets apparatus used to study fracture of the DNA molecules at strain rates up to 15 x 10(3) s-1. The molecular weight values were measured before and after fracture in elongational flow using the high-resolution technique of pulsed field gel electrophoresis (PFGE). The birefringent response incorporates both rigid and flexible components. The birefringence is nonlocalized and rises gradually to a plateau value, similar to rigid-rod behavior. In addition a certain minimum value in the strain rate is necessary, an onset value epsilon 0, before the signal appears, indicating a flexible component. This behavior is consistent with a hinged-rod model and is similar to that observed for the protein collagen molecule at elevated temperature. We propose that this type of behavior is likely for multistrand rope-like macromolecules where localized separation or partial untwisting of the intertwined chains occurs, creating temporary hinges, in accordance with biochemical evidence for sequence-specific sites of flexibility. Results are presented on the entanglement effects at high concentrations. We have calculated rotational diffusion rates as a function of concentration and molecular weight. Using PFGE to measure the molecular weight profiles, our fracture studies at high strain rates demonstrate chain halving and quartering in accordance with the predictions of the thermally activated barrier to scission theory for single-chain polymers.     

Modulation of HU–DNA interactions by salt concentration and applied force

HU is one of the most abundant proteins in bacterial chromosomes and participates in nucleoid compaction and gene regulation. We report experiments using DNA stretching that study the dependence of DNA condensation by HU on force, salt and HU concentration. Previous experiments at sub-physiological salt levels revealed that low concentrations of HU could compact DNA, whereas larger HU concentrations formed a DNA-stiffening complex. Here we report that this bimodal binding behavior depends sensitively on salt concentration. Only the compaction mode was observed for 150 mM and higher NaCl levels, i.e. for physiological salt concentrations. Similar results were obtained for the more physiological salt K-glutamate. Real-time studies of dissociation kinetics revealed that HU unbound slowly (minutes to hours under the conditions studied) but completely for salt concentrations at or above 100 mM NaCl; the lifetime of HU complexes was observed to increase with the HU concentration at which the complexes were formed, and to decrease with salt concentration. Higher salt levels of 300 mM NaCl completely eliminated observable HU binding to DNA. Finally, we observed that the dissociation kinetics depend on force applied to the DNA: increased applied force in the sub-piconewton range accelerates dissociation, suggesting a mechanism for DNA tension to regulate chromosome structure and gene expression.     

Molecular weight effect on liquid crystalline gel formation of curdlan

Curdlan dissolved in alkaline solution forms a unique gel consisting of liquid crystalline gel (LCG) and amorphous gel (AG) in alternating layers by a dialysis into aqueous calcium chloride. The unique structure has been investigated by measuring the birefringence of the gel Deltan, the ratio q of the thickness of LCG layer delta to the gel radius R, and the calcium content in the gel C(Ca) in a wide range of molecular weights of fractionated Curdlan, as well as unfractionated Curdlan as a control. With increasing molecular weight of Curdlan, Deltan increased and q = delta/R decreased, and both became saturated at high molecular weight. Deltan and q for unfractionated Curdlan were smaller and larger, respectively, than those for fractionated Curdlan. C(Ca) was constant irrespective of molecular weight and its distribution, which means that the abundance of calcium ions per glucose unit in the gel does not depend on the degree of orientation of mesogens. These results suggest that the amorphous phase appears when the size of the Curdlan molecules is larger than the average intermolecular distance, resulting from the random coil to triple helix transformation of Curdlan molecules associated with lowering hydroxide anion concentration in the dialysis process.     

ACTION OF HYDROXYUREA AND N-CARBAMOYLOXYUREA ON THE CELL CYCLE OF TETRAHYMENA

Addition of a 50 mm dosage of hydroxyurea (HU) to growing cultures of the cilitate Tetrahymena pyriformis allows cell growth to continue but inhibits DNA synthesis, and inhibits cell division after a 20–30% increase in cell number. Higher concentrations of HU cause cell death. T. pyriformis strain differences exist in sensitivity to HU. No cytotoxicity selective to a specific phase of the cell cycle could be demonstrated.
The inhibitory effects of HU are entirely reversed by removal of HU and this procedure can be used to induce cell cycle synchrony. Supplementing HU treated cells with deoxyribonucleosides relieves the inhibitory action of HU.
Carbamoyloxyurea (COU) is a reactive intermediate of HU and its action on Tetrahymena appears to be similar to that of HU. Because of this similarity and because COU is more potent than HU we postulate that COU is responsible for the unique properties previously ascribed to HU.     

E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA.

The incubation of the E coli DNA binding protein HU with relaxed circular SV40 DNA in the presence of pure nicking-closing enzyme introduces up to 18 negative superhelical turns in the DNA molecules as measured by agarose gel electrophoresis. The maximal density of supercoiling is obtained at a HU-DNA mass ratio of 1. Reconstituted DNA-HU complexes prefixed with glutaraldehyde appear as condensed circular structures having an average of 14 "beads" per circular SV40 DNA molecule, with a "bead" diameter of 180 +/- 23 A. The circular SV40 DNA is condensed by a ratio of 2.0-2.5 relative to naked DNA. This is similar to the ratio (2.4) measured for chromatin formed by reassociation of relaxed SV40 DNA with the four core histones.     

Characterization of hyaluronic acid and synovial fluid in stagnation point elongational flow

Hyaluronic acid (HA) is an important biomacromolecule, which fulfils a number of vital physiological functions (especially in the joint synovial fluid) and also has consumer and pharmaceutical applications. HA solution properties have already been quite thoroughly characterized in response to steady shear flows but are less well understood in highly deforming extensional flows. In this study, flow‐induced birefringence measurements are made as a function of the strain rate in planar elongational flow at the stagnation point of a cross‐slot device using HA solutions of a range of molecular weights and at dilute concentrations. The results provide macromolecular relaxation times, molecular weight distributions and the extensional viscosities and Trouton ratios of the fluids. The HA relaxation time is found to vary as ^1.8, which is consistent with a partially solvated, expanded coil. An intrinsic Trouton ratio is defined, which varies as ². The measurement of birefringence with strain rate is shown to be highly sensitive to the molecular weight distribution and can resolve subtle changes due to macromolecular degradation and the presence of fracture products. Mechanical degradation experiments in the cross‐slots indicate midchain scission of HA macromolecules, strongly suggesting near full extension of the high‐molecular weight fraction in the stagnation point extensional flow field. Taken together the results suggest a possible method for analysis of the HA in synovial fluid, and this concept is tested using synovial fluid obtained from porcine tarsal joint. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 287–305, 2014.     

In vivo and in vitro regulation of IgE production in murine hybridomas

Normal BALB/c mice injected i.p. with the IgE-secreting hybridomas B53 (epsilon, kappa anti-DNP), SE1.3 (epsilon, kappa, anti-arsonate) or A3B1 (epsilon, kappa, anti-TNP) were monitored for serum IgE concentrations and frequencies of splenic T lymphocytes with surface membrane receptors for the Fc portion of IgE (Fc epsilon R+ T lymphocytes). Mice with B53 or SE1.3 hybridomas initially developed high concentrations of IgE and CD8+ Fc epsilon R+ T lymphocytes, followed by a progressive decline in both serum IgE and expression of cytoplasmic epsilon-chains in the hybridoma cells. Serum IgE concentrations in mice with A3B1 hybridomas progressively increased without development of Fc epsilon R+ T lymphocytes nor a subsequent decline in IgE or change in cytoplasmic epsilon-chain expression in the A3B1 cells. An in vitro system in which the IgE-secreting hybridoma cells were cocultured with spleen cells harvested from mice with established B53 tumors was used to investigate the mechanisms involved in the inhibition of IgE production by the hybridoma cells. The results of these studies indicate that: 1) the induction/upregulation of Fc epsilon R on CD8+ T lymphocytes in vivo requires factors in addition to high serum IgE concentrations; 2) in addition to CD8+ Fc epsilon R+ T lymphocytes and monocytes, another, as yet unidentified, splenic cell component appears to contribute to the process by which epsilon-chain expression in IgE-secreting hybridoma cells is suppressed, and 3) a hybridoma (A3B1) that fails to induce CD8+, Fc epsilon R+ T lymphocytes in vivo and is not inhibited in IgE expression in vivo, nonetheless is inhibited in IgE expression in vitro when cocultured with spleen cells from mice with B53 tumors.     

Optico-hydrodynamic properties of high molecular weight DNA. II. Effect of aqueous glycerol solvents

The optical and hydrodynamic properties of T2 bacteriophage DNA have been determined by steady-state flow birefringence and viscosity in glycerol–aqueous buffer solvents at 25°C. Flow birefringence and extinction angle data were obtained over a velocity gradient range of 0.1 to 5 sec^?1 and at concentrations from 3 to 55 μg/ml in solvents containing approximately 30, 42, and 48 vol-% glycerol. Large optical backgrounds were observed in the mixed solvent flow birefringence studies which presented special experimental difficulties; these are described and their effect upon the flow birefringence data are discussed. The data on extinction angle provide no evidence for an internal viscosity effect on the stationary-state hydrodynamic properties of high molecular weight DNA over a range of solvent viscosity from 0.9 to 4.6 cP. Both the optical and hydrodynamic properties under present conditions of measurement appear to be self-consistent in terms of the values for these quantities in neutral aqueous buffer solution. Interpretation of the birefringence is complicated by uncertainties inherent in calculating the form anisotropy of DNA in non-aqueous solvents, but the data imply no large changes in helical structure with increasing glycerol concentration. Both intact and slightly degraded DNA samples were investigated, and no significant polydispersity effects were observed under the experimental conditions described.     

Effect of the number of nucleic acid oligomer charges on the salt dependence of stability (DeltaG 37degrees) and melting temperature (Tm): NLPB analysis of experimental data

For nucleic acid oligomers with variable chain lengths, the salt concentration ([salt]) dependences of the denaturation temperature (T(m)) and of the free energy of helix formation at 37 degrees C (Delta) are predicted using nonlinear Poisson-Boltzmann (NLPB) calculations. Analysis of experimental data reveals that the ratio of the [salt] derivative of melting temperature (ST(m) = dT(m)/d log[salt]) to the value for a polymer with the same base composition (ST(m)/ST(m, infinity)) is independent of base composition but strongly dependent on the number of DNA charges (/Z/) below approximately 8 bp for two-strand helices (formed from association of two complementary strands) and below approximately 18 bp for hairpin helices (formed from folding of one self-complementary strand). We interpret these ST(m)/ST(m, infinity) ratios in terms of the ratio of thermodynamic ion release from the oligomer (Deltan(u), per charge) to that from the same oligomer embedded in polymeric DNA (Deltan(u, infinity), per charge). Experimental values of ST(m)/ST(m, infinity) and its dependence on /Z/ are in good agreement with NLPB predictions for a preaveraged (essential structural) model of DNA. In particular, the NLPB calculations describe the stronger /Z/ dependence of ST(m) observed for melting of oligomeric hairpin helices than for melting of two-strand helices. These calculations predict an experimentally detectable (>or=10%) difference between ST(m) and ST(m, infinity) which increases strongly with decreasing length for two-strand helix lengths of <15 bp and for hairpin helix lengths of <30 bp. From NLPB values of Deltan(u)/Deltan(u, infinity), we predict Delta as a function of [salt] and /Z/. Predictions of thermodynamic and thermal stabilities of oligomeric helices as functions of length and [salt] are consistent with and represent a significant refinement of the average oligomer salt effect currently in use in nearest neighbor stability predictions.     

Orientation of DNA molecules in agarose gels by pulsed electric fields

The electric birefringence of DNA restriction fragments of three different sizes, 622, 1426, and 2936 base pairs, imbedded in agarose gels of different concentrations, was measured. The birefringence relaxation times observed in the gels are equal to the values observed in free solution, if the median pore diameter of the gel is larger than the effective hydrodynamic length of the DNA molecule in solution. However, if the median pore diameter is smaller than the apparent hydrodynamic length, the birefringence relaxation times increase markedly, becoming equal to the values expected for the birefringence relaxation of fully stretched DNA molecules. This apparent elongation indicates that end-on migration, or reptation is a likely mechanism for the electrophoresis of large DNA molecules in agarose gels. The relaxation times of the stretched DNA molecules scale with molecular weight (or contour length) as N2.8, in reasonable agreement with reptation theories.     

Effects of hydroxyurea on the mitotic activity and the G2 phase in hairless mouse epidermis

Hairless mice were given 5 mg hydroxyurea (HU) intraperitoneally (i.p.) followed by 0.15 mg Colcemid at various times after HU. The animals were killed at 2 and 4 hr after Colcemid, the epidermal mitotic counts in dorsal skin were determined and the mitotic rates calculated. These were compared with the normal mitotic rates, and the ratios between the results from HU-treated and -untreated animals were calculated. Hydroxyurea caused a considerable reduction in the mitotic rate with a trough at 6 hr, followed by a wave of increased mitotic rate with a peak at 14 hr, followed by a secondary drop at 20 hr, and then a return to normal. Another group of mice were given HU only, and the fraction of epidermal cells in G2 was measured by flow cytometry. From these animals, without previous injection of Colcemid, we also determined the mitotic counts and calculated the mitotic durations. Cells piled up in G2 for the first 6 hr after HU injection, then the G2 compartment was emptied. The results are discussed in relation to previous results from this department showing the effect of the same dose of HU on DNA synthesis in the same mouse strain. It is concluded that HU not only blocks or retards DNA synthesis in epidermal cells, but also affects the movement of cells through G2 and M. The cell kinetic effects of HU thus seem to be very complex.     

Fidelity of mammalian DNA replication and replicative DNA polymerases.

Current models suggest that two or more DNA polymerases may be required for high-fidelity semiconservative DNA replication in eukaryotic cells. In the present study, we directly compare the fidelity of SV40 origin-dependent DNA replication in human cell extracts to the fidelity of mammalian DNA polymerases alpha, delta, and epsilon using lacZ alpha of M13mp2 as a reporter gene. Their fidelity, in decreasing order, is replication greater than or equal to pol epsilon greater than pol delta greater than pol alpha. DNA sequence analysis of mutants derived from extract reactions suggests that replication is accurate when considering single-base substitutions, single-base frameshifts, and larger deletions. The exonuclease-containing calf thymus DNA polymerase epsilon is also highly accurate. When high concentrations of deoxynucleoside triphosphates and deoxyguanosine monophosphate are included in the pol epsilon reaction, both base substitution and frameshift error rates increase. This response suggests that exonucleolytic proofreading contributes to the high base substitution and frameshift fidelity. Exonuclease-containing calf thymus DNA polymerase delta, which requires proliferating cell nuclear antigen for efficient synthesis, is significantly less accurate than pol epsilon. In contrast to pol epsilon, pol delta generates errors during synthesis at a relatively modest concentration of deoxynucleoside triphosphates (100 microM), and the error rate did not increase upon addition of adenosine monophosphate. Thus, we are as yet unable to demonstrate that exonucleolytic proofreading contributes to accuracy during synthesis by DNA polymerase delta. The four-subunit DNA polymerase alpha-primase complex from both HeLa cells and calf thymus is the least accurate replicative polymerase. Fidelity is similar whether the enzyme is assayed immediately after purification or after being stored frozen.(ABSTRACT TRUNCATED AT 250 WORDS)     

Elongational flow studies on type IV collagen: Comparison with type I

Elongational flow techniques have been used to investigate the birefringent response of monodisperse type IV collagen in dilute solution and the results compared with type I. collagen. A four-roll mill apparatus was used to characterize the solutions at low strain rates, $\dot{\varepsilon}$ ? 300 s^?1. The birefringence is nonlocalized and rises gradually to a plateau value, in accordance with rigid-rod behavior. The gradients of the tangent to the curves at zero strain rate are estimated for types IV and I collagen. The concentrations of the solutions used were in the dilute to semidilute regimes. Using a value of 300 nm for the length of type I collagen, values of 364–408 nm were calculated for the length of the type IV collagen molecule, depending on the concentration regime chosen, which is consistent with biochemical predictions based on a rigid molecule. The results imply that the behavior of type IV collagen molecules in solution is similar to type I collagen, despite the presence of several sequence interruptions in the type IV helix. © 1993 John Wiley & Sons, Inc.     

Unique error signature of the four-subunit yeast DNA polymerase epsilon

We have purified wild type and exonuclease-deficient four-subunit DNA polymerase epsilon (Pol epsilon) complex from Saccharomyces cerevisiae and analyzed the fidelity of DNA synthesis by the two enzymes. Wild type Pol epsilon synthesizes DNA accurately, generating single-base substitutions and deletions at average error rates of 5' exonuclease activity is less accurate to a degree suggesting that wild type Pol epsilon proofreads at least 92% of base substitution errors and at least 99% of frameshift errors made by the polymerase. Surprisingly the base substitution fidelity of exonuclease-deficient Pol epsilon is severalfold lower than that of proofreading-deficient forms of other replicative polymerases. Moreover the spectrum of errors shows a feature not seen with other A, B, C, or X family polymerases: a high proportion of transversions resulting from T.dTTP, T.dCTP, and C.dTTP mispairs. This unique error specificity and amino acid sequence alignments suggest that the structure of the polymerase active site of Pol epsilon differs from those of other B family members. We observed both similarities and differences between the spectrum of substitutions generated by proofreading-deficient Pol epsilon in vitro and substitutions occurring in vivo in a yeast strain defective in Pol epsilon proofreading and DNA mismatch repair. We discuss the implications of these findings for the role of Pol epsilon polymerase activity in DNA replication.     

Effects of Hydroxyurea On the Mitotic Activity and the G2 Phase In Hairless Mouse Epidermis

Hairless mice were given 5 mg hydroxyurea (HU) intraperitoneally (i.p.) followed by 0.15 mg Colcemid® at various times after HU. the animals were killed at 2 and 4 hr after Colcemid, the epidermal mitotic counts in dorsal skin were determined and the mitotic rates calculated. These were compared with the normal mitotic rates, and the ratios between the results from HU-treated and -untreated animals were calculated. Hydroxyurea caused a considerable reduction in the mitotic rate with a trough at 6 hr, followed by a wave of increased mitotic rate with a peak at 14 hr, followed by a secondary drop at 20 hr, and then a return to normal. Another group of mice were given HU only, and the fraction of epidermal cells in G₂ was measured by flow cytometry. From these animals, without previous injection of Colcemid, we also determined the mitotic counts and calculated the mitotic durations. Cells piled up in G₂ for the first 6 hr after HU injection, then the G₂ compartment was emptied. the results are discussed in relation to previous results from this department showing the effect of the same dose of HU on DNA synthesis in the same mouse strain. It is concluded that HU not only blocks or retards DNA synthesis in epidermal cells, but also affects the movement of cells through G₂ and M. the cell kinetic effects of HU thus seem to be very complex.     

Orientation of DNA Molecules in Agarose Gels By Pulsed Electric Fields

Abstract

The electric birefringence of DNA restriction fragments of three different sizes, 622,1426, and 2936 base pairs, imbedded in agarose gels of different concentrations, was measured. The birefringence relaxation times observed in the gels are equal to the values observed in free solution, if the median pore diameter of the gel is larger than the effective hydrodynamic length of the DNA molecule in solution. However, if the median pore diameter is smaller than the apparent hydrodynamic length, the birefringence relaxation times increase markedly, becoming equal to the values expected for the birefringence relaxation of fully stretched DNA molecules. This apparent elongation indicates that end-on migration, or reptation is a likely mechanism for the electrophoresis of large DNA molecules in agarose gels. The relaxation times of the stretched DNA molecules scale with molecular weight (or contour length) as N^2.8, in reasonable agreement with reptation theories.     

A fluorescence study of the binding of poly(1,N6-ethenoadenylic acid) to Escherichia coli initiation factor 3

The binding of initiation Factor 3 (IF3) to poly (1,N6-ethenoadenylic acid) [poly(epsilon A)] was investigated by fluorescence spectroscopy. At low salt concentrations, IF3 evokes an increase in the fluorescence intensity of poly(epsilon A) due to the unstacking of the nucleotide bases. The poly(epsilon A) fluorescence enhancement titrates to an endpoint of 13 +/- 2 nucleotide residues per IF3. The maximum poly(epsilon A) fluorescence enhancement, at lattice saturation, decreases with increasing salt concentration. Even though IF3 does not produce a large fluorescence increase between 75 and 200 mM NaCl concentration, the protein still binds to poly(epsilon A) at these salt concentrations as measured by sedimentation partition chromatography; the value of Kobs for the IF3-poly(epsilon A) interaction is comparable to that of other synthetic polynucleotides. The binding of IF3 to poly(A) at 150 and 200 mM NaCl induces an increase in nucleotide base-base separation as determined by CD, yet IF3-induced disruption of base stacking of poly(epsilon A) at these same salt concentrations is not detected by fluorescence. It is likely that IF3 binds primarily to the phosphate backbone of poly(epsilon A) at low salt concentrations, producing an increase in the fluorescence intensity. But, at higher salt concentrations, the aromatic amino acids intercalate between the nucleotide bases quenching the poly(epsilon A) fluorescence.     

Deoxyribonucleoside triphosphate metabolism and the mammalian cell cycle. Effects of hydroxyurea on mutant and wild-type mouse S49 T-lymphoma cells

DNA precursor synthesis can be blocked specifically by the drug hydroxyurea (HU) which has therefore been used for anticancer therapy. High concentrations of HU, however, affect other processes than DNA synthesis; nevertheless, most studies on the biological action of HU have been made with concentrations at least one order of magnitude higher than those needed for cell-growth inhibition. In this study we characterized the effects of low concentrations of HU (i.e. concentrations leading to 50% inhibition of cell growth in 72 h) on cell cycle kinetics and nucleotide pools in mouse S49 cells with various defined alterations in DNA precursor synthesis. The effect of 50 microM HU on deoxyribonucleoside triphosphate pools was a 2-3-fold decrease in the dATP and dGTP pools, with no change in the dCTP pool and a certain increase in the dTTP pool. Addition of deoxycytidine or thymidine led to a partial reversal of the growth inhibition and cell-cycle perturbation caused by HU, and was accompanied by an increased level of the deoxyribonucleoside triphosphates. Addition of purine deoxyribonucleoside gave no protection, indicating that salvage of these nucleosides could not supply precursors for DNA synthesis in T-lymphoma cells. We observed a higher sensitivity to HU of cells lacking purine nucleoside phosphorylase or with a ribonucleotide reductase with altered allosteric regulation. Cells lacking thymidine kinase or deoxycytidine kinase were just as sensitive as wild-type cells.