Evidence for sequence preferences in the intercalative binding of ethidium bromide to dinucleoside monophosphates.

The rate of production of tandem duplications in phage λ has been measured in the presence and absence of known recombination systems. Two deletion phages have been used: tdel33, a deletion derivative of a φ80-λ hybrid phage, and λb221, which carries a large deletion of the central portion of the λ chromosome. Both phages are int⁻, and tdel33 is also red⁻, by virtue of their deletions. Stocks of these phages can be prepared free of long tandem duplication derivatives by CsCl density gradient purification. After a single cycle of lytic growth, lysates from these purified phage stocks contain tandem duplications at a frequency of 10⁻³ in the case of tdel33 and 10⁻⁵ in the case of λb221. These frequencies are unaffected by the presence of mutations in the host Rec system or the phage Red system. To investigate the difference in duplication frequency between tdel33 and λb221, the phages were grown in mixed infection. The result indicates that a trans-active product of tdel33 is responsible for its high frequency of duplication production.Tandem duplications have been detected by banding the phage lysates in CsCl density gradients. Long DNA addition mutants can be detected in this way if they arise with a frequency of at least 10⁻⁵ and if the duplication length is at least 0.14 λ lengths. To accomplish this it is necessary to distinguish them from contaminating parental phage and from dense phages with aberrant structures which arise at roughly comparable frequencies. The former can be done by rebanding and the latter by growth and rebanding. To distinguish these types we have also made use of a new mutant of Escherichia coli which does not plate λ deletion phages. All of the DNA addition mutants we have detected in this way are tandem duplications; evidently mutants with long insertions arise more rarely.     

A calorimetric study of the binding of 2'-deoxyuridine-5'-phosphate and 5-fluoro-2'-deoxyuridine-5'-phosphate to thymidylate synthetase.

The thermodynamic parameters, ΔH′, ΔG′, and ΔS′, and the stoichiometry for the binding of the substrate 2′-deoxyuridine-5′-phosphate (dUMP) and the inhibitor 5-fluoro-2′-deoxyuridine-5′-phosphate (FdUMP) to Lactobacillus casei thymidylate synthetase (TSase) have been investigated using both direct calorimetric methods and gel filtration methods. The data obtained show that two ligand binding sites are available but that the binding of the second mole of dUMP is extremely weak. Binding of the first mole of dUMP can best be illustrated by dUMP + TSase + H⁺?(dUMP-TSase-H⁺). [1] The enthalpy, ΔH₁′, for reaction [1] was measured directly on a flow modification of a Beckman Model 190B microcalorimeter. Experiments in two different buffers (I = 0.10 m) show that ΔH₁′ = ?28 kJ mol^?1 and that 0.87 mol of protons enters into the reaction. Analysis of thermal titrations for reaction [1] indicates a free energy change of ΔG₁′ = ?30 kJ mol^?1 (K₁ = 1.7 × 10⁵ m^?1). From these parameters, ΔS₁′ was calculated to be +5 J mol^?1 degree^?1, showing that the reaction is almost totally driven by enthalpy changes. Gel filtration experiments show that at very high substrate concentrations, binding to a second site can be observed. Gel filtration experiments performed at low ionic strength (I = 0.05 m) reveal a stronger binding, with ΔG₁′ = ?35 kJ mol^?1 (K₁ = 1.2 × 10⁶ m^?1), suggesting that the forces driving the interaction are, in part, electrostatic. Addition of 2-mercaptoethanol (0.10 m) had the effect of slightly increasing the dUMP binding constant. Binding of FdUMP to TSase is best illustrated by 2FdUMP + TSase + n_HH⁺?FdUMP₂ ? TSase ? (H⁺)_nH. [2] The enthalpy for this reaction, ΔH₂, was also measured calorimetrically and found to be ?30 kJ mol^?1 with n_H = 1.24 at pH 7.4 Assuming two FdUMP binding sites per dimer as established by Galivan et al. [Biochemistry15, 356–362 (1976)] our calorimetric results indicate different binding energies for each site. Based on the binding data, a thermodynamic model is presented which serves to rationalize much of the confusing physical and chemical data characterizing thymidylate synthetase.     

Analysis of protein self-association by combined calorimetric and molecular sieve studies: application to beta-lactoglobulin A

The application of isothermal calorimetry to the study of self-association reactions between identical protein subunits has been explored to assess the types of information obtainable from heat of dilution curves (i.e., the molar heat of dilution as a function of total solute concentration). Relationships between the heat of dilution, subunit association constants, and enthalpies of formation for the various association complexes in a self-associating system have been formulated. A method is described for constructing heat of dilution curves from sequential step-wise dilution experiments in a batch-type calorimeter. The relationship between calorimetric and van't Hoff enthalpies is formulated for systems undergoing self-association reactions. Comparison between the two is shown by numerical simulation to provide a very sensitive test for the presence of intermediate species.Calorimetric measurements were made on the self-association of β?lactoglobulin-A at 5.0 °C, pH 4.65, in 0.1 m NaCl and in 0.1 m acetate. Heat of dilution curves constructed from these data were used to estimate the equilibrium constant and enthalpy of formation, assuming a monomer-tetramer association process. Values of 31 ± 4 kcal/mole tetramer for the enthalpy and 1.3 ± 1.0 × 10¹¹ liter³/mole³ for the constant of tetramerization were determined from the calorimetric measurements in NaCl. The corresponding values for calorimetric measurements in acetate were 33 ± 4 kcal/mole and 1.6 ± 1.0 × 10¹¹ liter³/mole³.The calorimetric results were compared with thermodynamic information obtained from association data between 5 and 25 °C in 0.1 m acetate using molecular sieve chromatography. Within experimental error, the molecular sieve data at 5 °C could be fit to a monomer-tetramer association reaction with a monomer molecular weight of 36,000. From these studies a van't Hoff enthalpy of 38 ± 4 kcal/mole tetramer and an equilibrium constant of 4.6 ± 1.0 × 10¹¹ liter³ mole³ at 5 °C were obtained. Comparison between calorimetric and van't Hoff enthalpies indicates that the self-association of β-lactoglobulin-A under these conditions can be adequately described by a monomer-tetramer reaction. The results suggest that, a small fraction (e.g., 5–10%) of species having intermediate states of aggregation may be present, but preclude the presence of large fractions of intermediate species having appreciable enthalpies of association.     

Two-dimensional, computer-controlled film scanner: quantitation of fluorescence from ethidium bromide-stained DNA gels

A two-dimensional scanner based on a digital plotter is described. The device is used to analyze photographic negatives of ethidium bromide-stained DNA-agarose gels. Scanning is controlled by and photometric data transferred to a computer for processing, storage, display, and analysis such as integration of the areas under bands and determination of the mean distances of migration of polydisperse samples. An integral light source and detector module designed for reading optical "bar-codes" is mounted in place of the pen of the plotter. Spatial resolution and reproducibility are about 0.2 and 0.005 mm, respectively. Photometric precision as good as one part per thousand is achieved by sinusoidal modulation of the intensity of the light source and synchronous, phase-sensitive detection of the signal from the detector by a lock-in amplifier. No part of the sensor assembly touches the surface of the negative. In contrast to a densitometer, the computer transforms photometric data to values directly proportional to the amount of DNA at given points on the original gel. The ability to move the sensor in two dimensions over the negative allows for the integration across the width of a lane correctly allowing for the nonuniform distribution of the DNA.     

Preferential binding of bacteriophage Mu repressor to supercoiled Mu DNA

It was shown, using a relatively simple assay, that Mu repressor, cI, binds specifically to a region which spans the leftmost HindIII cleavage site on the phage genome. This extends the observations of Kwoh and Zipser [Nature (London) 277, 489-491 (1979)], who were able to define a binding region to the left of this site. These results provide support for the idea that the eight blocks of repeated DNA sequences, which also span the HindIII cleavage site, are involved in repressor binding. These results also indicate that cI repressor has a marked preference for supercoiled DNA.     

Two human colon tumor cell lines with similar nuclease sensitivities have different ethidium bromide binding characteristics

Chromatin from two human colon adenocarcinoma cell lines (HT-29 and LoVo) showed similar digestion kinetics when sensitivities to DNase I and micrococcal nuclease were examined. Chromatin conformations were probed by examining the binding of ethidium bromide. A Scatchard plot revealed that both chromatins bound the same amount of ethidium bromide per mole of DNA, but the DNA from LoVo cells was more accessible to the intercalator. The results indicate that differences in chromatin conformation are not necessarily accompanied by different nuclease sensitivities.     

Calorimetric study of carbohydrate binding to Concanavalin A

Flow microcalorimetry has been used to examine the ΔH of binding of two types of saccharides, a series of simple monosaccharides and a series of α-(1 → 4)-linked glucosides, to the lectin Concanavalin A. It has been found that the ΔH decreases with any change in the stereochemistry of a hydroxyl group relative to methyl α-d-mannopyranoside. The data have allowed the calculation of the relative contribution of two of the hydroxyl groups. The ΔH's of binding for the α-(1 → 4)-linked glucosides are approximately 31 kJ/mol, and the apparent association constants vary insignificantly with increasing length. This result indicates that only one glucose residue binds to concanavalin A by hydrogen bonds, and that the additional glucose residues have no interaction either by hydrogen bonds or by nonspecific hydrophobic interactions. This result confirms the absence of an extended binding site for α-(1 → 4)-linked glucopyranosides, in contrast to that proposed for α-(1 → 2)-linked mannopyranosides which show an increase in apparent association constants with increasing length.     

Ligand binding to dopamine-receptors: Analysis & interpretation

Dopamine receptor interaction was studied by concentration dependent inhibition of ³H-Spiperone binding to calf caudate nucleus homogenates with (+)-butaclamol, haloperidol, ergometrine, apomorphine and dopamine. The results were analyzed in terms of a one and a two site receptor model using computerized curve fitting procedures. Evidence is given in favour of a two site receptor model on basis of statistical criteria. The presence of two independent non-interconverting receptor sites for dopamine in calf caudate nucleus is consistent with binding data from others and with in vivo experiments.     

A fluorometric-HPLC assay for quantitating the binding of benzo[a]pyrene metabolites to DNA

A nonradiometric method is presented for quantitating low levels of benzo[a]pyrene (BP) derivatives that are covalently bound to the DNA of BP-treated mice. This method consists of hydrolyzing the DNA with acid to liberate the BP-adducts in the form of the isomeric tetrols of BP. These tetrols have fluorescence quantum yields of ～0.7 in deoxygenated solution at 298 K. Hence they are easily quantitated, following HPLC separation, by means of fluorescence detection. The sensitivity of the method is such that one bound BP residue per 10⁷ bases can be detected in 100 μg of DNA.     

Kinetic and quantitative measurements of catecholamine transport in chromaffin ghosts using a glassy carbon electrode

A method for the on-line kinetic measurement of net catecholamine uptake and release in ghosts derived from bovine chromaffin granules is described. Changes in free catecholamine concentration in 1 to 2 ml of media containing chromaffin ghosts were continuously measured through the amperometric detection of their oxidation products through a glassy carbon electrode set at 0.5-V potential vs a reference electrode. Parallel measurements of catecholamine uptake and release in the ghosts under various metabolic conditions show a good quantitative agreement between the values obtained with the electrode and those obtained through high-performance liquid chromatography after separation of the ghosts from the medium. Initial velocities of ATP-dependent uptake of epinephrine, norepinephrine, dopamine, and isoproternol by the ghosts are shown. This method permits, for the first time, quantitation of unidirectional movement of catecholamines in the presence of minute quantities of biological samples. The advantages, limitations, and suitability of this method to measure catecholamine transport in other systems are discussed.     

A thermodynamic description of the binding of iron to ferrioxamine B in aqueous solutions

The iron exchange reaction between nitrilotriacetate (NTA) and ferrioxamine B (DFO) has been investigated with titration calorimetry. Using characterization models for the initial and final states of the reaction solution based on the determination of the mole fractions of the individual species as a function of pH, the concentration of each participating species was calculated (B. L. Gould, 1980, Masters Thesis, Utah State University, Logan). The contribution of each component reaction to the overall exchange at various pH values was used to determine the enthalpy change for each of these individual reactions. The values determined for the enthalpy and entropy changes are shown below. An analysis of the thermodynamic parameters of the iron exchange system indicated the following interactions among the hydroxamate groups of the ferrioxamine B: (1) The ionization of the individual hydroxamate protons occurs independently with the same enthalpy change for each ionization, and (2) the heat of binding a hydroxamate group to the iron is dependent on the number of previously bound hydroxamates.     

Quantitation of radio-ligand binding data using a desk-top calculator in the program mode

Quantitation of specific estrogen-binding capacity was facilitated using an inexpensive procedure for the rapid processing of data from radioligand binding measurements from sucrose gradient analyses. Ligand-binding data from each fraction of a gradient were punched into a paper tape in ASCII code and, later, read by a tape reader into an Olivetti Programma 101. Using the total instructional capacity (120 steps) a program was written in symbolic language which describes: (a) the calculation of counting efficiency of the instrument for each fraction, (b) the conversion of counts/minute to disintegrations/minute, (c) the computation of the concentration of [³H]estradiol-17β in each fraction and (d) the summation of the quantity of [³H]estradiol-17β bound by specified regions of the gradient. The program can easily be adapted for use with data generated from separation procedures such as centrifugation, electrophoresis or chromatography in which large number of samples are analysed.     

Ouabain binding to preimplantation rabbit blastocysts

Ciliary ganglia (CG) from 8-day-old chick embryos were cultured as explants on a highly adhesive collagen substratum in the presence of the ciliary neuronotrophic factor (CNTF). A remarkable correlation was found between the formation of an outgrowth of ganglionic nonneuronal cells and the timing and extent of neuritic development outside the ganglion. Neurites were not seen to emerge from the ganglion before the onset (24 hr after explantation) of a nonneuronal cell outgrowth. After nonneurons began to migrate over the collagen substratum, neurites could be seen to extend up to, but not beyond the distal limit of the nonneuronal outgrowth. Time-lapse analysis showed that neuritic growth cones could move in synchrony with a nonneuron with which they were in contact as well as over the nonneuronal cell surface, but not on the collagen located distally to the external edge of the nonneuronal outgrowth.Freshly dissected CGs were also grown as secondary explants on preformed host monolayers of ganglionic nonneurons. These secondary explants showed considerable neuritic development within 24 hr, while control ganglia explanted on collagen had not produced neurites. Autoradiographic experiments indicated that this neuritic outgrowth occurred on nonneuronal cells emerging precociously from the secondary explant, rather than on the preexisting host nonneurons. Electron microscopy of 24-hr explants demonstrated that, inside the ganglion, neurites were also very closely associated with the surface of nonneuronal cells.Neuritic behavior in this nonneuron/collagen terrain is compared with previously described observations of CG explants on polyornithine (PORN) or dissociated CG neurons on PORN or collagen. These observations led to the identification of a PORN-bindable neurite promoting factor (PNPF) which does not bind to, and is not active on, collagen. The hypothesis is discussed that PNPF molecules are present on the surface of nonneuronal cells and that the cells owe to those molecules their competence as a suitable terrain for the elongation of neuritic processes.     

DNA binding site of the helix destabilizing protein gp32 from bacteriophage T4.

A helix destabilizing protein, the product of gene 32 (gp32) of bacteriophage T4, was subjected to limited proteolysis to produce three types of products with differing affinities for DNA. Previous work has suggested that the 18 amino acids at the N-terminus are required for tight binding to single-stranded DNA (Hosoda &; Moise, 1978). This paper reports the sequence of the N-terminal region and predicts the amino acid residues responsible for DNA binding.     

A comparison of the denatured states of alpha-lactalbumin and lysozyme

We have carried out a study of the denaturation of bovine α-lactalbumin by LiClO₄, LiCl, GuCl and urea, using difference spectroscopy, viscometry, polarimetry, and optical rotatory dispersion. These denaturants give rise to three different denatured states (GuCl and urea give the same state), which cannot be related to each other as members of a simple linear progression from the native state to the completely disordered state. The data require that LiClO₄ unfolds one part of the molecule, LiCl another, and GuCl or urea the whole molecule. There are striking parallels between the denaturation behaviour of lactalbumin and earlier observations on hen egg-white lysozyme, a protein with which it is about 40% homologous, and we believe the mass of the data supports the hypothesis, advanced by Browne et al. (1969), that the two proteins have similar backbone conformations.     

A structural comparison of the A and B subunits of Griffonia simplicifolia I isolectins

A structural comparison between the A and B subunits of the five tetrameric Griffonia simplicifolia I isolectins (A4, A3B, A2B2, AB3, B4) was undertaken to determine the extent of homology between the subunits. The first 25 N-terminal amino acids of both A and B subunits were determined following the enzymatic removal of N-terminal pyroglutamate blocking groups with pyroglutamate aminopeptidase. Although 21 amino acids were common to both subunits, there were four unique amino acids in the N-terminal sequence of A and B. Residues 8, 9, 17, and 19 were asparagine, leucine, lysine, and asparagine in subunit A and threonine, phenylalanine, glutamic acid, and serine in subunit B. The last six C-terminal amino acids, released by digestion with carboxypeptidase Y, were the same for both subunits: Arg-(Phe, Val)-Leu-Thr-Ser-COOH. Subunit B, which contains one methionyl residue, was cleaved by cyanogen bromide into two fragments, a large (Mr = 31,000) and a small (Mr = 2700) polypeptide. Failure of the small fragment to undergo manual Edman degradation indicated an N-terminal blocking group, presumably pyroglutamate. Both subunits were digested with trypsin and the tryptic peptides were analyzed using reverse-phase HPLC. Tryptic glycopeptides were identified by labeling the carbohydrate moiety of the A and B subunit using sodium [3H] borohydride. Cysteine-containing tryptic peptides were similarly identified by using [1-14C]iodoacetamide. Approximately 30% of the tryptic peptides were common to both subunits. Thus, although the N- and C-terminal regions of A and B are similar, the subunits each possess unique sequences.     

Alpha 2-macroglobulin binding to cultured fibroblasts: identification by affinity chromatography of high-affinity binding sites

Binding sites having the properties of high-affinity receptors for activated alpha 2-macroglobulin (alpha 2M) have been purified over 100-fold from membranes of spontaneously transformed NIH-3T3 cells (J. A. Hanover, S.-y. Cheng, M. C. Willingham, and I. H. Pastan [1983] J. Biol. Chem. 258, 370-377). To identify the molecular species involved in high-affinity binding, the solubilized receptor has been purified 500-fold by conventional procedures and further purified by affinity chromatography. After radioiodination of the 500-fold-purified preparation, the detergent-solubilized extract was applied to alpha 2M-Sepharose and an 85,000 +/- 5000 Mr species was selectively retained by the column. Binding of the 85,000 +/- 5000 Mr species to the affinity resin was inhibited by EDTA and by excess alpha 2M. Elution from the affinity column could be accomplished with bacitracin, a competitive inhibitor of alpha 2M binding, or with EDTA. Consistent with the previously reported characteristics of the high-affinity alpha 2M receptor, the 85,000 Mr species bound much more efficiently to methylamine-activated alpha 2M-Affigel than to alpha 2M-Affigel which had not been amine-activated. The present data suggest that a protein with a subunit Mr of 85,000 +/- 5000 may represent a component of the high-affinity alpha 2M receptor present on cultured fibroblasts.