Labelling of penicillin-binding proteins with a photoreactive peptidoglycan-peptide analogue

Transpeptidases, DD-carboxypeptidases and endopeptidases from bacteria are usually detected by labelling with radioactive beta-lactam antibiotics, due to a selective stabilization of the enzyme-antibiotic complex, and are therefore generally known as penicillin-binding proteins (PBPs). However, as a general rule, PBPs cannot be detected by labelling with real peptidoglycan substrate analogues other than beta-lactams, partly due to the fact that the acyl intermediates formed do not usually accumulate. We here report the chemical synthesis of a radioactive photoreactive derivative of the peptidoglycan substrate L-lysyl-D-alanyl-D-alanine which is able, due to the shortness of its activated state, to label a number of PBPs of Escherichia coli by quenching the reaction at the intermediate step. Furthermore, by using this derivative we have been able to label other PBPs of higher molecular mass (190, 170, 146, 125 and 87 kDa) that were previously detected only by using either photoreactive derivatives of beta-lactam or bis-beta-lactam antibiotics.     

Potentiometric characterization of ethidium bromide and of its reactions with nucleic acids

A liquid membrane electrode that allows the concentration of ethidium ion (Ed(+)) to be measured selectively and accurately in the range of 0.1 microM to 5 mM is made. For Ed(+) concentrations less than 1 microM or more than 0.1 mM, the trend is no longer linear, and the causes of this behavior are discussed. The mean activity coefficient of ethidium bromide exhibits deviations from the Debye-Huckel limiting law that are interpreted in terms of aggregate formation. The stability constants for Ed(2)(2+) and Ed(2)Br(+) are 230 kg mol(-1) and 3.0 x 10(4) kg(2) mol(-2), respectively. In NaCl solutions, clusters involving up to 4 Ed(+) units are detected and their stability constants are evaluated. The intercalation of ethidium into poly(A).poly(U) in 1M NaCl is investigated by the above electrode, and the results are compared with those obtained by spectrophotometry. The data are analyzed in terms of Scatchard plots. The potentiometric method is more accurate than the spectrophotometric one at low values of the binding degree (r) where negative deviations from linearity are observed. The deviations are ascribed to a cooperative behavior rather than to artifacts caused by minor systematic errors.     

Interaction of nucleic acids with electrically charged surfaces: II. Conformational changes in double-helical polynucleotides

The influence of adsorption of double-stranded (ds) DNA, ds RNA and homopolymeric pairs at a mercury electrode on conformation of these polynucleotides was studied. Changes in the polarographic reducibility of polynucleotides, which were followed by means of normal pulse polarography and linear sweep peak voltammetry at the dropping mercury electrode were exploited to indicate conformational changes. It was found that, as a consequence of adsorption of ds polynucleotides on the negatively charged electrode conformational changes similar to denaturation take place in a narrow potential region around ?1.2 V (the region U). After sufficiently long time of the contact with the electrode (under our conditions about 10 s) these changes reach limiting values, which can approach total denaturation. Upon adsorption of ds polynucleotides on the electrode charged to more positive potentials than the region U either (1) no conformational changes occur or (2) only a small part of the polynucleotide (probably labile regions of the ds molecule) is very quickly denatured - the remainder of the molecule preserves its ds structure. Conformational changes of adsorbed ds polynucleotides are influenced by factors which change the stability of ds polynucleotides in solution. It is supposed that denaturation of ds polynucleotides in the region U might result from the strains connected with the repulsion of certain segments of the molecule anchored on the electrode from the negatively charged surface.     

Spectroscopic properties of ethidium monoazide: a fluorescent photoaffinity label for nucleic acids.

The non-covalent binding of ethidium monoazide to nucleic acids is entirely analogous to that of ethidium (binding constant approximately 2-3 X 10(5) M). The ethidium monoazide can be photochemically covalently linked to nucleic acids in high yield, up to 75%, by long wavelength light. The fluorescence of ethidium monoazide and ethidium crosslinked to nucleic acids show the same environmental sensitivity as does the fluorescence of ethidium. These properties of ethidium monoazide indicate its use as a fluorescent photoaffinity label for nucleic acids. Ethidium diazide can be photochemically linked to nucleic acids but appears to have properties substantially different from those of ethidium.     

Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA

Molecular mechanical calculations were done on complexes of ethidium cation with various base-paired deoxydinucleoside monophosphates [(ApT)₂, (TpA)₂, (A₂ · T₂), (GpC)₂, (CpG)₂, and (G₂ · C₂)] and deoxyhexanucleoside pentaphosphates [(ATATAT)₂, (TATATA)₂, (A₆ · T₆), (GCGCGC)₂, (CGCGCG)₂, and G₆ · C₆]. Relative binding energies, sequence preferences, and conformational aspects of the intercalation complexes were studied. The most detailed models used (an all-atom force field) gave results in good agreement with previous calculations and experimental work. Less-sophisticated models did not perform as well.     

Binding of ethidium bromide and quinacrine hydrochloride to nucleic acids and reconstituted nucleohistones

Studies of binding of ethidium bromide and quinacrine hydrochloride to native DNA at low ionic strength indicate that for both compounds the binding is selective, with about one binding site for about four nucleotides. Annealing of unfractionated histones to DNA by a salt-gradient dialysis method slightly decreases the binding of the dyes to DNA. Similar observations made with reconstituted preparations by using individual histone fractions reveal that the arginine-rich histones (histones H3 and H4) are most effective in decreasing the binding. The binding studies with ethidium bromide at high ionic strength and with denatured DNA show that strong dye binding to DNA is strongly dependent on the ionic strength and on the secondary structure of DNA. The histones are not effective in decreasing the dye binding under conditions of high ionic strength. The results are consistent with the observations [Oliver & Chalkley (1974) Biochemistry13, 5093-5098; Axel, Melchoir, Sollner-Web & Felsenfield (1974) Proc. Natl. Acad. Sci. U.S.A.71, 4101-4105] that histones form some kind of surface structures on DNA through non-specific interactions and [Kornberg & Thomas (1974) Science184, 865-868; Kornberg (1974) Science184, 868-871; D'Anna & Isenberg (1974) Biochemistry13, 4992-4997; Vandegrift, Serra, Marve & Wagner (1974) Biochemistry13, 5087-5092] that the tendency of arginine-rich histones to aggregate may be an important factor in determining the structure of chromatin.     

Pharmacological analysis of the effect of natural double-helical nucleic acids on the detoxifying function of the liver

The effect of interferon inductors i.e. double stranded RNAs from S. cerevisiae and phage F6 on the liver detoxicating function was studied on noninbred albino mice. The liver detoxicating function was tested by duration of hexenal sleep. It was shown that intraperitoneal administration of the yeast and phage RNAs in doses of 1/5 LD50 for three times led to increasing of the narcotic sleep duration in the animals by 65 and 207 per cent, respectively. The effect was of the dose-dependent nature. The doses not inducing reliable inhibition of hexenal metabolism were equal to 1/10 LD50 for the yeast dsRNA and 1/27 LD50 for the phage dsRNA. The inhibitory effect of the dsRNAs was retained for 2-3 days after discontinuation of the drug use. When the dsRNAs were administered simultaneously with nembutal, an inductor of the liver microsomal enzymes, the dsRNAs eliminated its inducing effect. Simultaneous administration of alpha-tocopherol lowered the dsRNA effect on hexenal metabolism. The findings suggested that the dsRNA inhibitory effect on the liver detoxicating function was grounded on the mechanisms associated with inhibition of syntheses and activation of lipid peroxidation specific of the monooxygenase system under the action of the dsRNAs.     

Subcellular localization of photoreactive ethidium analogs in Trypanosoma brucei by fluorescence microscopy

To identify the in vivo targets of the trypanocide, ethidium bromide, the fluorescent staining of T. brucei was examined for a series of ethidium analogs using fluorescence microscopy. Determination of the biological targets for most drugs is limited by the reversible nature of their interactions. To overcome this limitation, photoaffinity (azido) analogs of ethidium, which are capable of covalent attachment with photoactivation, were used to identify the ethidium binding sites within the parasites. Two of these compounds, when covalently attached, demonstrated an enhancement of fluorescent staining and were selective for the kinetoplast at low drug concentrations. These compounds were also those found previously to have the highest trypanocidal activity. Propidium, a phenanthridinium analog identical to ethidium except for a larger, more ionic substitution at R5, showed more nonspecific binding as determined by its general staining of the cytoplasm.     

Chemical reactions in double-helical nucleic acids. VIII. Assembly of hybrid RNA-DNA-duplexes using water soluble condensing agents

Condensation of oligonucleotides containing ribonucleotide segments (from mononucleotide to full sequence) on DNA-template was studied, with cyanogen bromide and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide as condensing agents. Efficiency of the chemical ligation of RNA oligomers was much lower than that of DNA analogues. The yield of chemical ligation products was found to depend on the position of RNA segment in the hybrid duplexes and on the position of the phosphate group in the nick. The oligoribonucleotide's length does not affect the yield of condensation products. A nick in 5S RNA loop was repaired by means of the chemical ligation method.     

Preparation and application of a photoreactive thrombin analogue: binding to human platelets

alpha-Thrombin has previously been shown to bind to specific, saturable glycoproteins on the platelet surface. Modification of the thrombin active site with tosyllysyl chloromethyl ketone (TosLysCH2Cl) does not alter thrombin's binding characteristics. Interaction of alpha-thrombin with high-affinity binding sites (KD = 10(-9) M) initiates the platelet response which involves proteolytic hydrolysis of this glycoprotein. Although TosLysCH2Cl--thrombin binds to and competes for the same sites as alpha-thrombin, it cannot induce platelet stimulation because it is enzymatically inactive. In this study, we describe the preparation and application of photoreactive tritium-labeled thrombin analogues. The alpha-thrombin derivative retains its platelet-stimulating and enzymatic activities and, upon photoactivation, covalently binds to specific platelet membrane components. When freshly washed human platelets are exposed to less than saturation doses (less than or equal to 2 nM) of the thrombin derivatives in the dark and photoactivated, a single labeled complex is detected. The same experiment with greater than saturating doses (greater than or equal to 20 nM) of the thrombin derivative yields a similar complex as well as two additional ones. Molecular weight estimates of these thrombin-bound complexes were obtained by gel filtration and NaDodSO4--polyacrylamide gel electrophoresis. The low dose (high affinity) complex with TosLysCH2Cl--thrombin has an approximate molecular weight of 200 000, while that with active alpha-thrombin is smaller, approximately 120 000, due to enzymatic cleavage. The additional complexes detected with the high thrombin dose had estimated molecular weights of 400 000 and 46 000, respectively, and appeared to be the same for TosLysCH2Cl--thrombin and for the alpha-thrombin coupled platelets. These isolated complexes appear to correspond to the two previously detected populations of thrombin binding sites on the platelet.     

The fluorometric determination of nucleic acids in pea seeds by use of ethidium bromide complexes.

A method is described for the determination of RNA and DNA in plant tissues which depends on the effect of complex formation on the fluorescence of ethidium bromide. Previous methods were found to be inapplicable to the analysis of plant material because of the high activity of ribonuclease in tissue extracts. Treatment of extracts with bentonite overcomes this difficulty and also allows measurement of fluorescence without the need to use frontal illumination. The procedure described compares favourably with earlier methods as regards accuracy, sensitivity and simplicity.     

Calculations of the circular dichroism of double-helical nucleic acids. I. Effects involving pi leads to pi transitions

The circular dichroism of double-helical nucleic acids was calculated as a function of geometry using the theory of Tinoco and Johnson. This theory does not include contributions of near ultraviolet transitions that are not π → π* in nature. The calculated circular dichroism shows a strong dependence on the distance of base pairs from the helix axis and the tilt of the base pair. Smaller dependences are predicted for the propeller-like twist of a base pair and for variation of the angular increment per base pair. Moderately good agreement between calculated and many experimentally observed spectra could be generated.     

Calculations of the circular dichroism of double-helical nucleic acids. II. Effects involving n leads to pi transitions

The circular dichroism of double-helical nucleic acids was calculated as a function of geometry, including terms involving n → π* transitions. The “nonbonding” n or σ orbitals were of the azine type, delocalized, but concentrated at the nitrogen atoms of the purines and pyrimidines. Dynamic coupling of the magnetic moments of the n → π* transitions with the electric moments of π → π* transitions generated important terms. Mixing of electric dipole character into n → π* transitions by the static electric field perturbation of the molecule is of lesser importance. The largest contributions of n → π* transitions to the circular dichroism of double-helical nucleic acids are comparable in magnitude to the sum of π → π* terms only for geometries where the circular dichroism is weak. Using both n → π* and π → π* contributions one is able to match experimental and calculated circular dichroism spectra for DNA's over a much wider range of conditions than was possible previously.     

Interaction of nucleic acids. VI. Interaction of purine with nucleic acids

The interaction of purine with DNA, tRNA, poly A, poly C, and poly A. poly U complex was investigated. In the presence of purine, the nucleic acids in coil form (such as denatured DNA, poly A and poly C in neutral solutions, or tRNA) have lower optical rotations. In addition, hydrodynamic studies indicate that in purine solutions the denatured DNA has a higher viscosity and a decreased sedimentation coefficient. These findings indicate that through interaction with purine, the bases along the poly-nucleotide chain are unstacked and are separated farther from each other, resulting in increased assymmetry (and possibly volume) of the whole polymer. Thus, the de-naturation effect of purine reported previously can be explained by this preferential interaction of purine with the bases of nucleic acids in coil form through a hydrophobic-costacking mechanism. Results from studies on optical rotation and helix-coil transition show that the interaction of purine is greater with poly A than with poly C. The influence of temperature, Mg⁺⁺ concentration, ionic strength, and purine concentration on the effect of purine on nucleic acid conformation has also been investigated. In all these situations the unraveling of nucleic acid conformation occurs at much lower temperatures (20–40°C lower) in the presence of purine (0.2–0.6M).     

Pyrene intercalating nucleic acids with a carbon linker

We have synthesized a carbon linker analogue of INA (oligonucleotides containing insertions of 1-O-(1-pyrenylmethyl)glycerol). Thermal stability studies showed an increase in melting temperature in favor of the carbon linker analogue. We also synthesized a carbon linker analogue with two pyrenes geminally attached. Fluorescence studies of this intercalating nucleic acid with the pyrene moieties inserted as a bulge showed formation of an excimer band. When a mismatch was introduced at the site of the intercalator, an excimer band was formed for the destabilized duplexes whereas an exciplex band was observed when the stability of the duplex was retained.