Spin-labeled oxazolopyridocarbazole as a probe for studying nonintercalating DNA groove binding ligands

A spin-label (P-OPC) composed of the nitroxide-containing ring proxyl linked at the C1 position of the intercalating fluorescent chromophore oxazolopyridocarbazole (OPC) has been synthesized. The spin-labeled OPC was found to interact with DNA and polynucleotides according to an external minor groove binding mode with association constant values Kapp ranging from 10(5) to 10(6) M-1. External binding was obvious from the inability of P-OPC to increase the length of sonicated DNA upon binding, the low unwinding angle (9.6 degrees) of circular PM2 DNA, and the low energy transfer from DNA bases to bound chromophore. Binding of P-OPC to DNA or polynucleotide results in a strong immobilization of the proxyl moiety, resulting in the appearance of an asymmetric and broad ESR spectrum with a maximal hyperfine splitting of 56.5 G. In the equilibrium conditions, the occurrence of superimposed ESR spectra related to the P-OPC fraction undergoing rapid motion and to the P-OPC fraction immobilized allows the estimation of the concentrations of free and DNA-bound spin-label. The external mode of binding to DNA as well as the characteristics of the ESR spectra make P-OPC suitable for the determination of DNA binding parameters of nonintercalating ligands using competition experiments. The measurement of the binding constants of distamycin A to poly[d(A-T)] and poly[d(G-C)] is taken as an example.     

Molecular recognition between oligopeptides and nucleic acids. DNA sequence specificity and binding properties of an acridine-linked netropsin hybrid ligand

The binding to DNA of a mixed function ligand (NETGA) is described, in which a potential intercalating group, an acridine moiety, is incorporated at the carboxyl terminus of the minor groove binding oligopeptide netropsin skeleton. Scatchard analysis of absorption data provided evidence of two modes of binding to DNA with K1 = 9.1 x 10(5) M-1 at low r values (0.003-0.1), and a binding site size n = 10, indicative of binding of both moeities. At high binding ratios (greater than 0.1), K2 = 0.9 x 10(5) M-1 and n = 5 corresponding to external binding. Complementary strand MPE footprinting on a pBR322 restriction fragment showed NETGA binds to 5'-AAAT like netropsin. It causes enhanced cleavage by MPE, particularly at G-C rich sequences and remote from the preferred binding sites. Viscometry measurements provided evidence for biphasic modes of the two binding portions of NETGA. Fluorescence polarization and linear dichroism measurements were in accord with distinct modes of interaction of the acridine (intercalation) and oligopeptide (minor groove binding) portions of NETGA. LD measurements on NETGA indicate that the oligopeptide moiety (netropsin-like) has an orientation typical of minor groove binders, whereas the degree of intercalation of the acridine group is decreased by association of the oligopeptide moiety.     

Is the bithiazole moiety of bleomycin a classical intercalator?

Bleomycin is a widespread anticancerous drug, the biological activity of which having been extensively studied. Its metal ion-chelating portion has been shown to cleave DNA whereas the role of the bithiazole moiety is still questionable. In order to elucidate this problem some 2', 4-disubstituted bithiazoles structurally related to the "tripeptide S" moiety of bleomycin were synthesized and their interaction with DNA was studied using delta Tm, fluorescence, EPR and viscometry techniques. The results of delta Tm and fluorescence quenching determinations were in favour of a binding of the bithiazole part by an intercalation process. Nevertheless, the use of the spin-label probes indicated only a partial intercalation of the ring between the base-pairs. Moreover, viscometry data which clearly exhibited a slight decrease of DNA length in the presence of bithiazole derivative led to the proposal of a binding model involving a partial insertion of a thiazole ring which wedges in between the bases at a bending point of DNA.     

ESR study of intercalation: quantitative evaluation of drug-DNA binding through competition with a spin-labeled 9-aminoacridine

Interaction of a spin-labeled 9-aminoacridine with DNA was studied by electron spin resonance spectroscopy. Accurate determination of the binding parameters, equilibrium dissociation constant (K_D), and total number of ligand-binding sites was obtained using Scatchard and Lineweaver-Burk plots. The competition between 9-aminoacridine and its spin-labeled derivative was examined by a similar analysis of the spin-label signals. The practical interest of this method lies in the fact that the precision and the simplicity of the measurements allow the quantitative determination of the binding capacity of any intercalative drug which interacts specifically with adenine/thymine bases of DNA.     

The binding isotherms for the interaction of 5-doxyl stearic acid with bovine and human albumin.

Binding isotherms for the interaction of 5-doxyl stearic acid with bovine and human albumin are reported. The critical micelle concentration (CMC) and the limiting solubility of 5-doxyl stearic acid were determined using the electron spin resonance (ESR)-spin label method. The CMC and the limiting solubility of this spin-label stearic acid in saline-phosphate buffer are 3.5 x 10(-5) M and 2 x 10(-4) M, respectively. We found no ESR line width evidence for pre-association of the spin-label stearate below the CMC. Maximum binding of the spin-label stearate to both bovine and human albumin occurs before micelle formation. The binding isotherm for spin-label stearic acid interaction with bovine albumin is in agreement with data obtained by others using [1-(14)C]stearic acid. For human albumin, comparison is difficult since previous data obtained with [1-(14)C]stearic acid vary widely. Comparison of the ESR 2T(||) values (the splitting between low and high field extremes, a measure of the degree of immobilization of protein-bound spin-label stearate) for bovine and human albumin indicates a greater immobilization of the spin-label molecules bound to human albumin. The binding data indicate that complexes are formed with bound spin-label stearate/albumin ratios of at least 18. The computed equilibrium constants for both bovine and human albumin indicate that the first seven spin-label molecules are tightly bound, log K > 5.0. The species predicted to form in solution by these equilibrium constants are reported.     

Probing the topography of lectins with site-specific spin-labeled glycosides

Three new spin-labeled glycosides, spin-label I [1-[4-(beta-D-galactopyranosyloxy)phenyl]-3-(2,2,6,6-tetramethyl-1 -oxypiperidin-4-yl)-2-thiourea], spin-label II (2,2,6,6-tetramethyl-1-oxypiperidin-4-yl alpha-D-galactopyranoside), and spin-label III [1-(methyl 2-deoxy-alpha-D-galactopyranosid-2-yl)-3-(2,2,6,6- tetramethyl-1-oxypiperidin-4-yl)-2-thiourea], were investigated as structural probes of Griffonia simplicifolia I isolectins (GS I) A4 and B4, respectively, by electron spin resonance (ESR) and inhibition of guaran isolectin precipitation. The p-aminophenyl beta-galactoside spin-label I was strongly immobilized by the B4 isolectin (Kd = 0.42 mM; 2T parallel = 54.0 +/- 0.3 G), while binding to the A4 isolectin was so weak (KI congruent to 2 mM) that binding was undetectable by ESR. The preference for the B4 isolectin was indicative of a more extended hydrophobic binding locus adjacent to the carbohydrate-specific binding site. The alpha-galactosyl spin-label II bound slightly more strongly to the A4 than to the B4 isolectin, as evidenced in both Kd values and particularly by differences in the degree of immobilization (2T parallel = 53.5 vs. 51.5 G, respectively). The 2-N-substituted methyl galactoside spin-label III was so poor an inhibitor of both isolectins (KI congruent to 1-2 mM) that ESR detection of the bound complex was not feasible. In all cases above, the spin-labels were displaced by specific monosaccharide haptens.     

A Spin-Label Study on Lipids in Dough Formed at Various Concentrations of Oxygen

The effect of oxygen on wheat flour lipids during dough mixing was investigated by analysis of the lipid composition and by an ESR technique with a fatty acid spin-label (4,4’-dimethyl-oxazolidine-N-oxyl derivative of 5-ketostearic acid). Dough was prepared in the presence of the spin-label under an atmosphere of air, nitrogen, 95% nitrogen—5% oxygen or oxygen, and the gluten was obtained by washing out the starch. ESR spectra of the spin-label incorporated into the gluten showed decreases in the order parameter, rotational correlation time and activation energy for rotational viscosity with increasing atmospheric oxygen concentration. During dough mixing in oxygen, oxidation of lipids proceeded and bound lipids slightly decreased. These data indicate that modification of lipids by incorporated oxygen leads to an increase in their fluidity and to a decrease in their hydrophobic interaction with protein in dough.     

Involvement of the 3' side of the anticodon loop of yeast tRNATyr in messenger-free binding to ribosomes. An electron-spin resonance study

Electron-spin resonance (ESR) spectra of a nitroxide spin-label attached to residue i6A-37 of yeast tRNATyr were measured in complexes of deacylated tRNATyr with Escherichia coli ribosomes. A Scatchard plot, obtained in the absence of mRNA, indicated strong binding with an association constant of 1 X 10(7) l X mol-1, suggesting the P-site binding. The ESR spectrum of free tRNATyr, characteristic for a rapidly tumbling nitroxide, changes to a spectrum with extensively broadened lines in the ribosome-tRNA complex. The original spectrum can be restored upon long incubations of the complex with an excess of extraneous tRNA. ESR spectra suggest that the spin-label motion is drastically perturbed though not completely blocked in the ribosome-tRNATyr complex. Since ESR spectra of a spin-label attached to the opposite, i.e. 5', side of the anticodon loop are only slightly perturbed by the messenger-free binding to ribosomes [Rodriguez et al. (1980) J. Biol. Chem. 255, 8116-8120], it is concluded that the two sides of the anticodon loop face entirely different environments when bound to the P site, the 3' side being oriented towards the surface of the ribosome, and the other side towards its environment or a large cavity.     

Spin-labeling studies of rat liver NADPH-cytochrome p450 reductase: conformation and function relationship.

ESR spin-labeling studies designed to yield information regarding the relationship between function and conformation of rat liver NADPH-cytochrome P450 reductase (EC 1.6.4.2) were carried out. The purified enzyme was spin labeled by a nitroxide derivative of p-chloromercuribenzoate. Two conditions for spin labeling were employed: (i) the presence of NADP+, yielding an active site-protected spin-labeled reductase, and (ii) the absence of NADP+, yielding completely spin-labeled reductase. Reductase in which the active site was protected by binding NADP+ and then spin-labeled retains most of its enzymatic activity; on the other hand, completely spin-labeled reductase is devoid of any enzymatic activity. Completely spin-labeled reductase yields a two-component resolved ESR spectrum that reflects two classes of spin-labeled binding sites, a strongly immobilized (S) and a weakly immobilized (W) site. The ratio of W/S provides a valuable parameter for studying the relationship between function and conformation. Structural perturbants, such as urea, KCl, and pH, were employed to determine their effects on the activity of the enzyme and their relationship to changes in the conformational state of the reductase. It was further observed that the enzymatically active spin-labeled derivative generated superoxide radical in the presence of NADPH and cytochrome c, which in turn reduced completely the attached spin-label.     

Methionine-90-spin-labeled bovine alpha-lactalbumin: electron spin resonance and NMR distance measurements

The unique methionine residue of bovine alpha-lactalbumin was modified by irreversible alkylation with the bromoacetamido nitroxide spin-label 4-(2-bromoacetamido)-2,2,6,6-tetramethylpiperidine-N-oxyl. The line shape of the electron spin resonance (ESR) spectrum was indicative of a fairly mobile spin-label and was sensitive to the calcium-induced conformational change. Paramagnetic broadening of the spin-label ESR lines by a Gd(III) ion substituted at the high-affinity calcium site of the protein yielded a distance between the spin-label and the metal-binding site of 8.0 +/- 1.0 A. The extent of the paramagnetic line broadening by the covalently attached nitroxide spin-label on the proton resonances of several amino acid residues of the protein at 500 MHz allowed estimation of intramolecular distances between the methionine-90 residue and several resolvable protons.     

Conformational transition of polypeptide chain elongation factor G as determined by electron spin resonance.

The conformational transition of the polypeptide chain elongation factor G (EF-G) induced by interaction with guanine nucleotide has been investigated by means of the spin-labeling technique. Various spin-label probes were attached specifically to the sulfhydryl group of the protein that is essential for binding to ribosomes, and the effects of these ligands on the electron spin resonance (ESR) spectra were examined. It was found that the ESR spectra of EF-G labeled with nitroxide maleimide reagents were modified by the addition of various guanine nucleotides such as GDP, GTP and, to a lesser extent, by Gpp(NH)p and Gpp(CH2)p, indicating that conformational changes accompany the binding of nucleotide ligand. However, the ESR spectra of labeled EF-G-GDP and EF-G-GTP were almost identical. On the other hand, when EF-G was labeled with nitroxide iodoacetamide reagents, a clear difference in the ESR spectra of EF-G-GDP and EF-G-GTP derivatives was observed. In this case, the spectral shape of the spin-labeled EF-G in the presence of GTP or its analogs, Gpp(NH)p or Gpp(CH2)p, was quite similar to that of free, unliganded EF-G derivative. These results, together with those previously obtained using hydrophobic probes (Arai, Arai, & Kaziro (1975) J. Biochem. 78, 243-246) demonstrate the existence of an EF-G-guanine nucleotide binary complex. They also indicate that there is a substantial difference in conformation between free EF-G, EF-G-GDP, and EF-G-GTP near the active site essential for interaction with ribosomes.     

Synthesis of a photoaffinity-spin-labeled derivative of ATP and its first application to F1-ATPase

The synthesis of an ATP derivative is described, in which a spin-label is attached to the 3'-position of the ribose moiety and an azido group to C8 of the adenine ring (SL-N3-ATP). Irradiation of this compound at 350 nm generates a nitrene, which will react with any functional group in its vicinity. SL-N3-ATP exhibits a strongly immobilized ESR spectrum in a complex with F1-ATPase from beef heart mitochondria. It was covalently incorporated into this enzyme. SL-N3-ATP may be employed in ESR investigations under conditions in which non-covalent interactions are too weak for motionally restricted species to be easily observed.     

Structural information on a membrane transport protein from nuclear magnetic resonance spectroscopy using sequence-selective nitroxide labeling.

The lactose transport protein (LacS) from Streptococcus thermophilus bearing a single cysteine mutation, K373C, within the putative interhelix loop 10-11 has been overexpressed in native membranes. Cross-polarization magic-angle spinning nuclear magnetic resonance spectroscopy (NMR) could selectively distinguish binding of (13)C-labeled substrate to just 50-60 nmol of LacS(K373C) in the native fluid membranes. Nitroxide electron spin-label at the K373C location was essentially immobile on the time scale of both conventional electron spin resonance spectroscopy (ESR) (<10(-8)s) and saturation-transfer ESR (<10(-3)s), under the same conditions as used in the NMR studies. The presence of the nitroxide spin-label effectively obscured the high-resolution NMR signal from bound substrate, even though (13)C-labeled substrate was shown to be within the binding center of the protein. The interhelix loop 10-11 is concluded to be in reasonably close proximity to the substrate binding site(s) of LacS (<15 A), and the loop region is expected to penetrate between the transmembrane segments of the protein that are involved in the translocation process.     

Segmental flexibility of single-, double-, and triple-stranded polyribonucleotides from the data of spin label method. Formation of the triple-stranded poly(A.A.U) polynucleotide helix

Segmental mobility dynamic peculiarities of poly(U), poly(A) and poly(C) synthetic polymers and their complexes were investigated by spin-label method. Imidazolide spin-label was introduced into 2'-oxi-groups of polymer ribose in correlation: one spin-label on 18-20 bases. Formation of complexes was observed by ESR spectra at two pH: 4.2 and 7.2. Segmental mobility of only single strand spin-labelled polymer segment and in the complex was evaluated by measuring rotational correlation time (tau) determined by dependence of distances between outer wide extrema in ESR spectra from solvent viscosity at different temperatures. It turned out that correlation time tau of single strand structures in a high degree depend on pH and temperature. For three strand structures abrupt increase of tau because of appearance of rigidity was observed. It is possible to evaluate part of triple complexes poly(U.A.A) and poly(U.U.A) existing in dynamic equilibrium depending on pH and temperature by the form of outer wide extrema. Adding of dye to complex of poly(U).poly(A) causes an increase of rigidity of the supermolecular structure. Quantitative characteristics of formed complexes were obtained by simulation of ESR spectra on computer.     

Preparation and characterization of spin-labeled derivatives of epidermal growth factor (EGF) for investigations of the interactions of EGF with its receptor by electron paramagnetic resonance spectroscopy.

We prepared, purified, and characterized derivatives of epidermal growth factor (EGF) having a nitroxide spin-label attached covalently at the amino terminus. Characterization of these derivatives with regard to the positions of attachment of the spin-label was accomplished by a combination of peptide mapping, protein sequencing, and fast atom bombardment-mass spectrometry. One derivative was chosen for use in initial investigations by electron paramagnetic resonance (EPR) spectroscopy of receptor-bound EGF and its dissociation kinetics. This derivative was found to be equipotent with the native hormone in competitive binding assays, in activating the EGF receptor kinase, and in stimulating the formation of EGF receptor dimers in solubilized cell extracts. Upon binding to solubilized EGF receptor, the spin-labeled EGF derivative became immobilized, giving rise to a visually distinct slow-motion EPR spectrum. The resulting spectrum showed no detectable dipolar interaction between nitroxides, indicating that the nitroxide moieties of spin-labels reacted at the amino termini of receptor-bound spin-labeled EGF molecules are separated by a distance of at least 16 A. An EPR study of the kinetics of dissociation of spin-labeled EGF in the presence of excess unlabeled EGF revealed a rapid component with a k off approximately 2 x 10(-2) s-1 and a less well resolved slow component.     

Progress towards a DNA-based model system for the study of electron spin-spin interactions

A DNA-based model system is described for studying electron spin-spin interactions between a paramagnetic metal ion and a nitroxide spin label. The modified base deoxythymidine-EDTA (dT-EDTA) chelates the divalent or trivalent metal ion and produces a new feature in the circular dichroism (CD) spectra that makes it possible to monitor local DNA melting. Based on the results of optical and electron paramagnetic resonance (EPR) experiments, we find that the terminus of the DNA duplex that incorporates dT-EDTA and the spin-label melts at a higher temperature than the rest of the DNA duplex. EPR microwave progressive power saturation experiments performed at 77 K are consistent with the specific binding of Dy(III) at the EDTA site and an intramolecular dipole-dipole interaction between the nitroxide spin-label and the chelated Dy(III). This model system should be suitable for studying the relaxation properties of metal ions by saturation-recovery EPR.     

Interaction of spin-labeled tryptophan with sickle hemoglobin: probing the microenvironment of the contact sites by spin-probe--spin-label techniques

The spin-labeled tryptophan was used as a structural probe of hemoglobin contact sites. The ESR spectral data indicated that the probe exhibits weak binding to hemoglobin with a dissociation constant of 3.2.10(-5) and 4.0 mol bound per hemoglobin tetramer. The spectrum suggested that the bound tryptophan was 'partially immobilized' with a correlation time reflecting the environment of the tryptophan binding site of 8.2 ns. The topology of the contact sites was investigated by using dual spin-label methodology in which spin-labeled tryptophan and (2H,15N) substituted and deuterated maleimide spin label [2H-15N]MSL covalently-bound to Cys-beta 93 residue were used. The ESR spectral data suggested that the tryptophan binding sites were located within 8-10 A of the nitroxide free radical of spin-labeled hemoglobin. The environment of the contact sites is discussed.     

Spin-label studies of erythrocyte deformability. IV. Relation of electron spin resonance spectral change with deformation and orientation of erythrocytes in shear flow.

Electron spin resonance (ESR) spectra of spin-labeled human erythrocytes in shear flow are simulated to derive semi-empirical relations of the ESR spectral change with deformation and orientation of the cells by using a modified theoretical model developed for deformation and orientation of liquid drops. The six observed spectra at different shear stress values were simultaneously simulated by adjusting only two parameters. One parameter can be related to the ratio of the internal to the external viscosity, and the other to the elastic property of the cell membrane. From these results we have derived a semi-empirical relationship between the average deformation index or the orientation angle with a spectral measure, which characterizes the spectral shape change induced by shear stress. Thus, it becomes possible to obtain improved quantitative information on the rheological behavior of red blood cells by using the spin-label ESR method.     

Sequence-selective binding of an ellipticine derivative to DNA.

The DNA sequence specificity of an ellipticine derivative bearing an aminoalkyl side chain has been determined by a variety of footprinting methods. The drug exhibits sequence selective binding and discriminates against runs of adenines or thymines. Binding is shown to occur at various sequences with a preference for GC rich regions of DNA. A large enhancement of DNAase I and of hydroxyl radical cleavage in regions rich in A's or T's is observed together with hyperreactivity of adenines towards diethylpyrocarbonate in the presence of drug. This indicates the occurrence of drug-induced changes in critical conformational features of DNA. The total absence of hyperreactivity of guanine residues towards diethylpyrocarbonate appears to be related to the sequence selectivity of drug binding. No alteration of the dimethyl sulphate and methylene blue-induced cleavage of DNA is observed. Irradiation of ellipticine derivative-DNA complexes with UV light followed by alkali treatment leads to selective photocleavage at guanine residues, consistent with the deduced degree of selectivity of the binding reaction.