7-Azidoactinomycin D: a novel probe for examining actinomycin D-DNA interactions

The technique of photoaffinity labeling is applied to the actinomycin D system to provide a novel probe for the examination of the interactions of actinomycin D with nucleic acids. The capacity for covalent attachment of actinomycin D will aid greatly in the study of target-site specificities and the correlations of biological effects with biophysical DNA interactions. Through chemical modification of the parent actinomycin D molecule with a photoreactive azido substituent, a functional analog of the parent actinomycin D is generated having equilibrium binding properties identical to those of the parent molecule yet with the capacity to form a covalent attachment to DNA upon photolysis. The results presented here describe the noncovalent interactions of this photoreactive probe to DNA (absence of light) and compares the binding properties observed to those of the parent actinomycin D and 7-aminoactinomycin D analog. These studies demonstrate that the DNA binding properties (i.e. binding affinity, binding site size, and sequence specificity) retained by the 7-azidoactinomycin D, thus providing a suitable probe for examining actinomycin D-DNA interactions.     

A study of the interaction of avidin with 2-anilinonaphthalene-6-sulfonic acid as a probe of the biotin binding site

The environment of the biotin binding site on avidin was investigated by determining the fluorescence enhancement of a series of fluorescent probes that are anilinonaphthalene sulfonic acid derivatives. Of the compounds tested, 2-anilinonaphthalene-6-sulfonic acid (2,6-ANS) exhibited the greatest enhancement under the conditions used (which would reflect both molar fluorescence enhancement and binding affinity) and exhibited more than 95% reversal upon addition of biotin. Thus, 2,6-ANS was chosen for more detailed characterization of the interaction with avidin. Only a single class of binding sites for 2,6-ANS was identified; the mean value for the Kd was 203 +/- 16 microM (X +/- 1 S.D.), and the molar ratio of 2,6-ANS binding sites to biotin binding sites was approx. 1. These results provide evidence that the biotin binding site and the 2,6-ANS binding site are at least partially overlapping, but the possibility that the probe binding site is altered by a conformational change induced by biotin binding cannot be excluded. At excitation = 328 nm and emission = 408 nm, the molar fluorescence of the bound probe was 6.8 +/- 1.0 microM-1 and that of the free probe was 0.061 +/- 0.008 microM-1 giving an enhancement ratio (molar fluorescence of bound probe/molar fluorescence of free probe) of 111 +/- 22. Upon binding, the wavelength of maximum fluorescence decreases. These findings also provide evidence that the fluorescence enhancement associated with the interaction of 2,6-ANS and avidin reflects the environment of the biotin binding site. The Kosower's Z factor, an empirical index of apolarity, was 82.1 for the 2,6-ANS binding site on avidin. This value reflects a degree of apolarity that is similar to apolar environments observed for substrate binding sites on several enzymes; although not the dominant factor, this environment may contribute to the strong binding of biotin.     

A degenerate alpha satellite probe, detecting a centromeric deletion on chromosome 21 in an apparently normal human male, shows limitations of the use of satellite DNA probes for interphase ploidy analysis.

A degenerate alpha satellite DNA probe specific for a repeated sequence on human chromosomes 13 and 21 was synthesized using the polymerase chain reaction (PCR). Fluorescence in situ hybridization (FISH) with this probe to normal metaphase spreads revealed strong probe binding to the centromeric regions of human chromosomes 13 and 21 with negligible cross-hybridization with other chromosomes. FISH to normal interphase cell nuclei showed four distinct domains of probe binding. However, hybridization with probe to interphase and metaphase preparations from one apparently normal human male resulted in only three major binding domains. Metaphase chromosome analysis revealed a centromeric deletion on one chromosome 21 that caused greatly reduced probe binding. The result suggest caution in the interpretation of interphase ploidy studies performed with chromosome-specific alphoid DNA probes.     

Interaction of a paramagnetic analogue of oxaloacetate with citrate synthase.

Electron paramagnetic resonance studies have indicated that nitrosodisulfonate binds to pig heart citrate synthase. Titration of the enzyme with nitrosodisulfonate revealed several binding sites for the probe per subunit with one site (KD approximately 0.1 mM) having a greater affinity than the others. The substrate, oxaloacetate, competed very effectively for one of the nitrosodisulfonate binding sites (KD less than 10(-2) mM) at the same time eliminating the weaker probe binding sites. Citrate and (R)- and (S)-malates also displaced the probe. Failure to resolve low- and high-field shoulder in the high gain--high modulation electron paramagnetic resonance spectra of the enzyme--nitrosodisulfonate system indicated that the bound probe was "weakly immobilized". However, the electron paramagnetic resonance spectrum of the bound probe changed to one typical of a "strongly immobilized" nitroxide upon the addition of a saturating concentration of the substrate acetyl coenzyme A (acetyl-CoA) to the enzyme--nitrosodisulfonate system, indicating the formation of a ternary acetyl-CoA-enzyme-probe complex. Titration of the acetyl-CoA saturated enzyme with the probe indicated one binding site per subunit (KD = 0.37 mM). Thus, nitrosodisulfonate may be considered as a paramagnetic analogue of oxaloacetate in its interaction with citrate synthase. These results are compared with our previous studies with this enzyme, employing a spin-labeled acyl coenzyme A (acyl-CoA) derivative [Weidman, S. W., Drysdale, G. R., & Mildvan, A. S. (1973) Biochemistry 12, 1874--1883].     

Insertion of amphiphilic molecules into membranes is catalyzed by a high molecular weight non-ionic surfactant

We have employed an amphiphilic fluorescent probe to elucidate the mechanism by which a class of oxyethylene-oxypropylene copolymers catalyzes the insertion of hydrophobic or amphiphilic molecules into membranes. The rate of binding can be accelerated by over two orders of magnitude in the presence of the catalyst which does not itself disrupt the lipid bilayer. The rate of probe binding to lipid vesicles does not depend on the lipid concentration in the presence or absence of catalyst but is linearly related to the concentration of the catalyst. Probe binding to the polyol surfactant appears to be a component of the catalytic mechanism and equilibrium binding parameters can be determined; these are used to indirectly establish quantitative binding parameters for the probe to the vesicle membrane. The polyol surfactant is also shown to catalyze insertion of the probe into the outer leaflet of a hemispherical lipid bilayer and the plasma membrane of HeLa cells. The latter were also stained by catalyzed transfer of a fluorescent lipid from lipid vesicles. The permeability of the cell membrane is not significantly altered under any of the catalytic conditions. These data, taken together, suggest that the polyol surfactant extracts a monomeric substrate molecule from its aggregate or microcrystal and passes it to the membrane via a loose and transient contact.     

Internalization of iron-transferrin complex by murine L1210 leukemia cells and rat reticulocytes demonstrated by a minibead probe

To determine if the cellular uptake of iron is associated with internalization of iron-transferrin (TF) complex by the cell, we synthesized a visual probe in which TF is covalently bound to amide-modified latex minibead, submicrometer in size (0.345 micron). Incubation of the probe with L1210 leukemia cells and rat reticulocytes led to the binding of the probe to the cell surface visualized and semiquantified by scanning and transmission electron microscopy. The binding was inhibited by preincubation with nonderivatized iron-TF complex. Internalization of the probe occurred through clathrin-coated pits and vesicles. Minibeads derivatized by nontransport proteins or glycine as well as nonderivatized minibeads did not appreciably bind to the cells and were not internalized. Ethylamine, an inhibitor of receptor-mediated endocytosis abolished the internalization but not the binding of the probe which, then, accumulated on the cell surface. These findings provide direct evidence for internalization of TF during the iron uptake.     

Identification of a rRNA/chloramphenicol interaction site within the peptidyltransferase center of the 50 S subunit of the Escherichia coli ribosome.

We have used oligodeoxyribonucleotide probes to investigate possible interactions between chloramphenicol and portions of the rRNA contained within the peptidyltransferase center of the Escherichia coli ribosome. Oligodeoxyribonucleotide probes complementary to bases 2448-2454, 2468-2482, and 2497-2505 of 23 S rRNA were hybridized to 50 S subunits in situ. Probe binding was qualitatively assessed by sucrose gradient centrifugation. Each probe was shown to bind specifically with its intended binding site through digestion of the rRNA within the RNA/DNA hetero-duplexes with RNase H and analysis of the digestion fragments using gel electrophoresis. Competitive binding experiments were conducted between each probe and the antibiotics chloramphenicol and erythromycin. The binding of a probe complementary to bases 2497-2505 was attenuated by 70% upon the binding of chloramphenicol. A probe complementary to bases 2468-2482 showed an increase in binding of 14% while binding of a probe complementary to bases 2448-2454 was not affected by chloramphenicol binding. Erythromycin did not affect the binding of any of these probes to 50 S subunits. These results suggest that bases within the 2497-2505 region of 23 S rRNA in E. coli may be involved in a chloramphenicol/rRNA interaction.     

The migration of divalent cations in mitochondria visualized by a fluorescent chelate probe

Summary The use of the fluorescent chelate probe, chlorotetracycline, in mitochondria is described. The probe shows a high fluorescence in the presence of mitochondria which may be ascribed to binding of the probe to membrane-associated Ca⁺⁺ and Mg⁺⁺. The fluorescence excitation and emission spectra are diagnostic of binding of the probe to Ca⁺⁺ in coupled mitochondria and Mg⁺⁺ in uncoupled mitochondria. The fluorescence polarization spectra are diagnostic of the cations having a moderately high mobility in the membrane environment. The effects of exogenous EDTA and of endogenous Mn⁺⁺ indicate that the probe is primarily visualizing actively accumulated Ca⁺⁺ on the inner surface of the inner membrane. By employing the Ca⁺⁺ transport inhibitor, Tb⁺⁺⁺, the fluorescence changes associated with metabolic alterations are shown to arise partly from cation transport and partly through alterations in the binding properties of the inner surface of the membrane. Chlorotetracycline is a probe for divalent cations associated with the membrane and is of general utility in the study of cation migrations in cellular and subcellular systems.     

Tubulin photoaffinity labeling study with a plinabulin chemical probe possessing a biotin tag at the oxazole

A new bioactive photoaffinity probe KPU-252-B1 (4) possessing a biotin tag on the oxazole ring of a potent plinabulin derivative KPU-244 (2) was synthesized via the Cu^I-catalyzed Huisgen’s cycloaddition reaction to understand the precise binding mode of the diketopiperazine-based anti-microtubule agent plinabulin on tubulin. Probe 4 showed significant binding affinity toward tubulin and cytotoxicity against an HT-29 cells. A photoaffinity labeling study suggested that probe 4 specifically recognizes tubulin at a binding site that binds plinabulin or colchicine, most likely near or at the colchicine binding site, which is located at the interfacial region formed by ??-and ??-tubulin association. The results also demonstrated that probe 4 may serve as a useful plinabulin chemical probe to investigate the molecular mechanism by which anti-microtubule diketopiperazine derivatives operate.     

Ruthenium red as a paramagnetic probe in NMR spectroscopy

It is shown that ruthenium red acts as a paramagnetic probe in NMR spectroscopy. Unlike lanthanide and calcium ions it acts as a substitution probe for polyamine binding sites in biological systems, although it also binds at sites where calcium binds.     

Screening for oligonucleotide binding affinity by a convenient fluorescence competition assay.

A competitive homogeneous quenched fluorescence assay system is described for the high throughput screening of DNA conjugates that bind to single-stranded DNA. Fluorescence signal is generated by competitive binding of the sample molecule to a target strand labelled with a quencher probe, which is otherwise hybridised to a complementary strand containing a fluorescent probe. Thus fluorescence generated is related to the affinity of the sample. Competitive analysis of a number of peptide-oligonucleotide conjugates gave data that correlated well with the corresponding UV melting data. The assay will be useful for screening of large numbers of potential single-stranded binding molecules.     

Conformational dynamics of a transposition repressor in modulating DNA binding

The repressor of bacteriophage Mu functions in the establishment and maintenance of lysogeny by binding to Mu operator DNA to shut down transposition. A domain at its N terminus functions in DNA binding, and temperature-sensitive mutations in this domain can be suppressed by truncations at the C terminus. To understand the role of the C-terminal tail in DNA binding, a fluorescent probe was attached to the C terminus to examine its environment and its movement with respect to the DNA binding domain. The emission spectrum of this probe indicated that the C terminus was in a relatively hydrophobic environment, comparable to the environment of the probe attached within the DNA-binding domain. Fluorescence of two tryptophan residues located within the DNA-binding domain was quenched by the probe attached to the C terminus, indicating that the C terminus is in close proximity to this domain. Addition of DNA, even when it did not contain operator DNA, reduced quenching of tryptophan fluorescence, indicating that the tail moves away from the DNA-binding domain as it interacts with DNA. The presence of the tail also produced a trypsin hypersensitive site within the DNA-binding domain; mutant repressors with an altered or truncated C terminus were relatively resistant to cleavage at this site. Interaction of the wild-type repressor with DNA greatly reduced cleavage at the site. A repressor with a temperature-sensitive mutation in the DNA-binding domain was especially sensitive to cleavage by trypsin even in the presence of DNA, and the C-terminal tail failed to move in the presence of DNA at elevated temperatures. These results indicate that the tail sterically inhibits DNA binding and that it moves during establishment of repression. Such conformational changes are likely to be involved in communication between repressor protomers for cooperative DNA binding.     

Design and synthesis of a biotin-tagged photoaffinity probe of paeoniflorin

A trifunctional probe (binding element-photoreactive group-affinity tag) of natural product paeoniflorin was designed and synthesized based on the previous primary structure-activity relationship. This new probe is a potential tool for labeling, purification, and identification of the target proteins.     

5-Methylcytosine containing CG decamer as Z-DNA embedded sequence for a potential Z-DNA binding protein probe

Abstract

Attempting to elucidate biological significance of the left-handed Z-DNA is a research challenge due to Z-DNA potential role in many diseases. Discovery of Z-DNA binding proteins has ignited the interest in search for Z-DNA functions. Biosensor with Z-DNA forming probe can be useful to study the interaction between Z-DNA conformation and Z-DNA binding proteins. In this study, 5-methylcytosine (^mC) containing CG decamers were characterized for their suitability to form Z-DNA and to be used in Z-DNA forming probe. The 5′-thiol oligonucleotide embedded with 5′-^mCG^mCG^mCG^mCG^m CG-3′ was designed and developed as a potential Z-DNA forming probe for Z-DNA binding protein screening.     

Evidence for a tRNA/rRNA interaction site within the peptidyltransferase center of the Escherichia coli ribosome

A nine-base oligodeoxyribonucleotide complementary to bases 2497-2505 of 23S rRNA was hybridized to both 50S subunits and 70S ribosomes. The binding of the probe to the ribosome or ribosomal subunits was assayed by nitrocellulose filtration and by sucrose gradient centrifugation techniques. The location of the hybridization site was determined by digestion of the rRNA/cDNA heteroduplex with ribonuclease H and gel electrophoresis of the digestion products, followed by the isolation and sequencing of the smaller digestion fragment. The cDNA probe was found to interact specifically with its rRNA target site. The effects on probe hybridization to both 50S and 70S ribosomes as a result of binding deacylated tRNA(Phe) were investigated. The binding of deacylated tRNA(Phe), either with or without the addition of poly(uridylic acid), caused attenuation of probe binding to both 50S and 70S ribosomes. Probe hybridization to 23S rRNA was decreased by about 75% in both 50S subunits and 70S ribosomes. These results suggest that bases within the 2497-2505 site may participate in a deacylated tRNA/rRNA interaction.     

罗丹明类荧光分子探针与血清白蛋白之间相互作用的研究

本研究旨在对罗丹明类荧光探针ZM-6与人血清白蛋白(HSA)的相互作用进行研究。采用了荧光光谱法、三维荧光光谱法、同步荧光光谱法以及CD光谱法在模拟生理条件下对二者的相互作用以及HSA的构象进行了研究。研究结果表明,探针与ZM-6之间的猝灭机理主要是静态猝灭方式。根据热力学数据确定了二者之间的作用力,类型为范德华力和氢键。二者之间的结合距离为4.45 nm。同时得出,ZM-6对HSA的构象产生了影响。此研究对于探针分子的设计以及修饰提供有效的数据以及理论支持。     

S-(N-dansylaminoethyl)-6-mercaptoguanosine as a fluorescent probe for the uridine transport system in human erythrocytes.

A fluorescent derivative of 6-mercaptoguanosine, S-(N-dansylaminoethyl)-6-mercaptoguanosine, was synthesized, and found to be a strong inhibitor of the uridine transport system of erythrocyte (Ki approximately 0.3 microM). The emission spectrum of this compound has peaks at 400 and 550 nm. The emission at 550, but not that a 400 nm, in environment-sensitive. A method was devised for preparing a suspension of erythrocyte-membrane fragments with sufficiently low light scattering so that a detailed study could be made of the fluorescence of the probe when bound to membranes. Direct binding measurements showed the existence of a tight binding site, with a dissociation constant of the same order of magnitude as the inhibition constant. Binding of probe and substrate are not mutually exclusive, but the fluorescence and affinity of the bound probe are sensitive to the presence of uridine. The emission spectrum suggests that the bound probe penetrates into the bilayer region of the membrane.     

125I]iodopindolol: a new beta adrenergic receptor probe

When utilizing iodohydroxybenzylpindolol (IHYP) as an adrenergic receptor probe in muscle membrane systems, the data demonstrated an unacceptably high nonspecific binding component. Bearer et al. have reported that chloramine-T induced iodination of hydroxybenzylpindolol (HYP) results in the incorporation of iodine into the indole ring rather than into the phenolic moiety as noted previously by others. These results suggest that pindolol itself can also be iodinated. Therefore, the usefulness of carrier free 125I-labeled iodopindolol (IPIN) as an adrenergic receptor probe was investigated. Using between 0.01 nM and 0.1 nM [125I]IPIN in two different muscle membrane systems, we found the nonspecific binding component to be 10% or less of total binding. When [125I]IPIN was used with membranes prepared from rat skeletal muscle, we found it to interact with a single set of high affinity binding sites (KD = 0.13 +/- 0.01 nM) with the characteristics of beta adrenergic receptors and a density of 48.5 fmoles/mg protein. IPIN binding was also studied with purified dog cardiac sarcolemma. A single set of binding sites was detected having a KD of 1.64 +/- 0.5 nM; the density of these sites was 289 fmoles/mg membrane protein. [125I]IPIN may be a useful probe for the beta adrenergic receptor of tissues in which [125I]IHYP and other beta adrenergic receptor probes have a non-specific binding component which approaches that of the specific binding component.     

Synthesis of a new Ni-phenanthroline complex and its application as an electrochemical probe for detection of nucleic acid

A new DNA sensor using a nickel(II) phenanthroline complex ([Ni(phen)(2)PHPIP]·2ClO(4)) as the electrochemical probe was developed. The sensor is very sensitive and selective for calf thymus DNA (ctDNA) detection in aqueous medium. The Ni-phenanthroline probe was synthesized by a two-step preparation using p-hydroxy-phenylimidazo-1,10-phenanthroline (PHPIP) as the ligand and characterized with IR, UV and MS. Some interesting electrochemical properties of the Ni-complex and the interactions of the complex with ctDNA were reported. The calculated dynamics parameters of the electrode process indicate that there are obvious interactions between the probe and the ctDNA in aqueous solution. Under constant potential conditions, the redox current peak of the probe (Ni-complex) decreases obviously as the probe interacts/binds with ctDNAs. This unexpected electrochemical behavior may suggest that a new adduct through the binding of Ni-phenanthroline complex with ctDNA is formed electrochemically. By estimation, the binding ratio of the probe and ctDNA was found to be 1:1 with a binding constant β=4.29×10(5) mol L(-1) in aqueous solution at room temperature.     

Membrane potential and surface potential in mitochondria. Binding of a cationic spin probe

The interaction of the cationic spin probe 4-(N,N-dimethyl-N-dodecyl)-ammonium-2,2,6,6-tetramethyl-piperidine-1-oxyl (Cat12) with intact mitochondria and submitochondrial particles was investigated as a function of salt concentration, pH and energization by ATP. In the presence of 1 mM Fe(CN)-36, which inhibits the probe reduction by the mitochondria, the probe signal is stable and shows both bound and free forms. The partition of the probe into mitochondrial membranes is decreased by various salts depending on the cation valency, indicating that the membrane is negatively charged (-10 to -15 mV at pH 7.0). The surface potential increases with pH from -3 mV at pH 5.0 to -18 mV at pH 8.0. Energization of intact mitochondria by ATP reduces the magnitude of both bound and free signals by more than 50%; the signal of the bound form slowly disappears on further incubation. The ATP effect is inhibited and also reversed by either oligomycin or CCCP. Similar effects of ATP were observed in mitoplasts but not in submitochondrial particles. In submitochondrial particles ATP has no effect on the probe signal or binding. These results suggest that the formation of membrane potential in mitochondria induces uptake and internal binding of the probe which results in broadening of the EPR signal of the internally bound probe. It is concluded that Cat12 is not a suitable probe for measurement of surface potential in energized mitochondria.