A new generation of fluorescent chemosensors demonstrate improved analyte detection sensitivity and photobleaching resistance

Molecular chemosensors have found increased utility in the development of precise and sensitive detection devices. However, chemosensors that report binding via fluorescence through UV excitation are susceptible to destruction via photodegradation of the fluorophore. In the following report, the dansyl fluorophore in a previously reported chemosensor for peptides is replaced with an acridone derivative that is highly resistant to photobleaching. Its spectral properties are closely matched to those of the original dansyl fluorophore, and although quite structurally dissimilar, the new more photostable acridone chemosensor analogue exhibits only minor differences in binding/detection characteristics.     

Recognition and Binding of a Helix-Loop-Helix Peptide to Carbonic Anhydrase Occurs via Partly Folded Intermediate Structures

We have studied the association of a helix-loop-helix peptide scaffold carrying a benzenesulfonamide ligand to carbonic anhydrase using steady-state and time-resolved fluorescence spectroscopy. The helix-loop-helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, interpreted as differently interacting peptide/protein structures. We characterize these peptide/protein complexes as mostly bound but unfolded, bound and partly folded, and strongly bound and folded. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using the amplitudes of these times, we can correlate the lifetime groups with the corresponding fluorescence anisotropy component. The 23-ns rotational correlation time, which appears with the same amplitude as a 17-ns fluorescence lifetime, shows that the dansyl fluorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide/protein complex. A partly folded and partly hydrated interfacial structure is manifested in an 8-ns dansyl fluorescence lifetime and a 1.2-ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure, which allows segmental movement and has a higher degree of solvent exposure of dansyl. Indirect excitation of dansyl on the helix-loop-helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase shows that the helix-loop-helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that binding of the peptide to carbonic anhydrase involves a transition from a disordered to an ordered structure of the helix-loop-helix scaffold.     

Dynamic fluorescence of extrinsic fluorophores as a tool for studying protein conformational substates

Summary The fluorescence lifetime distribution of 2-p-toluidinyl-6-naphthalene sulfonic acids (TNS) bound to the heme site of apomyoglobin has been examined. The results were compared to those observed for the free fluorophore in isotropic nonviscous solvent. Two different excitation wavelengths were used, i.e. 290 and 350 nm. The results showed that the distribution of TNS bound to apomyoglobin is wider than that of the free fluorophore, thus indicating the existence of a large number of conformational substates originating from the interaction between TNS and the protein matrix. The comparison of the distribution obtained at two different excitation wavelengths allowed the emission arising from conformational substates, in which the excited state of fluorophore moiety has a higher probability to be populated by Forster energy transfer mechanism, to be distinguished.     

Fluorimetric studies of actin labeled with dansyl aziridine.

F-actin has been specifically labeled with a fluorescent probe, dansyl aziridine, at cysteine-373 of the protein. The fluorescence property of the conjugated probe serves as a spectroscopic indicator of several processes in which actin participates. The sulfhydryl modification does not impair the G-F transformation of actin, nor does it affect the complex formation of actin and myosin or the dissociation of the complex by ATP as judged by viscosity measurements. However, both labeled actin and actin modified by N-ethylmaleimide, which also reacts at cysteine-373, stimulate the Mg²⁺-ATPase of myosin only about 75% as well as unmodified actin. The probe attached to actin exhibits a 65-nm blue shift of its emission maximum from 560 to 495 nm and a sixfold fluorescence enhancement indicating that it is located in a hydrophobic environment. The excitation spectrum of labeled actin indicates that a tryptophan and a tyrosine residue are close to the probe and transfer excitation energy to the dansyl fluorophore. Upon depolymerization of F-actin, the fluorescence intensity of labeled actin increases about 20%. The fluorescence of labeled actin is also enhanced by the addition of EDTA, ATP, and pyrophosphate, but Mg²⁺ antagonizes this effect reversibly. However, in the presence of 10 mm orthophosphate buffer (pH 7.4) these effects disappear. When labeled F-actin binds with myosin subfragment-1 (SF-1) or heavy meromyosin (HMM), the fluorescence of the actin adduct is enhanced. The fluorescence properties of labeled acto-SF-1 and acto-HMM become insensitive to EDTA and polyphosphates even in the absence of orthophosphate. These results suggest that the two-stranded helical structure of the F-actin filament is stabilized by the presence of phosphate and/or the binding of the myosin “head”.     

Isotope-edited nuclear magnetic resonance study of Fv fragment of anti-dansyl mouse monoclonal antibody: recognition of the dansyl hapten.

An isotope-edited proton nuclear magnetic resonance study is reported of Fv, which is the smallest antigen recognition unit composed of VH and VL domains. Fv has been obtained by clostripain digestion of a short-chain anti-dansyl mouse IgG2a monoclonal antibody [Igarashi, T., Sato, M., Katsube, Y., Takio, K., Tanaka, T., Nakanishi, M., & Arata, Y. (1990) Biochemistry 29, 5727-5733]. A variety of stable-isotope-labeled anti-dansyl Fv analogues have been prepared. The aromatic proton resonances for all Tyr residues of the Fv fragment have been assigned in the absence and presence of epsilon-dansyl-L-lysine by means of isotope-edited homonuclear and heteronuclear two-dimensional NMR experiments. On the basis of the established assignments, it has been concluded that the dansyl ring is bound through Tyr-96H and Tyr-104H to both ends of H3, the third hypervariable region of the heavy chain. We also suggest that the antigen binding results in the formation of a hydrophobic core comprising the dansyl ring and the aromatic rings of Tyr-96H and Tyr-104H.     

Synthesis and photophysical properties of dansyl-based polyamine ligands and their Zn(II) complexes

The synthesis, potentiometric studies and photophysical properties of two new polyamine ligands (L1 and L2) possessing the dansyl chromophore were studied in aqueous 0.15 M NaCl. The compounds show the absorption and emissions bands characteristic of the dansylamide fluorophore and both present intramolecular excited state proton transfer at intermediate pH ranges. One of the ligands (L2) strongly coordinates Zn(II) leading to fluorescence quenching. A model compound (L3) of the dansyl moiety was also investigated.     

Human serum albumin binding assay based on displacement of a non selective fluorescent inhibitor

In this paper, we describe a fluorescent antibacterial analog, 6, with utility as a competition probe to determine affinities of other antibacterial analogs for human serum albumin (HSA). Analog 6 bound to HSA with an affinity of 400+/-100 nM and the fluorescence was environmentally sensitive. With 370 nm excitation, environmental sensitivity was indicated by a quenching of the 530 nm emission when the probe bound to HSA. Displacement of dansylsarcosine from HSA by 6 indicated it competed with compounds that bound at site II (ibuprofen binding site) on HSA. Analog 6 also shifted the NMR peaks of an HSA bound oleic acid molecule that itself was affected by compounds that bound at site II. In addition to binding at site II, 6 interacted at site I (warfarin binding site) as indicated by displacement of dansylamide and the shifting of NMR peaks of an HSA bound oleic acid molecule affected by warfarin site binding. Additional evidence for multiple site interaction was discovered when a percentage of 6 could be displaced by either ibuprofen or phenylbutazone. A competition assay was established using 6 to determine relative affinities of other antibacterial inhibitors for HSA.     

Binding of heparin to antithrombin III: The use of dansyl and rhodamine labels

Low molecular weight heparin of low-anticoagulant activity and high molecular weight heparin of correspondingly high activity were prepared by chromatography on protamine-Sepharose; preparations subjected to limited N-desulfation (5–10% free amino groups) by solvolysis were labeled with 5-dimethylaminonaphthalene-1-sulfonyl chloride (dansyl chloride) or rhodamine B isothiocyanate (RITC). The fluorescent heparins retained approximately 50% of the original anticoagulant activities. Dansyl-heparin on binding to antithrombin III (ATIII) exhibited a 2.5-fold enhancement of dansyl fluorescence intensity. This effect could be prevented by excess unlabeled heparin. A 7900 molecular weight dansyl-heparin preparation bound to ATIII with a stoichiometry of close to 2:1 and with an apparent association constant for binding (K_a) of 4.9 × 10⁵, m^?1, whereas a 21,600 molecular weight fraction bound at 0.7:1 with the protein and with an apparent K_a = 7.9 × 10⁵, m^?1. When ATIII reacted with a mixture of low molecular weight dansyl-heparin and low molecular weight RITC-heparin, there was enhancement of RITC fluorescence emission when excited at the dansyl excitation maximum; this effect was not observed when either of the labeled heparin species was prepared from high molecular weight material. The results are consistent with the proposal that a single molecule of high molecular weight, high-activity heparin occupies two sites when it binds to ATIII, whereas low molecular weight, low-activity heparin binds to the two sites separately.     

Characterization of the binding domain of the beta-adrenergic receptor with the fluorescent antagonist carazolol. Evidence for a buried ligand binding site

The antagonist carazolol has been used as a fluorescent probe for the binding site of the beta-adrenergic receptor (beta AR). The fluorescence properties of carazolol are dominated by the emission of the carbazole group, with the fine structure of the spectrum, but not the quantum yield, sensitive to the environment of the probe. The fluorescence emission spectrum of the bound probe is consistent with an extremely hydrophobic environment in the binding site of the receptor. Binding of carazolol to the purified beta AR increases the polarization of the fluorophore. Exposure to collisional quenchers has demonstrated the bound carazolol to be completely inaccessible to the solvent. Furthermore, the fluorescence of bound carazolol is not quenched by exposure to sodium nitrite, a F?rster energy acceptor which has an R0 value of 11.7 A with carazolol. Thus, physical analysis of the binding site of the beta AR by carazolol fluorescence indicates that the antagonist binds to the beta AR in a rigid hydrophobic environment which is buried deep within the core of the protein.     

Analysis of endo-beta-N-acetylglucosaminidase activity by high-pressure liquid chromatography on a silica-based chemically bonded octadecyl column

We have devised a new method for assaying the endo-β-N-acetylglucosaminidase activity by using the dansyl asparaginyl oligosaccharide, (Man)₅(GlcNAc)₂-Asn-DNS, as the substrate and analyzing the product, GlcNAc-Asn-DNS, by a reverse-phase high-pressure liquid chromatography using a silica-based chemically bonded octadecyl column (Waters μBondapack C₁₈). The column is eluted with 8% acetonitrile in 25 mm sodium borate buffer, pH 7.5, at 3 ml/min. The effluent is monitored by a Perkin-Elmer LC-75 uv monitor at 213 nm and a Perkin-Elmer LC-1000 fluorescence monitor (excitation, 313 nm; emission, 540 nm). Under these conditions, GlcNAc-Asn-DNS is well separated from (Man)₅(GlcNAc)₂-Asn-DNS and the analysis can be completed in 5 min. The peak height is used to quantify the dansyl derivatives. Under the conditions described above, the lower limit of detection is 0.1 nmol of dansyl glycopeptides.     

Use of Fluorescence Polarization to Observe Changes in Attitude of S-1 Moieties in Muscle Fibers

The fluorophore, N(iodoacetylamino)-1-naphthylamine-5-sulfonic acid (1,5-IAEDANS), incubated with glycerinated psoas fibers primarily labels the S-1 moieties of such fibers, but it does not impair fiber contractility even when the degree of labeling is as high as 0.8 moles fluorophore per mole myosin. The polarization of the on-axis fluorescence from either the IAEDANS fluorophore, or the intrinsic tryptophane fluorophore, depends on whether the fiber is relaxed, in rigor, or developing isometric tension; furthermore, the changes in polarization on going from one state to another are much the same with either tryptophane or IAEDANS fluorophores. The foregoing is true whether the plane of the exciting light is parallel or perpendicular to the fiber axis. Also, if a fiber is first freed of its myosin by extraction, and is then incubated with IAEDANS-labeled S-1 the resulting polarization approaches that observed with a labeled, unextracted fiber in rigor. By contrast, incubation with the fluorophore, 7-nitro-4-chlorobenz-2-oxa-1,3-diazole (NBD-Cl) confers fluorescence only on actin, without impairing contractility, but the polarization of such fluorescence changes in a different direction and magnitude from myosin-originating fluorescence. It is concluded from these various observations that whether the fluorophore is IAEDANS or tryptophane the polarization change with change in physiological state originates in the S-1 moieties of fibers, and relates to the space attitude of these moieties.     

Human serum albumin–malathion complex study in the presence of silver nanoparticles at different sizes by multi spectroscopic techniques

The binding of malathion to human serum albumin (HSA) in the presence of silver nanoparticles (AgNPs) was investigated for the first time by multiple spectroscopic methods such as fluorescence quenching, fluorescence resonance energy transfer (FRET), circular dichroism, red-edge excitation shift (REES), synchronous fluorescence and three dimensional fluorescence spectroscopy under physiological conditions .The results indicated that binding of malathion to HSA induced fluorescence quenching through static mechanism. The number of binding sites was calculated by double logarithmic equation. Changes in the micro-environment of the fluorophore residues were also probed by synchronous fluorescence spectroscopy and REES. Changes of secondary structure of HSA in HSA–malathion complex was verified by circular dichroism approach in the presence of AgNPs that showed the electrostatic interaction changes in the protein structure. The binding average distance (r) between the donor (HSA) and the acceptor (malathion) was measured and found to be 1.63?nm according to the Forster’s theory of non-radiation energy transfer which was <7?nm confirmed the existence of static quenching in the presence of AgNPs. The conformational changes of HSA by three-dimensional fluorescence spectroscopy were studied. By comparing the resonance light scattering in the binary and ternary systems, we could estimate the effect of AgNPs on the precipitation of the malathion on the HSA. Generally we have discussed the toxicity reduction effect of malathion in food industrial by the results of spectroscopy techniques.     

A real-time PCR-based method for determining the surface coverage of thiol-capped oligonucleotides bound onto gold nanoparticles

Here we report a real-time PCR-based method for determining the surface coverage of dithiol-capped oligonucleotides bound onto gold nanoparticles alone and in tandem with antibody. The detection of gold nanoparticle-bound DNA is accomplished by targeting the oligonucleotide with primer and probe binding sites, amplification of the oligonucleotide by PCR, and real-time measurement of the fluorescence emitted during the reaction. This method offers a wide dynamic range and is not dependant on the dissociation of the oligonucleotide strands from the gold nanoparticle surface; the fluorophore is not highly quenched by the gold nanoparticles in solution during fluorescence measurements. We show that this method and a fluorescence-based method give equivalent results for determining the surface coverage of oligonucleotides bound onto 13 or 30 nm gold nanoparticles alone and in tandem with antibody. Quantifying the surface coverage of immobilized oligonucleotides on metallic nanoparticle surfaces is important for optimizing the sensitivity of gold nanoparticle-based detection methods and for better understanding the interactions between thiol-functionalized oligonucleotides and gold nanoparticles.     

Structural and fluorescent study of zinc complexes of dansyl aminoquinoline

We have shown previously that 8-(5′-N,N-dimethylamino-1′-naphthalene)-sulfonamidoquinoline (DANQUIN) demonstrated a remarkable selectivity and sensitivity for the Zn(II) ion. In this work, the crystal structures of DANQUIN, Cu(DANQUIN)₂ and Cu(DANPY)₂ (DANPY, N-2-picolyl-(5′-N,N-dimethylamino-1′-naphthalene)-sulfonamide) are reported and compared with the simulated structure of Zn(DANQUIN)₂, which is important for the understanding of the factors that govern the fluorescence of DANQUIN. Free DANQUIN mainly displays the fluorescence of the dansyl group at 547 nm while the Zn(II)-DANQUIN complex mainly shows the enhanced fluorescence of aminoquinoline at 469 nm, while the emission of the dansyl group shifted to 517 nm with an almost constant intensity. This result demonstrates the advantage of this hybrid fluorescent chemosensor for Zn(II), and also makes it a potential candidate for ratiometric Zn(II) detection.     

The interaction of cyclosporin and calmodulin

The interaction of cyclosporin A and dansyl cyclosporin A with bovine and wheat germ calmodulin has been monitored by measurements of induced changes in dansyl and bound toluidinyl naphthalene sulfonate fluorescence. The interaction is Ca2(+)-dependent and 1:1. Measurements of the efficiency of radiationless energy transfer from bound dansyl cyclosporin A to an acceptor group located on Cys-27 of wheat germ calmodulin suggest that the primary binding site is not located on the N-terminal lobe (residues 1-65). However, studies with proteolytic fragments of calmodulin indicate that elements of the N-terminal half-molecule (residues 1-77) may be involved in the stabilization of the binding site. The binding of cyclosporin alters the physical properties of calmodulin and, in particular, reduces the localized rotational mobility of a fluorescent probe.     

Development of a fluorogenic sensor for activated Cdc42

Cdc42, a member of the Rho GTPase family, is a fundamental regulator of the actin cytoskeleton during cell migration. To generate a sensor for Cdc42 activation, we employed a multi-pronged approach, utilizing cysteine labeling and expressed protein ligation, to incorporate the environment sensitive fluorophore 4-N,N-dimethylamino-1,8-naphthalimide (4-DMN) into the GTPase binding domain of the WASP protein. These constructs bind only the active, GTP-bound conformation of Cdc42 to produce a fluorescence signal. Studies with a panel of five sensor analogs revealed a derivative that exhibits a 32-fold increase in fluorescence intensity in the presence of activated Cdc42 compared to incubation with the inactive GDP-bound form of the protein. We demonstrate that this sensor can be exploited to monitor Cdc42 nucleotide exchange and GTPase activity in a continuous, fluorescence assay.     

Orientation of substrate and two conformations of lactose permease

The accessibility of substrate bound to lactose permease of Escherichia coli was investigated by using the fluorescent substrate dansyl galactoside and a membrane-impermeable fluorescence quencher. To determine the orientation of bound substrate, both cells and inside-out vesicles were used. The substrate is oriented with the dansyl group toward the cytoplasm and the galactoside group toward the periplasm. Only half of the dansyl groups are accessible to quencher, irrespective of their orientation. This is interpreted as evidence for two different conformations of lactose permease, one with the binding site open to the cytoplasm and closed to the periplasm and vice versa for the other state.     

Molecular dynamics investigation of an antibody binding site by the fluorescence-photochrome method

A combined fluorescence-photochrome approach was used for investigation of the molecular dynamics antiDNP antibody binding site and its cavity. A 4-(N-2,4-dinitrophenylamino)-4'-(N,N'-dimethylamino)stilbene (StDNP) fluorescence DNP analog was incorporated into the antibody binding site. This was followed by measurements of fluorescence and photochrome parameters such as the StDNP excitation and emission spectra, fluorescence lifetime, steady-state and time-resolved fluorescence polarization, kinetics of trans-cis and cis-trans photoisomerization, and fluorescence quenching by nitroxide radicals freely diffused in solution. In parallel, computational modeling studies on the location and dynamics of DNP/TEMPO spin-label (NslDNP) and StDNP guests within a model of the binding site were performed. When all the experimental evidence is considered (including data from the antibody X-ray study), one can conclude that wobbling of the Trp 91 L/Trp 96 H binding-site.bound-hapten moiety (StDNP), can be responsible for the label's nanosecond dynamics monitored by fluorescence polarization techniques. A similar conclusion may be reached as a result of data analysis on NslDNP mobility within the antibody binding site. The mobility of Trp 91 L and Trp 96 H moieties provides the induced fit needed for effective stacking and release of the DNP epitope. Analysis of the above-mentioned data allows one to explore the mechanism of the probe's movement within the binding site and enables one to discuss the local dynamics of the binding site region. The combined fluorescence-photochrome approach can be used for investigation of local medium molecular dynamics in the immediate vicinity of specific sites of proteins and nucleic acids, as well as for other biologically important structures and synthetic analogues.     

Elongation factor EF-Ts interacts with the aminoacyl-tRNA.EF-Tu.GTP complex]

The fluorescence polarization technique has been used to study the interaction of the EF-Ts dansyl derivative with EF-Tu after nucleotide exchange and binding of the aminoacyl-tRNA to EF-Tu.GTP. It is shown that the ternary complex formation results in the increase of EF-Ts affinity to EF-Tu and EF-Ts remains bound to EF-Tu up to the GTP hydrolysis stage on the ribosome.     

Conformational dynamics of complementarity-determining region H3 of an anti-dansyl Fv fragment in the presence of its hapten

Antigen-induced structural changes in the Fv fragment of an anti-dansyl immunoglobulin G were studied by X-ray crystallography and stopped-flow fluorescence measurement. The crystal structure of the Fv fragment complexed with dansyl-lysine was determined at a resolution of 1.85 A. The dansyl-lysine molecule bound to a narrow cavity formed by the complementarity-determining regions H3 and H1, the N-terminal region of the VH domain and L2 of the VL domain. The structure of the binding site in the crystal structure explained well the results of the previous nuclear magnetic resonance measurements. The hapten binding caused remarkable conformational changes in H3 and its environmental structures, including the hydration structure from those observed in the unliganded state. The tip of H3 moved about 12 A from its position in the unliganded state. In addition, because of the contacts of H3 with the VL domain at the domain interface, the conformational changes of H3 resulted in the relative rotation of the variable domains by 5 degrees from their association observed in the unliganded state. The hydrophobic interactions at the domain interface seemed to be particularly important for the mutual rotation of the domains. The stopped-flow fluorescence measurement monitoring the interaction of the dansyl group and the binding pocket revealed that H3 was in a conformational equilibrium of three consecutive conformational states in the presence of dansyl-lysine in solution; an unliganded state preventing the access of the hapten, another unliganded state able to bind the hapten and the complex. The conformational dynamics of H3 in recognizing and binding the hapten molecule are discussed on the basis of the structural information from the present and previous studies.