Increased resonance energy transfer between fluorophores bound to DNA in proximity to metallic silver particles

We examined the effects of metallic silver particles on resonance energy transfer (RET) between fluorophores covalently bound to DNA. A coumarin donor and a Cy3 acceptor were positioned at opposite ends of a 23-bp double helical DNA oligomer. In the absence of silver particles the extent of RET is near 9%, consistent with a Forster distance R(0) near 50 A and a donor to acceptor distance near 75 A. The transfer efficiency increased when the solution of AMCA-DNA-Cy3 was placed between two quartz plates coated with silver island films to near 64%, as determined by both steady-state and time-resolved measurements. The apparent R(0) in the presence of silver island films increases to about 110 A. These values of the transfer efficiency and R(0) represent weighted averages for donor-acceptor pairs near and distant from the metallic surfaces, so that the values at an optimal distance are likely to be larger. The increased energy transfer is observed only between two sandwiched silvered slides. When we replaced one silvered slide with a quartz plate the effect vanished. Also, the increased energy transfer was not observed for silvered slides separated more than a few micrometers. These results suggest the use of metal-enhanced RET in PCR, hybridization, and other DNA assays, and the possibility of controlling energy transfer by the distance between silver surfaces.     

Fluorescence spectral properties of cyanine dye labeled DNA near metallic silver particles

Recent studies have demonstrated that silver metallic particles can increase the quantum yield and decrease the lifetimes of nearby fluorophores. These studies are extended to double stranded DNA oligomers labeled with N,N'-(dipropyl)-tetramethylindocarbocyanine (Cy3) or N,N-(dipropyl)-tetramethylindodicarbocyanine (Cy5). The proximity to silver particles increases the apparent quantum yields and decreases the lifetimes of the double helical DNA 23-mer labeled individually with Cy3 or Cy5. The decreased lifetimes are accompanied by apparently increased photostability of the labeled oligomers near silver particles. Because of spatial averaging across the sample these results are likely to significantly underestimate the effects of silver particles on labeled DNA localized at an optimal distance from the metallic surface. These results suggest that DNA arrays fabricated on substrates with silver particles can display increased sensitivity and photostability in the analysis of gene expression.     

Radiative decay engineering. 2. Effects of Silver Island films on fluorescence intensity, lifetimes, and resonance energy transfer

Metallic surfaces can have unusual effects on fluorophores such as increasing or decreasing the rates of radiative decay and the rates of resonance energy transfer (RET). In the present article we describe the effects of metallic silver island films on the emission spectra, lifetimes, and energy transfer for several fluorophores. The fluorophores are not covalently coupled to the silver islands so that there are a range of fluorophore-to-metal distances. We show that proximity of fluorophores to the silver islands results in increased fluorescence intensity, with the largest enhancement for the lowest-quantum-yield fluorophores. Importantly, the metal-induced increases in intensity are accompanied by decreased lifetimes and increased photostability. These effects demonstrate that the silver islands have increased the radiative decay rates of the fluorophore. For solvent-sensitive fluorophores the emission spectra shifted to shorted wavelengths in the presence of the silver islands, which is consistent with a decrease of the apparent lifetime for fluorophores near the metal islands. We also observed an increased intensity and blue spectral shift for the protein human glyoxalase, which displays a low quantum yield for its intrinsic tryptophan emission. In this case the blue shift is thought to be due to increased emission from a buried low-quantum-yield tryptophan residue. Increased intensities were also observed for the intrinsic emission of the nucleic acid bases adenine and thymine and for single-stranded 15-mers poly(T) and poly(C). And finally, we observed increased RET for donors and acceptors in solution and when bound to double-helical DNA. These results demonstrate that metallic particles can be used to modify the emission from intrinsic and extrinsic fluorophores in biochemical systems.     

Effects of metallic silver particles on resonance energy transfer in labeled bovine serum albumin

Resonance energy transfer (RET) is widely used to detect proximity between biomolecules. In transparent solution the maximum donor-to-acceptor distance for RET is about 70 A. We measured the effects of metallic silver island films on RET from the intrinsic tryptophan of a protein to a bound probe as the acceptor. These preliminary experiments revealed a dramatic increase in the apparent F?rster distance increasing from 28.6 to 63 A. These results suggest the use of silver island films for detecting long range proximity between biomolecules and for biotechnology applications based on RET.     

Onion aphid (Neotoxoptera formosana) attractants, in the headspace of Allium fistulosum and A. tuberosum leaves

Abstract:  Attractancy of Allium fistulosum L. and Allium tuberosum Rottl. to adult apterae of the onion aphid, Neotoxoptera formosana (Takahashi), an oligophagous aphid pest of Allium crops, was investigated with a Y-tube olfactometer. The aphids were significantly attracted to both A. fistulosum and A. tuberosum . The headspace components of both plants were extracted with solid-phase microextraction (SPME) and analysed by gas chromatography-mass spectrometry (GC-MS). The main volatile components of A. fistulosum were dipropyl disulphide (relative contents: 67%), 1-propenyl propyl disulphide (23%) and dipropyl trisulphide (6%). In the headspace of A. tuberosum , diallyl disulphide was detected as the main component (58%). Attractancy of dipropyl disulphide, dipropyl trisulphide and diallyl disulphide to the aphids was examined with the Y-tube olfactometer. The aphids were significantly attracted to dipropyl trisulphide and diallyl disulphide at a concentration of 0.01%. Dipropyl disulphide did not significantly attract the aphids at any concentrations tested. It was revealed that attractancy of A. fistulosum and A. tuberosum was caused by dipropyl trisulphide and diallyl disulphide, respectively. The findings suggest that N. formosana uses these sulphur compounds, characteristic components of Allium plants, as olfactory cues to find the host plants.     

Zinc depletion efficiently inhibits pancreatic cancer cell growth by increasing the ratio of antiproliferative/proliferative genes

We investigated the ability of the zinc chelator N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (TPEN) to reduce pancreatic cancer cell viability. TPEN was much more efficient to inhibit pancreatic adenocarcinoma cell growth than a panel of anti-cancer drugs, including 5-fluorouracil, irinotecan, cisplatin, edelfosine, trichostatin A, mitomycin C, and gemcitabine, the gold standard chemotherapeutic agent for pancreatic cancer. Moreover, TPEN showed a dose- and time-dependent anti-proliferative effect significantly higher on pancreatic cancer cells than on normal primary fibroblasts. This effect may be explained by a significantly higher zinc depletion by TPEN in pancreatic cancer cells as compared to fibroblasts. Cell viability reduction by TPEN was associated to both G1-phase cell cycle arrest and apoptosis, and to the increased ratio of the expression level of cyclin-Cdk inhibitor versus cyclin genes and apoptotic versus anti-apoptotic genes. Finally, we show that apoptotic cell death induced by TPEN involved mitochondrial injury and caspase 3 and caspase 8 activation. In this study, we suggest that zinc depletion may be an efficient strategy in the treatment of pancreatic cancer because of its reduced antiproliferative effect on normal cells.     

Positions of the sites labeled by N-cyclohexyl-N'-(4-dimethylamino-1-naphthyl)carbodiimide on the (Ca2+ + Mg2+)-ATPase

N-Cyclohexyl-N'-(4-dimethylamino-1-naphthyl)carbodiimide (NCD-4) labels (Ca2+ + Mg2+)-ATPase at Ca2+-protectable sites, believed to be at or near the two Ca2+ binding sites on the ATPase, and at nonspecific sites. The labeled ATPase has been reconstituted into lipid bilayers containing phosphatidylethanolamine labeled with fluorescein isothiocyanate. The distance between NCD-4 and fluorescein groups was measured using Forster energy transfer and the NCD-4 labels were found to be approx. 20 A from the lipid/water interface suggesting that the Ca2+ binding sites on the ATPase are also 20 A from the lipid/water interface. Addition of vanadate causes no change in the efficiency of energy transfer, suggesting that the Ca2+ binding sites on the E1 conformation of the ATPase do not move significantly with respect to the lipid/water interface in the E1-E2 transition.     

Effects of fluorophore-to-silver distance on the emission of cyanine-dye-labeled oligonucleotides

We examined the fluorescence spectral properties of Cy3- and Cy5-labeled oligonucleotides at various distances from the surface of silver island films. The distance to the surface was controlled by alternating layers of biotinylated bovine serum albumin (BSA) and avidin, followed by binding of a biotinylated oligonucleotide. The maximum enhancement of fluorescence near a factor of 12 was observed for the first BSA-avidin layer, with the enhancement decreasing to 2-fold for six layers. The minimum lifetimes were observed for the first BSA-avidin layer, and were about 25-fold shorter than on quartz slides without silver, with the lifetimes being about 2-fold shorter for six BSA-avidin layers. These results suggest that maximum fluorescence enhancements occur about 90A from the silver surface, a distance readily obtained by one or two layers of proteins.     

Distance distributions in proteins recovered by using frequency-domain fluorometry. Applications to troponin I and its complex with troponin C

We used resonance energy transfer to examine the distribution of distances between two sites on troponin I (TnI). The donor (D) was the single tryptophan residue at site 158 (Trp 158), and the acceptor (A) was cysteine 133 (Cys 133) which was labeled with N-(iodoacetyl)-N'-(1-sulfo-5-naphthyl)ethylenediamine (IE). A distribution of D-A distances results in a distribution of donor decay times, which were resolved by using frequency-domain fluorometry. In the native state we recovered a relatively narrow distribution of D-A distances. The widths of the distance distributions were found to increase progressively and dramatically with increasing concentrations of guanidine hydrochloride. Binding of calcium-free troponin C (TnC) to troponin I did not alter the distance distribution. Addition of Ca2+ to the TnI.TnC complex resulted in a sharper distance distribution and protected against the guanidine hydrochloride induced increase in the width of the distance distribution. Additionally, the same distance distributions were recovered for native and denatured TnI when the Forster distance for energy transfer was decreased by acrylamide quenching. These results demonstrate that distance distributions can be recovered with good accuracy, to the extent of revealing modest changes due to binding of other components. This technique should have widespread applications in studies of protein folding.     

一种植物生长激素-N'-(5-硝基-2-羟基苯亚甲基)-3,5-二羟基苯甲酰肼的合成、晶体结构和抗菌活性

目的:合成并表征一种属于植物生长激素的席夫碱类化合物.方法:由5-硝基水杨醛和3,5-二羟基苯甲酰肼在甲醇溶液中反应得到N′-(5-硝基-2-羟基苯亚甲基)-3,5-二羟基苯甲酰肼.结果:用单晶X-射线衍射法测得其结构并表征,同时通过抗菌实验证明其在一定浓度下具有明显的抗菌活性.结论:这种席夫碱类化合物在某种程度上具有明显的抗菌活性.     

Distance between Cys-201 in erythrocyte band 3 and the bilayer measured by single-photon radioluminescence.

Single-photon radioluminescence (SPR), the excitation of fluorophores by short-range beta-decay electrons, was developed for the measurement of submicroscopic distances. The cytoplasmic domain of band 3 (cdb3) is the primary, multisite anchorage for the erythrocyte skeleton. To begin to define the membrane arrangement of the highly asymmetrical cdb3 structure, the distance from the bilayer of Cys-201 next to the "hinge" of cdb3 was measured by both SPR and resonance energy transfer (RET). cdb3 was labeled at Cys-201 with fluorescein maleimide. For SPR measurements, the bilayer was labeled with [3H]oleic acid. The corrected cdb3-specific SPR signal was 98 +/- 2 cps microCi-1 [mumol band 3]-1. From this and the signal from a parallel sample in which 3H2O was substituted for [3H]oleic acid to create uniform geometry between 3H and the fluorophores, a Cys-201-to-bilayer separation of 39 +/- 7 A was calculated. Confirmatory distances of 40 and 43 A were obtained by RET between fluorescein on Cys-201 and eosin and rhodamine B lipid probes, respectively. This distance indicates that Cys-201 lies near band 3's vertical axis of symmetry and that the subdomain of cdb3 between the hinge and the membrane is not significantly extended. In addition, these results validate SPR as a measure of molecular distances in biological systems.     

Fluorescence properties of labeled proteins near silver colloid surfaces

The fluorescence properties of a monolayer of labeled avidin molecules were studied near silver island films. We first adsorbed a monolayer of biotinylated-BSA as a base that was used to capture labeled avidin molecules. For labeled avidin on silver island films, we observed an increase of the fluorescence intensity of between 18 and 80 with one-photon excitation and up to several hundredfold or larger with two-photon excitation. The probes were moderately more photostable in the presence of silver islands. There was also a dramatic decrease in the lifetimes with the amplitude-weighted values decreasing from 7- to 35-fold. The data suggest that these spectral changes are due to both increased rates of excitation near the metallic particles and increases in the rates of radiative decay. Because these silver island surfaces are very heterogeneous, we are hopeful that larger increases in intensity and photostability can be obtained for probes situated at an optimal distance from the ideal island surfaces.     

Resonance energy transfer between tryptophan 57 in the epsilon subunit and pyrene maleimide labeled gamma subunit of the chloroplast ATP synthase

The intrinsic fluorescence of the catalytic portion of the chloroplast ATP synthase (CF1) is quenched when cysteine 322, the penultimate amino acid of the gamma subunit, is specifically labeled with pyrene maleimide (PM). The epsilon subunit of CF1 contains the only two residues of tryptophan, which dominate the intrinsic fluorescence of unlabeled CF1. CF1 deficient in the epsilon subunit (CF1-epsilon) was reconstituted with mutant epsilon subunits in which phenylalanine replaced tryptophan at position 15 (epsilonW15F) and position 57 (epsilonW15/57F). CF1(epsilonW15F) containing a single tryptophan, epsilonW57, was labeled with PM at gammaC322. Resonance energy transfer (RET) from epsilonW57 to PM on gammaC322 occurred with an efficiency of energy transfer of 20%. RET was also observed from epsilonW57 to PM attached to the disulfide thiols of the gamma subunit (gammaC199,205) with an efficiency of approximately 45%. The R(o) (the distance at which the efficiency of energy transfer is 50%) for the epsilonW57 and PM donor/acceptor pair is 30 A, indicating that both gammaC322 and gammaC199,205 must be within 40 A of epsilonW57. These RET measurements show that both gammaC322 and gammaC199,205 are located near the base of the alpha/beta hexamer. This places the C-terminus of CF1 gamma much closer to epsilon than hypothesized based on homology to crystal structures of mitochondrial F1. These new RET measurements also allow the alignment of the predicted epsilon subunit structure. The orientation is similar to that predicted from cross-linking and mutational studies for the epsilon subunit of Escherichia coli F1.     

Sulfide oxidation with H2O2 catalyzed by manganese complex of N,N′,N″-tris(2-hydroxypropyl)-1,4,7-triazacyclononane

[MnL](ClO₄)₂ (L = N,N′,N″-tris(2-hydroxypropyl)-1,4,7-triazacyclononane) has been tested for catalyzing sulfide oxidation. In the presence of this complex, ethyl phenyl sulfide, butyl sulfide and phenyl sulfide are completely oxidized to the corresponding sulfoxides and sulfones with H₂O₂ as the oxidant. 2-Chloroethyl phenyl sulfide oxidation yield 2-chloroethyl phenyl sulfone and phenyl vinyl sulfone. In ethyl phenyl sulfide oxidation, effects of complex and H₂O₂ concentration and temperature on the reaction rate have been discussed. Through controlling reaction conditions, ethyl phenyl sulfoxide and ethyl phenyl sulfone may be produced selectively. The UV–Vis and electron paramagnetic resonance (EPR) studies on catalyst solution indicate that metal centre of the complex is transformed from Mn(II) to Mn(IV) after the addition of H₂O₂. At 25 °C, rate constant for ethyl phenyl sulfide oxidation is 4.38 × 10⁻³ min⁻¹.     

Precipitation by polycation as capture step in purification of plasmid DNA from a clarified lysate

The demand for highly purified plasmids in gene therapy and plasmid-based vaccines requires large-scale production of pharmaceutical-grade plasmid. Large-scale purification of plasmid DNA from bacterial cell culture normally includes one or several chromatographic steps. Prechromatographic steps include precipitation with solvents, salts, and polymers combined with enzymatic degradation of nucleic acids. No method alone has so far been able to selectively capture plasmid DNA directly from a clarified alkaline lysate. We present a method for selective precipitation of plasmid DNA from a clarified alkaline lysate using polycation poly(N, N'-dimethyldiallylammonium) chloride (PDMDAAC). The specific interaction between the polycation and the plasmid DNA resulted in the formation of a stoichiometric insoluble complex. Efficient removal of contaminants such as RNA, by far the major contaminant in a clarified lysate, and proteins as well as 20-fold plasmid concentration has been obtained with about 80% recovery. The method utilizes a inexpensive, commercially available polymer and thus provides a capture step suitable for large-scale production.     

Donor-donor energy migration for determining intramolecular distances in proteins: I. Application of a model to the latent plasminogen activator inhibitor-1 (PAI-1).

A new fluorescence spectroscopic method is presented for determining intramolecular and intermolecular distances in proteins and protein complexes, respectively. The method circumvents the general problem of achieving specific labeling with two different chromophoric molecules, as needed for the conventional donor-acceptor transfer experiments. For this, mutant forms of proteins that contain one or two unique cysteine residues can be constructed for specific labeling with one or two identical fluorescent probes, so-called donors (d). Fluorescence depolarization experiments on double-labeled Cys mutant monitor both reorientational motions of the d molecules, as well as the rate of intramolecular energy migration. In this report a model that accounts for these contributions to the fluorescence anisotropy is presented and experimentally tested. Mutants of a protease inhibitor, plasminogen activator inhibitor type-1 (PAI-1), containing one or two cysteine residues, were labeled with sulfhydryl specific derivatives of 4,4-difluoro-4-borata-3a-azonia-4a-aza-s-indacence (BODIPY). From the rate of energy migration, the intramolecular distance between the d groups was calculated by using the Forster mechanism and by accounting for the influence of local anisotropic orientation of the d molecules. The calculated intramolecular distances were compared with those obtained from the crystal structure of PAI-1 in its latent form. To test the stability of parameters extracted from experiments, synthetic data were generated and reanalyzed.     

Yeast N(alpha)-terminal acetyltransferases are associated with ribosomes

N-terminal acetylation is one of the most common modifications, occurring on the vast majority of eukaryotic proteins. Saccharomyces cerevisiae contains three major NATs, designated NatA, NatB, and NatC, with each having catalytic subunits Ard1p, Nat3p, and Mak3p, respectively. Gautschi et al. (Gautschi et al. [2003] Mol Cell Biol 23: 7403) previously demonstrated with peptide crosslinking experiments that NatA is bound to ribosomes. In our studies, biochemical fractionation in linear sucrose density gradients revealed that all of the NATs are associated with mono- and polyribosome fractions. However only a minor portion of Nat3p colocalized with the polyribosomes. Disruption of the polyribosomes did not cause dissociation of the NATs from ribosomal subparticles. The NAT auxiliary subunits, Nat1p and Mdm20p, apparently are required for efficient binding of the corresponding catalytic subunits to the ribosomes. Deletions of the genes corresponding to auxiliary subunits significantly diminish the protein levels of the catalytic subunits, especially Nat3p, while deletions of the catalytic subunits produced less effect on the stability of Nat1p and Mdm20p. Also two ribosomal proteins, Rpl25p and Rpl35p, were identified in a TAP-affinity purified NatA sample. Moreover, Ard1p copurifies with Rpl35p-TAP. We suggest that these two ribosomal proteins, which are in close proximity to the ribosomal exit tunnel, may play a role in NatA attachment to the ribosome.     

Studies on the reactions of ruthenium(II) substrates with tridentate (N,N,O) azo ligands

Reactions of 1-{[2-(arylazo)phenyl]iminomethyl}-2-phenol, HL_sal, 1, [where H represents the dissociable protons upon complexation and aryl groups of HL_sal are phenyl for HL¹_sal, p-methylphenyl for HL²_sal, and p-chlorophenyl for HL³_sal], ligands with Ru(H)(CO)(Cl)(PPh₃)₃ afforded complexes of composition [(L_sal)Ru(CO)(Cl)(PPh₃)] and (L_sal)₂Ru where the N,N,O donor tridentate (L_sal)⁻ ligands coordinated the metal centre facially and meridionally, respectively. Stepwise formation of [(L_sal)₂Ru] has been ascertained. Reaction of 1-{[2-(arylazo)phenyl]iminomethyl}-2-napthol, HL_nap, 2, [where H represents the dissociable protons upon complexation and aryl groups of HL_nap are phenyl for HL¹_nap, p-methylphenyl for HL²_nap, and p-chlorophenyl for HL³_nap], ligands with Ru(H)(CO)(Cl)(PPh₃)₃ afforded exclusively the complexes of composition [(L_nap)Ru(CO)(Cl)(PPh₃)], where N,N,O donor tridentate (L_nap)⁻ was facially coordinated. The ligand 1-{[2-(phenylazo)phenyl]aminomethyl}-2-phenol, HL, 3, was prepared by reducing the aldimine function of HL¹_sal. Reaction of HL with Ru(PPh₃)₃Cl₂ afforded new azosalen complex of Ru(III) in concert with regiospecific oxygenation of phenyl ring of HL. All the new ligands were characterized by analytical and spectroscopic techniques. The complexes were characterized by analytical and spectroscopic techniques and subsequently confirmed by the determination of X-ray structures of selected complexes.     

Trade-off in short- and long-distance communication in tungara (Physalaemus pustulosus) and cricket (Acris crepitans) frogs

Female phonotaxis in túngara (Physalaemus pustulosus)and cricket (Acris crepitans) frogs is biased toward male advertisementcalls or call components of lower frequency. This behavioralbias might result in part from a mismatch between the spectralcharacteristics of the advertisement call and the most sensitive frequencyof the peripheral end organ implicated in reception of thesesounds. In both species, females are tuned to frequencies lowerthan average for the calls in their population. This mismatch,however, represents the situation during short-distance communication.Female frogs can also use the call to detect choruses at longdistances, and the spectral distribution of call energy canvary with transmission distance. We used computer simulationsto test the hypothesis that there is a better match betweentuning and call spectral energy at long distances from the callingmale than at short distances by comparing the performance (soundenergy received) of the natural tuning curve relative to anoptimal tuning curve (i.e., one centered at the call's dominantfrequency). The relative performance of the natural tuning curveincreased with distance in túngara frogs. For the twosubspecies of cricket frogs, however, the relative performancedecreased at longer distances. The performance did not equalthe optimal tuning curve at the distances tested. The resultsindicate that the relationship between calls and auditory tuningcannot be optimal for both long and short distance reception.The relationship between female tuning and call dominant frequencymay represent a compromise between short and long distance communication,and the bias toward short or long distances may vary among species.     

Conformations within soluble oligomers and insoluble aggregates revealed by resonance energy transfer

A fluorescently labeled 20‐residue polyglutamic acid (polyE) peptide 20 amino acid length polyglutamic acid (E₂₀) was used to study structural changes which occur in E₂₀ as it co‐aggregates with other unlabeled polyE peptides. Resonance energy transfer (RET) was performed using an o‐aminobenzamide donor at the N‐terminus and 3‐nitrotyrosine acceptor at the C‐terminus of E₂₀. PolyE aggregates were not defined as amyloid, as they were nonfibrillar and did not bind congo red. Circular dichroism measurements indicate that polyE aggregation involves a transition from α‐helical monomers to aggregated β‐sheets. Soluble oligomers are also produced along with aggregates in the reaction, as determined through size exclusion chromatography. Time‐resolved and steady‐state RET measurements reveal four dominant E₂₀ conformations: (1) a partially collapsed conformation (24 Å donor–acceptor distance) in monomers, (2) an extended conformation in soluble oligomers (>29 Å donor–acceptor distance), (3) a minor partially collapsed conformation (22 Å donor‐acceptor distance) in aggregates, and (4) a major highly collapsed conformation (13 Å donor–acceptor distance) in aggregates. These findings demonstrate the use of RET as a means of determining angstrom‐level structural details of soluble oligomer and aggregated states of proteins. © 2009 Wiley Periodicals, Inc. Biopolymers 93: 299–317, 2010. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com