Practical syntheses of dyes for difference gel electrophoresis

An efficient route to the synthesis of novel zwitterionic pyridinium-cyanopropenides with 3-heteroaryl-substituted trimethinium salts

In this study, eight new zwitterionic derivatives were synthesized using a simple design method from the reaction of various 2-substituted 1,3-bis(dimethylamino)-trimethinium salts with malononitrile or ethyl 2-cyanoacetate in excellent yields in the presence of triethylamine in ethanol at reflux. The molecular structures of the new compounds were confirmed by IR, UV/vis, mass, ¹H, and ¹³C NMR spectra as well as by elemental analyses.

Synthesis of new zwitterionic derivatives via the reaction of 2-substituted 1,3-bis(dimethylamino)-trimethinium salts with malononitrile or ethyl cyanoacetate in the presence of Et₃N in ethanol at reflux.

A flowerlike FePt/MnO2/GOx-based cascade nanoreactor with sustainable O2 supply for synergistic starvation-chemodynamic anticancer therapy

The development of versatile nanotheranostic agents has received increasing interest in cancer treatment. Herein, in this study, we rationally designed and prepared a novel flowerlike multifunctional cascade nanoreactor, BSA-GOx@MnO2@FePt (BGMFP), by integrating glucose oxidase (GOx), manganese dioxide (MnO2) and FePt for synergetic cancer treatment with satisfying therapeutic efficiency. In an acidic environment, intratumoral H2O2 could be decomposed to O2 to accelerate the consumption of glucose catalyzed by GOx to induce cancer starvation. Moreover, the accumulation of gluconic acid and H2O2 generated along with the consumption of glucose would in turn promote the catalytic efficiency of MnO2 and boost O2 evolution, which could enhance the efficiency of starvation therapy. Moreover, FePt as an excellent Fenton agent could simultaneously convert H2O2 to the toxic hydroxyl radical (˙OH), subsequently resulting in amplified intracellular oxidative stress and cell apoptosis. Therefore, BGMFP could catalyze a cascade of intracellular biochemical reactions and optimize the unique properties of MnO2, GOx and FePt via mutual promotion of each other to realize O2 supply, chemodynamic therapy (CDT) and starvation therapy. The anticancer results in vitro and in vivo demonstrated that BGMFP possessed remarkable tumor inhibition capacity through enhancing the starvation therapy and CDT. It is appreciated that BGMFP could be a promising platform for synergetic cancer treatment.

Stable, Fluorescent Polymethylmethacrylate Particles for the Long-Term Observation of Slow Colloidal Dynamics

Suspensions of solid micron-scale colloidal particles in liquid solvents are a foundational model system used to explore a wide range of phase transitions, including crystallization, gelation, spinodal decomposition, and the glass transition. One of the most commonly used systems for these investigations is the fluorescent spherical particles of polymethylmethacrylate (PMMA) suspended in a mixture of nonpolar solvents that match the density and the refractive index of the particles to minimize sedimentation and scattering. However, the particles can swell in these solvents, changing their size and density, and may leak the fluorescent dye over days to weeks; this constrains the exploration of slow and kinetically limited processes, such as near-boundary phase separation or the glass transition. In this paper, we produce PMMA colloidal particles that employ polymerizable and photostable cyanine-based fluorescent monomers spanning the range of visible wavelengths and a polymeric stabilizer prepared from polydimethylsiloxane, PDMS-graft-PMMA. Using microcalorimetry, we characterize the thermodynamics of an accelerated equilibration process for these dispersions in the buoyancy- and refractive-index-matching solvents. We use confocal differential dynamic microscopy to demonstrate that they behave as hard spheres. The suspended particles are stable for months to years, maintaining fixed particle size and density, and do not leak dye. Thus, these particles enable longer term experiments than may have been possible earlier; we demonstrate this by observing spinodal decomposition in a mixture of these particles with a depletant polymer in the microgravity environment of the International Space Station. Using fluorescence microscopy, we observe coarsening over several months and measure the growth of the characteristic length scale to be a fraction of a picometer per second; this rate is among the slowest observed in a phase-separating system. Our protocols should facilitate the synthesis of a variety of particles.

IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters

Cell communications are essential to the organization, development, and maintenance of multicellular organisms. Much of this communication involves changes in RNA transcription and is dynamic. Most methods for studying transcription require interrupting the continuity of cellular function by sacrificing the communicating cells and capturing gene expression information by periodic sampling of individual cells or the population. The IMAGEtag technology to quantify RNA levels in living cells, demonstrated here in yeast, allows individual cells to be tracked over time as they respond to different environmental cues. IMAGEtags are short RNAs consisting of strings of a variable number of tandem aptamers that bind small-molecule ligands. The aptamer strings can vary in length and in configuration of aptamer constituents, such as to contain multiples of the same aptamer or two or more different aptamers that alternate in their occurrence. A minimum effective length is about five aptamers. The maximum length is undefined. The small-molecule ligands are enabled for imaging as fluorophore conjugates. For each IMAGEtag, two fluorophore conjugates are provided, which are FRET pairs. When a cell expresses an RNA containing an IMAGEtag sequence, the aptamers bind their ligands and bring the fluorophores into sufficiently close proximity to allow FRET. The background fluorescence of both fluorophores is minimal in the FRET channel. These features endow IMAGEtags with the sensitivity to report on mRNA expression levels in living cells.

Targeting tumor hypoxia: a third generation 2-nitroimidazole-indocyanine dye-conjugate with improved fluorescent yield

Tumor hypoxia is associated with the rapid proliferation and growth of malignant tumors, and the ability to detect tumor hypoxia is important for predicting tumor response to anti-cancer treatments. We have developed a class of dye-conjugates that are related to indocyanine green (ICG, ) to target tumor hypoxia, based on in vivo infrared fluorescence imaging using nitroimidazole moieties linked to indocyanine fluorescent dyes. We previously reported that linking 2-nitroimidazole to an indocyanine dicarboxylic acid dye derivative () using an ethanolamine linker (ethanolamine-2-nitroimidazole-ICG, ), led to a dye-conjugate that gave promising results for targeting cancer hypoxia in vivo. Structural modification of the dye conjugate replaced the ethanolamine unit with a piperazineacetyl unit and led a second generation dye conjugate, piperzine-2-nitroimidazole-ICG (). This second generation dye-conjugate showed improved targeting of tumor hypoxia when compared with . Based on the hypothesis that molecules with more planar and rigid structures have a higher fluorescence yield, as they could release less absorbed energy through molecular vibration or collision, we have developed a new 2-nitroimidazole ICG conjugate, , with two carbon atoms less in the polyene linker. Dye-conjugate was prepared from our new dye (), and coupled to 2-nitroimidazole using a piperazine linker to produce this third-generation dye-conjugate. Spectral measurements showed that the absorption/emission wavelengths of 657/670 were shifted ∼100 nm from the second-generation hypoxia dye of 755/780 nm. Its fluorescence quantum yield was measured to be 0.467, which is about 5 times higher than that of (0.083). In vivo experiments were conducted with balb/c mice and showed more than twice the average in vivo fluorescence intensity in the tumor beyond two hours post retro-orbital injection as compared with . These initial results suggest that may significantly improve in vivo tumor hypoxia targeting.

Symmetrical and asymmetrical cyanine dyes. Synthesis, spectral properties, and BSA association study

New cyanines were prepared by an efficient and practical route with satisfactory overall yield from low-cost starting materials. The photophysical behavior of the cyanines was investigated using UV-vis and steady-state fluorescence in solution, as well as their association with bovine serum albumin (BSA) in phosphate buffer solution (PBS). No cyanine aggregation was observed in organic solvents or in phosphate buffer solution. The alkyl chain length in the quaternized nitrogen was shown to be fundamental for BSA detection in PBS in these dyes.

Tumor targeting profiling of hyaluronan-coated lipid based-nanoparticles

Hyaluronan (HA), a naturally occurring high Mw (HMw) glycosaminoglycan, has been shown to play crucial roles in cell growth, embryonic development, healing processes, inflammation, and tumor development and progression. Low Mw (LMw, <10 kDa) HA has been reported to provoke inflammatory responses, such as induction of cytokines, chemokines, reactive nitrogen species and growth factors. Herein, we prepared and characterized two types of HA coated (LMw and HMw) lipid-based targeted and stabilized nanoparticles (tsNPs) and tested their binding to tumor cells expressing the HA receptor (CD44), systemic immunotoxicity, and biodistribution in tumor bearing mice. In vitro, the Mw of the surface anchored HA had a significant influence on the affinity towards CD44 on B16F10 murine melanoma cells. LMw HA-tsNPs exhibited weak binding, while binding of tsNPs coated with HMw HA was characterized by high binding. Both types of tsNPs had no measured effect on cytokine induction in vivo following intravenous administration to healthy C57BL/6 mice suggesting no immune activation. HMw HA-tsNPs showed enhanced circulation time and tumor targeting specificity, mainly by accumulating in the tumor and its vicinity compared with LMw HA-tsNPs. Finally, we show that methotrexate (MTX), a drug commonly used in cancer chemotherapy, entrapped in HMw HA-tsNPs slowly diffused from the particles with a half-life of 13.75 days, and improved the therapeutic outcome in a murine B16F10 melanoma model compared with NPs suggesting an active cellular targeting beyond the Enhanced Permeability and Retention (EPR) effect. Taken together, these findings have major implications for the use of high molecular weight HA in nanomedicine as a selective and safe active cellular targeting moiety.

Modulation of drug resistance in ovarian adenocarcinoma using chemotherapy entrapped in hyaluronan-grafted nanoparticle clusters

Resistance to anticancer drugs is considered a major cause of chemotherapy failure. One of the major mediators of resistance is the multidrug extrusion pump protein, P-glycoprotein (P-gp), an ATP-binding cassette (ABC) transporter with broad substrate specificity. In order to bypass this drug resistance mechanism, we have devised phospholipid-based nanoparticle clusters coated with the glycosaminoglycan hyaluronan, the major ligand of CD44, which is upregulated and undergoes different splice variations in many types of cancer cells. These particles, termed glycosaminoglycan particle nanoclusters or gagomers (GAGs), were self-assembled into ∼500 nm diameter clusters, with zeta-potential values of ∼-70 mV. Flow cytometry analysis provided evidence that, unlike free doxorubicin (DOX), a model chemotherapy, DOX entrapped in the GAGs (DOX-GAGs) accumulated in P-gp-overexpressing human ovarian adenocarcinoma cell line and dramatically decreased cell viability, while drug-free GAGs and the commercially available drug DOXIL (PEGylated liposomal DOX) did not produce therapeutic benefit. Furthermore, by using RNA interference strategy, we showed that DOX-GAGs were able to overcome the P-gp-mediated resistant mechanism of these cells. Most importantly, DOX-GAGs showed a superior therapeutic effect over free DOX in a resistant human ovarian adenocarcinoma mouse xenograft model. Taken together, these results demonstrated that GAGs might serve as an efficient platform for delivery of therapeutic payloads by bypassing P-gp-mediated multidrug resistance.

Trivalent galactosyl-functionalized mesoporous silica nanoparticles as a target-specific delivery system for boron neutron capture therapy

A multi-functional mesoporous silica nanoparticle (MSN)-based boron neutron capture therapy (BNCT) agent, designated as T-Gal-B-Cy3@MSN, was synthesized with hydrophobic mesopores for incorporating a large amount of o-carborane (almost 60% (w/w) boron atoms per MSN), and the amines on the external surface were conjugated with trivalent galactosyl ligands and fluorescent dyes for cell targeting and imaging, respectively. The polar and hydrophilic galactosyl ligands enhance the water dispersibility of the BNCT agent and inhibit the possible leakage of o-carborane loaded in the MSN. Confocal microscopic images showed that T-Gal-B-Cy3@MSNs were endocytosed by cells and were then released from lysosomes into the cytoplasm of cells. Moreover, in comparison with the commonly used clinical BNCT agent, sodium borocaptate (BSH), T-Gal-B-Cy3@MSN provides a higher delivery efficiency (over 40-50 fold) of boron atoms and a better effect of BNCT in neutron irradiation experiments. MTT assays show a very low cytotoxicity for T-Gal-B-Cy3@MSN over a 2 h incubation time. The results are promising for the design of multifunctional MSNs as potential BNCT agents for clinical use.

A peptide nucleic acid (PNA) heteroduplex probe containing an inosine-cytosine base pair discriminates a single-nucleotide difference in RNA

Selective discrimination of a single-nucleotide difference in single-stranded DNA or RNA remains a challenge with conventional DNA or RNA probes. A peptide nucleic acid (PNA)-derived probe, in which PNA forms a pseudocomplementary heteroduplex with inosine-containing DNA or RNA, effectively discriminates a single-nucleotide difference in a closely related group of sequences of single-stranded DNA and/or RNA. The pseudocomplementary PNA heteroduplex is easily converted to a fluorescent probe that distinctively detects a member of highly homologous let-7 microRNAs.

Optimized design and synthesis of a cell-permeable biarsenical cyanine probe for imaging tagged cytosolic bacterial proteins

To optimize cellular delivery and specific labeling of tagged cytosolic proteins by biarsenical fluorescent probes built around a cyanine dye (Cy3) scaffold, we have systematically varied the polarity of the N-alkyl chain (i.e., 4-5 methylene groups appended by a sulfonate or methoxy ester moiety) and arsenic capping reagent (ethanedithiol versus benzenedithiol). Optimal live-cell labeling and visualization of tagged cytosolic proteins is reported using an ethanedithiol capping reagent with the uncharged methoxy ester functionalized N-alkyl chains. These measurements demonstrate the general utility of this new class of photostable and highly fluorescent biarsenical probes based on the cyanine dye scaffold for in vivo labeling of tagged cellular proteins for live cell imaging measurements of protein dynamics.

Synthesis and validation of cyanine-based dyes for DIGE

The application of difference gel electrophoresis (DIGE), in particular its most common "minimal labeling" variety, utilizes N-hydroxysuccinimide esters of Cy2, Cy3, and Cy5 dyes, which are commercially available. We describe methods for the efficient synthesis of all three dyes from relatively inexpensive and commercially available precursors in only a few steps and with relatively high yields. In model DIGE experiments, the newly synthesized dyes proved to be indistinguishable from commercially available ones and have been shown to be stable for years while stored under argon as dry solids or after being dissolved in N,N-dimethylformamide.

Combination of highly efficient hexapeptide ligand library-based sample preparation with 2D DIGE for the analysis of the hidden human serum/plasma proteome

Blood serum/plasma samples provide the major source to identify diagnostically relevant or treatment response-related proteins. But its complexity and the enormous dynamic range hinders comprehensive analysis. Therefore, more detailed analysis, in particular, of low-abundant peptides/proteins requires extensive pre-fractionation, which frequently influences the native composition and may lead to a loss of potentially important information. In order to overcome these barriers, we describe an innovative sample preparation tool utilizing combinatorial hexapeptide ligand libraries to efficiently enrich low-abundance proteins with a simple protocol. In contrast to the most common approaches based on the immuno-depletion of antibody-targeted high-abundance proteins, this technology concentrates low-abundance proteins and concurrently reduces the high-abundance species. Thus, the dynamic range is compressed, and low-abundance proteins become more easily detectable. We show how this sample preparation technique can be easily combined with 2D DIGE analysis to enable more comprehensive and quantitative profiling of complex biological samples.

1-(5-Carboxy-pent-yl)-2,3,3-trimethyl-3H-indol-1-ium bromide monohydrate

In the title compound, C(17)H(24)NO(2) (+)·Br(-)·H(2)O, the pentyl group chain in the cation extends nearly perpendicular [N-C-C-C = -64.4 (3)°] to the mean plane of the indole ring with the carboxyl end group twisted such that the dihedral angle between the mean planes of the indole and carb-oxy groups measures 43.2 (4)°. Both ions in the salt form inter-molecular hydrogen bonds (O-H⋯Br and O-H⋯O) with the water mol-ecule. As a result of the Br⋯H-O-H⋯Br inter-actions, a zigzag chain is formed in the c-axis direction. The crystal packing is influenced by the collective action of the O-H⋯O and O-H⋯Br inter-molecular inter-actions as well as π-π stacking inter-molecular inter-actions between adjacent benzyl rings of the indole group [centroid-centroid distance = 3.721 (13) Å] and inter-molecular C-H⋯π inter-actions between a methyl hydrogen and the benzyl ring of the indole group. The O-H⋯Br inter-actions form a distorted tetra-hedral array about the central Br atom. A MOPAC AM1 calculation provides support to these observations.

Validation of self-made fluorescent cyanine dyes for 2D gel-based multi-fluorescence protein analysis

Two-dimensional gel electrophoresis (2-DE) in combination with quantitative multi-fluorescence protein analysis (MFA) is the most versatile methodical tool for differential analysis of protein mixtures or even complex proteomes. It is based on covalent labelling of proteins with fluorescent cyanine dyes (Ethyl-Cy2, Propyl-Cy3 or Methyl-Cy5) before isoelectric focussing, enabling differential tagging of up to three samples which are finally separated on the same 2-D gel. To minimize costs and to increase the number of possible experiments, the cyanine dye NHS esters were synthesized in our own lab according to a protocol published by Jung and Kim (2006) . Self-made cyanine dyes were tested by studying their labelling and fluorescent properties and possible effects on the electrophoretic mobility of labelled proteins. To validate the potential use as labels in 2-DE/MFA experiments, dyes were used for the differential analysis of the proteome of thrombin-stimulated human vascular smooth muscle cells (VSMCs).

Differential activity-based gel electrophoresis for comparative analysis of lipolytic and esterolytic activities

We established a novel technique for differential activity-based gel electrophoresis (DABGE) of lipolytic enzymes from two different biological samples. For this purpose, a set of three fluorescent suicide inhibitors was developed. These probes possess the same substrate analogous structures but carry different cyanine dyes (Cy2b, Cy3, and Cy5) as reporter fluorophores. For comparison of enzyme profiles, two samples are individually labeled with a different probe followed by mixing, gel electrophoresis, fluorescence imaging, and identification of the tagged proteins by MS/MS. Protocols for quantitative determination of active enzymes were developed on the basis of lipolytic proteomes that had been admixed with defined amounts of known lipases and esterases. A detailed analysis of the fluorescence intensities showed that the found enzyme ratios very closely reflected the relative amounts of the labeled enzymes that were used for spiking. The DABGE method was used to compare the lipolytic proteomes of brown and white adipose tissue showing specific enzyme patterns of both samples. This study represents the first application of this technology for comparative analysis of lipases and esterases. Further applications of this technique can be expected to provide entirely new information on lipid enzymology in health and disease with high precision.

Catch and release microwave mediated synthesis of cyanine dyes

Unsymmetrical functionalised cyanine dyes, covering the whole colour range, were readily synthesised (in 100 mg amounts) by a combination of microwave and solid-phase methodologies.

Microwave synthesis of quaternary ammonium salts

The microwave synthesis of several quaternary ammonium salts is described. The synthesis provides comparable or better yields than published methods with reduced reaction times and in the absence of solvent.

A Spiroisoxazolinoproline-Based Amino Acid Scaffold for Solid Phase and One-Bead−One-Compound Library Synthesis

An efficient, multigram synthesis of a spiroisoxazolinoproline-based amino acid, 7, requiring minimal purification, delivering good cis:trans diastereoselectivity (approximately 1:4), and providing good yields is reported. Surface-bound studies of the reduction of an arylnitro group in the presence of an isoxazoline ring with tin(II) dichloride dihydrate were undertaken to confirm the stability of the isoxazoline ring. Full derivitization of this spiroisoxazolinoproline-based amino acid scaffold was performed during the synthesis of a sample library with high yields and high purity that validated the efficiency of the chemistry that was employed in resin-bound library synthesis. A 129,600 member one-bead-one-compound (OBOC) library based on the scaffold 7 was synthesized utilizing a dual amino acid encoding method and bifunctionalization of TentaGel resin.