Effect of phenyl numbers in polyphenyl ligand on retention properties of aromatic stationary phases

Aromatic phase, as one type of reversed-phase stationary phases, shows complementary selectivity to the n-alkyl counterparts especially for certain challenging separation tasks. However, effect of phenyl numbers in aromatic ligands on retention behaviors has rarely been addressed compared with the alkyl stationary phases. To illustrate the issue, a series of polyphenyl stationary phases were facially prepared via the coupling chemistry of isocyanate with amine, including aniline (π¹), 4-aminobiphenyl (π²), 4-amino-p-terphenyl (π³) and [1,1':4',1'':4'',1'''-quaterphenyl]-4-amine (π⁴), respectively. The chromatographic behaviors of the new stationary phases as well as the traditional C18 were systematically compared in terms of retention mode, hydrophobic and aromatic selectivity, shape selectivity and π-π interaction by various analytes, including alkylbenzenes, polycyclic aromatic hydrocarbons congeners and substituted benzenes with electron-withdrawing groups. Due to the homologous structure of four polyphenyl ligands, the hydrophobic selectivity, aromatic selectivity and shape selectivity of stationary phases increase with phenyl numbers in the bonded polyphenyl ligands, whereas the increment becomes insignificant from U-π³ to U-π⁴. This phenomenon is explained by the insertion degree of analytes in the polyphenyl ligand brushes. Compared with the homemade C18, the polyphenyl phases indicate insignificant changes of shape selectivity with temperature. Notably, the new polyphenyl phases demonstrate the great selective separation towards the electron-deficient compounds through the π-π interaction. These findings make up for the understanding of the retention behavior of aromatic stationary phases.

Design and synthesis of a stable supramolecular trigonal prism formed by the self-assembly of a linear tetrakis(Zn2+-cyclen) complex and trianionic trithiocyanuric acid in aqueous solution and its complexation with DNA (cyclen = 1,4,7,10-tetraazacyclododecane)

A new supramolecular complex, {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+), was designed and synthesized by the 3:4 self-assembly of a linear tetrakis(Zn(2+)-cyclen) complex (Zn(4)L(4))(8+) and trianionic trithiocyanurate (TCA(3-)) in aqueous solution (cyclen = 1,4,7,10-tetraazacyclododecane). The {(Zn(4)L(4))(3)-(TCA(3-))(4)}(12+) complex, which should have a trigonal prism configuration, was found to be very stable in aqueous solution at neutral pH and 25 degrees C, as evidenced by (1)H NMR titration, potentiometric pH and UV titrations, and MS measurements. The complex does not dissociate into the starting building blocks in the presence of Zn(2+)-binding anions such as phosphates and double-stranded DNA. The results of the competitive binding assays with ethidium bromide and calf-thymus DNA, thermal melting experiments, gel mobility shift assays, and dynamic light-scattering data strongly indicated that the trigonal prism functions as a polycationic template to induce the aggregation of double-stranded DNA.

Design, synthesis, and evaluation of phenanthridine derivatives targeting the telomerase RNA/DNA heteroduplex

We are targeting molecules to the RNA/DNA heteroduplex that forms during the enzyme telomerase's catalytic cycle. Telomerase is a potential universal anti-cancer target that we have previously shown can be inhibited by molecules that target this heteroduplex. The aim of this work was to make derivatives of our lead, ethidium, that would allow its straightforward incorporation into molecules in both solid and solution phase. The heteroduplex targeting intercalator will act as a scaffold to allow the incorporation of new functionalities that will interact with specific protein surfaces of telomerase, thereby potentially increasing affinity and specificity. In examining multiple new derivatives of ethidium, with literature precedent or novel, we have identified one, a 5-benzylic acid ethidium derivative that is synthesized in three steps as a single isomer, and completely retains the inhibition efficacy of the parent compound. Furthermore, we have demonstrated that it can be effectively incorporated into resin bound amines on the solid phase. As such it represents an ideal monomer for the exploration of telomerase inhibition or for other applications which would benefit from hybrid molecules that can target duplexes.

On the electronic structure of ethidium

The electronic structure of the common intercalating agent ethidium bromide (3,8-diamino-5-ethyl-6-phenylphenanthridinium bromide) is dominated by an interplay of electron donating and withdrawing effects mediated by its nitrogen atoms. X-ray crystallography, UV/Vis and IR absorption, fluorescence emission, and NMR spectroscopy are used to probe the electronic properties of the phenanthridinium "core" of ethidium as well as its exocyclic amines and 6-phenyl groups. Interestingly, despite its positive charge, most of ethidium's aromatic carbon and hydrogen atoms have high electron densities (compared to both 6-phenylphenanthridine and benzene). The data suggest that electron donation by ethidium's exocyclic amines dominates over the electron withdrawing effects of its endocyclic iminium in their combined influence on the electron densities of these atoms. Ethidium's nitrogen atoms are, conversely, electron deficient where the 5-position is the most electropositive, followed by the 3-amino, and lastly the 8-amino group. These results have been used to generate an empirically-based pi-electron density map of ethidium that may prove useful to understanding its nucleic acid binding specificity.

Influence of the amino substituents in the interaction of ethidium bromide with DNA

A key step in the rational design of new DNA binding agents is to obtain a complete thermodynamic characterization of small molecule-DNA interactions. Ethidium bromide has served as a classic DNA intercalator for more than four decades. This work focuses on delineating the influence(s) of the 3- and 8-amino substituents of ethidium on the energetic contributions and concomitant fluorescent properties upon DNA complex formation. Binding affinities decrease by an order of magnitude upon the removal of either the 3- or 8-amino substituent, with a further order-of-magnitude decrease in the absence of both amino groups. The thermodynamic binding mechanism changes from enthalpy-driven for the parent ethidium to entropy-driven when both amino groups are removed. Upon DNA binding, fluorescence enhancement is observed in the presence of either or both of the amino groups, likely because of more efficient fluorescence quenching through solvent interactions of free amino groups than when buried within the intercalation site. The des-amino ethidium analog exhibits fluorescence quenching upon binding, consistent with less efficient quenching of the chromophore through interactions with solvent than within the intercalation site. Determination of the quantum efficiencies suggests distinct differences in the environments of the 3- and 8-amino substituents within the DNA binding site.

Synthesis, photophysical properties, and nucleic acid binding of phenanthridinium derivatives based on ethidium

A series of substituted phenanthridine derivatives has been synthesized by converting the amines at the 3- and 8-positions of ethidium bromide into guanidine, pyrrole, urea, and various substituted ureas. The resulting derivatives exhibit unique spectral properties that change upon binding nucleic acids. The compounds were analyzed for their ability to inhibit the HIV-1 Rev-Rev Response Element (RRE) interaction, as well as for their affinity to calf thymus DNA. One derivative (3,8-bis-urea-ethylenediamine-5-ethyl-6-phenylphenanthridinium trifuroracetate) has an enhanced affinity and specificity for HIV-1 RRE as compared to ethidium bromide. These results indicate that the nucleic acid affinity and specificity of an intercalating agent can be tuned by synthetic modification of its exocyclic amines.

The effect of inducing agents on the metabolism of ethidium bromide by isolated rat hepatocytes

The metabolism of ethidium bromide by isolated rat hepatocytes is significantly enhanced by pre-treatment of animals with phenobarbitone (PB) and 3-methylcholanthrene (3-MC). Pre-treatment with PB and 3-MC results in a 2.5- and 1.5-fold increase, respectively in the amount of the principal metabolite, ethidium 8-N-glucuronide, compared with that formed by hepatocytes from untreated rats. The formation of ethidium 3-N-glucuronide is not enhanced by pre-treatment with either PB or 3-MC. Two new metabolites, hydroxyethidium glucuronide and a transient unidentified species, have been detected by HPLC and are formed only by hepatocytes from animals pre-treated with 3-MC.

Intracellular localization and metabolism of the phenanthridinium trypanocide, ethidium bromide, by isolated rat hepatocytes

1. Confocal laser scanning microscopy (CLSM) has shown that ethidium (3 ,8-diamino-5-ethyl-6-phenylphenanthridinium) bromide, an aromatic phenanthridinium trypanocide, is taken up rapidly into the nucleoli and nuclear membranes of isolated rat hepatocytes. 2. It is biotransformed by the hepatocytes and at least five metabolites have been detected by high-performance liquid chromatography (HPLC). 3. Two new metabolites, 3- and 8-N-glucuronosylethidium, have been identified by HPLC-electrospray mass spectrometry and they represent the major pathway of metabolism, accounting for 6.4 +/- 0.7 and 19.5 +/- 1.2% respectively of total recovered drug after incubation. A third metabolite, 3,8-diacetylethidium, is formed in trace quantities. 4. The other two metabolites, 3-acetylethidium and 8-acetylethidium, have been reported previously.

Chemical cross-linking of ethidium to DNA by glyoxal

Ethidium was found to be efficiently cross-linked to DNA by glyoxal. Kinetic studies showed that the rate of the cross-linking reaction is strongly dependent on the glyoxal concentration. Comparative studies using a series of phenanthridines and acridines showed that NH2 groups at both the 2 and 7 positions on the phenanthridine ring are necessary for efficient cross-linking. Studies using synthetic polydeoxynucleotides showed that the 2-amino group of guanine is absolutely required for cross-linking. Fluorescence contact energy transfer and relative viscosity experiments showed that the cross-linked drug remains intercalated into DNA. DNA gel electrophoresis and melting studies demonstrated that cross-linked ethidium does not dissociate the DNA double helix to single strands.

Use of drug-specific antibodies to identify ethidium adducts produced in Trypanosoma brucei by photoaffinity labeling

A photoreactive azido analog of the trypanocide ethidium bromide, 3-amino-8-azido-5-ethyl-6-phenylphenanthridinium chloride, attached covalently to calf thymus DNA (CT DNA) by photoaffinity labeling, was used to generate antibodies for the drug analog. The specificity of the antiserum was tested using enzyme-linked immunoadsorbant assays (ELISA) against immobilized antigen (photoaffinity labeled DNA) and by both the avidin-biotin peroxidase reaction and indirect immunofluorescence performed on smears of drug treated trypanosomes. The reaction of the antiserum with the covalently bound drug adduct was diminished effectively by prior incubation with an excess of ethidium monoazide, ethidium diazide, and ethidium bromide, and to a lesser extent by the DNA-ethidium complex, the diazide-DNA or RNA adduct, and the monoazide-RNA adduct. DNA which had been photoaffinity labeled with either the propidium or the acridine moiety did not react. The antiserum recognition of DNA photoaffinity labeled with ethidium monoazide was based on the substituted phenanthridinium ring system of the parent ethidium, as evidenced by competition binding studies involving the free monoazido analog (EA1), the diazido analog (EA2), and the parent compound, ethidium bromide (EB). This approach and the sensitivity it provides should prove useful for identifying the distribution and fate of covalently bound drugs resulting from antiparasitic drug treatment, and for studying their roles in antiparasitic action.

Use of a photolabeling technique to identify nonviable cells in fixed homologous or heterologous cell populations

Flow cytometric determination of viable versus nonviable cells in fixed samples can be accomplished by utilizing the irreversible binding of photoactivated ethidium monoazide (EMA). EMA is a positively charged molecule which is excluded by cells with intact membranes (viable cells), included by cells with damaged membranes, and can be photochemically crosslinked to nucleic acids using visible light. EMA fluorescence can be excited using a standard argon laser operating at 488 nm and is able to be distinguished from fluorescein and phycoerythrin. Fixation is important when analyzing cells from a potentially infectious origin. EMA is photochemically crosslinked and therefore unable to leak out of cells when removed from the extracellular media, unlike propidium iodide (PI) or other viability stains, which were heretofore commonly used. We demonstrate the usefulness of EMA in combination with fluoresceinated and phycoerythrin labeled monoclonal antibodies in immunophenotyping. The photoaffinity labeling technique allows for a quick and efficient means of identifying nonviable cells which cannot be distinguished on the basis of light-scattering properties.