Phototoxicity of Peptidoconjugates Modulated by a Single Amino Acid

Stacked Thiazole Orange Dyes in DNA Capable of Switching Emissive Behavior in Response to Structural Transitions

Functional nucleic acids with the capability of generating fluorescence in response to hybridization events, microenvironment or structural changes are valuable as structural probes and chemical sensors. We now demonstrate the enzyme-assisted preparation of nucleic acids possessing multiple thiazole orange (TO) dyes and their fluorescent behavior, that show a spectral change from the typical monomer emission to the excimer-type red-shifted emission. We found that the fluorescent response and emission wavelength of the TO dyes were dependent on both the state of the DNA structure (single- or double-stranded DNA) and the arrangement of the TO dyes. We showed that the fluorescent behavior of the TO dyes can be applied for the detection of RNA molecules, suggesting that our approach for preparing the fluorescent nucleic acids functionalized with multiple TO dyes could be useful to design a fluorescence bioimaging and detection technique of biomolecules.

pH-Sensitive micelles with mitochondria-targeted and aggregation-induced emission characterization: synthesis, cytotoxicity and biological applications

Subcellular organelle-specific reagents for simultaneous tumor targeting, imaging, and treatment are of enormous interest in cancer therapy. Herein, we present a mitochondria targeting micelle (PEG-AIE-TPP) by conjugating a triphenylphosphonium (TPP) with a fluorogen which can undergo aggregation-induced emission (AIE). At first, the in vitro and in vivo properties of the PEG-AIE-TPP micelle were characterized in detail. It was found that the micelle was reasonably stable at physiological pH and highly sensitive to mildly acidic pH stimuli. Importantly, this micelle could selectively localize and accumulate in the mitochondria, thus generating an aggregation-induced emission (AIE) effect as confirmed by the green fluorescence. Additionally, the micelle exhibited selective cytotoxicity to cancer cells and negligible toxicity to normal cells in vitro. The in vivo imaging and ex vivo imaging results showed that the accumulation tendency of the micelle at the tumor region was obvious. We also further proved the biocompatible, tumor targeting ability and antitumor activity of the PEG-AIE-TPP micelle in MCF-7 tumor-bearing mice. Accordingly, this mitochondria-targeted therapeutic micelle with good stability, biocompatibility, and tumor-targeting and antitumor activity provides a potentially unique tumor-targeted system for cancer therapy.

Light-Controlled Cellular Internalization and Cytotoxicity of Nucleic Acid-Binding Agents: Studies in Vitro and in Zebrafish Embryos

We synthesized octa-arginine conjugates of DNA-binding agents (bisbenzamidine, acridine and Thiazole Orange) and demonstrated that their DNA binding and cell internalization can be inhibited by appending a (negatively charged) oligoglutamic tail through a photolabile linker. UV irradiation released the parent conjugates, thus restoring cell internalization and biological activity. Assays with zebrafish embryos demonstrates the potential of this prodrug strategy for controlling in vivo cytotoxicity.

Rationally designed molecular beacons for bioanalytical and biomedical applications

Nucleic acids hold promise as biomolecules for future applications in biomedicine and biotechnology. Their well-defined structures and compositions afford unique chemical properties and biological functions. Moreover, the specificity of hydrogen-bonded Watson-Crick interactions allows the construction of nucleic acid sequences with multiple functions. In particular, the development of nucleic acid probes as essential molecular engineering tools will make a significant contribution to advancements in biosensing, bioimaging and therapy. The molecular beacon (MB), first conceptualized by Tyagi and Kramer in 1996, is an excellent example of a double-stranded nucleic acid (dsDNA) probe. Although inactive in the absence of a target, dsDNA probes can report the presence of a specific target through hybridization or a specific recognition-triggered change in conformation. MB probes are typically fluorescently labeled oligonucleotides that range from 25 to 35 nucleotides (nt) in length, and their structure can be divided into three components: stem, loop and reporter. The intrinsic merit of MBs depends on predictable design, reproducibility of synthesis, simplicity of modification, and built-in signal transduction. Using resonance energy transfer (RET) for signal transduction, MBs are further endowed with increased sensitivity, rapid response and universality, making them ideal for chemical sensing, environmental monitoring and biological imaging, in contrast to other nucleic acid probes. Furthermore, integrating MBs with targeting ligands or molecular drugs can substantially support their in vivo applications in theranositics. In this review, we survey advances in bioanalytical and biomedical applications of rationally designed MBs, as they have evolved through the collaborative efforts of many researchers. We first discuss improvements to the three components of MBs: stem, loop and reporter. The current applications of MBs in biosensing, bioimaging and therapy will then be described. In particular, we emphasize recent progress in constructing MB-based biosensors in homogeneous solution or on solid surfaces. We expect that such rationally designed and functionalized MBs will open up new and exciting avenues for biological and medical research and applications.

Mitochondria-targeted cancer therapy using a light-up probe with aggregation-induced-emission characteristics

Subcellular organelle-specific reagents for simultaneous tumor targeting, imaging, and treatment are of enormous interest in cancer therapy. Herein, we present a mitochondria-targeting probe (AIE-mito-TPP) by conjugating a triphenylphosphine (TPP) with a fluorogen which can undergo aggregation-induced emission (AIE). Owing to the more negative mitochondrial membrane potential of cancer cells than normal cells, the AIE-mito-TPP probe can selectively accumulate in cancer-cell mitochondria and light up its fluorescence. More importantly, the probe exhibits selective cytotoxicity for studied cancer cells over normal cells. The high potency of AIE-mito-TPP correlates with its strong ability to aggregate in mitochondria, which can efficiently decrease the mitochondria membrane potential and increase the level of intracellular reactive oxygen species (ROS) in cancer cells. The mitochondrial light-up probe provides a unique strategy for potential image-guided therapy of cancer cells.

Metal complex catalysis in living biological systems

This feature article discusses synthetic metal complexes that are capable of catalyzing chemical transformations in living organisms. Photodynamic therapy exemplifies what is probably the most established artificial catalytic process exploited in medicine, namely the photosensitized catalytic generation of cell-damaging singlet oxygen. Different redox catalysts have been designed over the last two decades to target a variety of redox alterations in cancer and other diseases. For example, pentaazamacrocyclic manganese(ii) complexes catalyze the dismutation of superoxide to O(2) and H(2)O(2)in vivo and thus reduce oxidative stress in analogy to the native enzyme superoxide dismutase. Recently, piano-stool ruthenium and iridium complexes were reported to influence cellular redox homeostasis indirectly by catalytic glutathione oxidation and catalytic transfer hydrogenation using the coenzyme NADH, respectively. Over the last few years, significant progress has been made towards the application of non-biological reactions in living systems, ranging from the organoruthenium-catalyzed cleavage of allylcarbamates and a gold-catalyzed intramolecular hydroarylation to palladium-catalyzed Suzuki-Miyaura and Sonogashira cross-couplings within the cytoplasm or on the surface of living cells. The design of bioorthogonal catalyst/substrate pairs, which can passively diffuse into cells, combines the advantages of small molecules with catalysis and promises to provide exciting new tools for future chemical biology studies.

Improved efficacy of fosmidomycin against Plasmodium and Mycobacterium species by combination with the cell-penetrating peptide octaarginine

Cellular drug delivery can improve efficacy and render intracellular pathogens susceptible to compounds that cannot permeate cells. The transport of physiologically active compounds across membranes into target cells can be facilitated by cell-penetrating peptides (CPPs), such as oligoarginines. Here, we investigated whether intracellular delivery of the drug fosmidomycin can be improved by combination with the CPP octaarginine. Fosmidomycin is an antibiotic that inhibits the second reaction in the nonmevalonate pathway of isoprenoid biosynthesis, an essential pathway for many obligate intracellular pathogens, including mycobacteria and apicomplexan parasites. We observed a strict correlation between octaarginine host cell permeability and its ability to improve the efficacy of fosmidomycin. Plasmodium berghei liver-stage parasites were only partially susceptible to an octaarginine-fosmidomycin complex. Similarly, Toxoplasma gondii was only susceptible during the brief extracellular stages. In marked contrast, a salt complex of octaarginine and fosmidomycin greatly enhanced efficacy against blood-stage Plasmodium falciparum. This complex and a covalently linked conjugate of octaarginine and fosmidomycin also reverted resistance of Mycobacteria to fosmidomycin. These findings provide chemical genetic evidence for vital roles of the nonmevalonate pathway of isoprenoid biosynthesis in a number of medically relevant pathogens. Our results warrant further investigation of octaarginine as a delivery vehicle and alternative fosmidomycin formulations for malaria and tuberculosis drug development.

Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base

A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).

Thiazole orange and Cy3: improvement of fluorescent DNA probes with use of short range electron transfer

Thiazole orange was synthetically incorporated into oligonucleotides by using the corresponding phosphoramidite as the building block for automated DNA synthesis. Due to the covalent fixation of the TO dye as a DNA base surrogate, the TO-modified oligonucleotides do not exhibit a significant increase of fluorescence upon hybridization with the counterstrand. However, if 5-nitroindole (NI) is present as a second artificial DNA base (two base pairs away from the TO dye) a fluorescence increase upon DNA hybridization can be observed. That suggests that a short-range photoinduced electron transfer causes the fluorescence quenching in the single strand. The latter result represents a concept that can be transferred to the commercially available Cy3 label. It enables the Cy3 fluorophore to display the DNA hybridization by a fluorescence increase that is normally not observed with this dye.

Site-specific oxidative stress induction

In this issue of Chemistry & Biology, Kelly and colleagues describe the development of two novel ROS-generating compounds [1] that specifically localize in the nucleus or mitochondrion. Their application reveals that nuclei and mitochondria respond differently to oxidative stress, in terms of gene expression and survival pathway activation.

Approach for assessing total cellular DNA damage

The capability to relate phenotypic effects to damage associated with either the mitochondrial or nuclear genome is especially useful under a number of circumstances. Potential hazardous exposures can be evaluated for genotoxicity and related to diseases, particularly cancer. The correlation of DNA damage with adverse health effects is also important in evaluating the safety of various chemical agents and prospective therapeutics. Many techniques exist that afford the ability to identify and measure cellular DNA damage upon exposure to a suspected genotoxic agent; however, quite often these techniques are limited either by the advanced instrumentation and skill needed to perform the analyses or the amount of time needed and limited information obtained regarding the types of DNA damage generated. Recent advances in cellular-based methods have resulted in the timely and straightforward collection of reliable and specific data regarding levels of damage and the identity of the damage products. Antibodies developed for DNA damage lesions allow for the direct measurement of those lesions within a population of exposed cells, while the automation of the single-cell gel electrophoresis (comet) assay and the use of scoring software have led to rapid and standardized data collection. This essay describes the usefulness of these approaches, while providing a brief experimental overview of the techniques.

Ion Pair Recognition of Quaternary Ammonium and Iminium Salts by Uranyl−Salophen Compounds in Solution and in the Solid State

Efficient ditopic receptors for quaternary ammonium and iminium salts have been obtained upon functionalization of the uranyl-salophen unit with conformationally flexible side arms bearing phenyl or beta-naphthyl substituents. Binding affinities in chloroform solution have been measured for a large number of quaternary salts comprising tetramethylammonium (TMA), tetrabutylammonium (TBA), acetylcholine (ACh), N-methylpyridinium (NMP), and N-methylisoquinolinium (NmiQ) cations. Recognition of the anion partner is ensured by coordination to the hard Lewis acidic uranyl center, whereas cation-pi/CH-pi interactions of the quaternary ions are established with the aromatic pendants. The role of the cation-anion interactions on the dynamics of exchange between the free and complexed species is discussed. Solid-state structures have been obtained for a few salt-receptor combinations. In the solid state, side-armed receptor molecules form assemblies that enclose ion pair aggregates of varying composition and structure, including AChCl dimers, two different kinds of tetrameric (TMA)Cl clusters, and unidimentional salt strips of (NMP)Br. The lack of side arms as preferential binding sites for the polar quaternary cations prevents association patterns of the kinds formed with the side-armed receptors, as shown by the crystal structure of the complex of (TMA)Cl with the parent uranyl-salophen receptor.

Calix[4]pyrrole as a chloride anion receptor: solvent and countercation effects

The interaction of calixpyrrole with several chloride salts has been studied in the solid state by X-ray crystallography as well as in solution by isothermal titration calorimetry (ITC) and (1)H NMR spectroscopic titrations. The titration results in dimethylsulfoxide, acetonitrile, nitromethane, 1,2-dichloroethane, and dichloromethane, carried out using various chloride salts, specifically tetraethylammonium (TEA), tetrapropylammonium (TPA), tetrabutylammonium (TBA), tetraethylphosphonium (TEP), tetrabutylphosphonium (TBP), and tetraphenylphosphonium (TPhP), showed no dependence on method of measurement. The resulting affinity constants (K(a)), on the other hand, were found to be highly dependent on the choice of solvent with K(a)'s ranging from 10(2)-10(5) M(-1) being recorded in the test solvents used for this study. In dichloromethane, a strong dependence on the countercation was also seen, with the K(a)'s for the interaction with chloride ranging from 10(2)-10(4) M(-1). In the case of TPA, TBA, and TBP, the ITC data could not be fit to a 1:1 binding profile.

Synthesis, Structure, Anion Binding, and Sensing by Calix[4]pyrrole Isomers

The synthesis, structure, and anion binding properties of chromogenic octamethylcalix[4]pyrroles (OMCPs) and their N-confused octamethylcalix[4]pyrrole isomers (NC-OMCPs) containing an inverted pyrrole ring connected via alpha'- and beta-positions are described. X-ray diffraction analyses proved the structures of two synthesized isomeric pairs of OMCPs and NC-OMCPs. The addition of anions to solutions of chromogenic OMCPs and NC-OMCPs resulted in different colors suggesting different anion-binding behaviors. The chromogenic NC-OMCPs showed significantly stronger anion-induced color changes compared to the corresponding chromogenic OMCP, and the absorption spectroscopy titrations indicated that chromogenic OMCPs and NC-OMCPs also possess different anion binding selectivity. Detailed NMR studies revealed that this rather unusual feature stems from a different anion-binding mode in OMCPs and NC-OMCPs, one where the beta-pyrrole C-H of the inverted pyrrole moiety participates in the hydrogen-bonded anion-NC-OMCP complex. Preliminary colorimetric microassays using synthesized chromogenic calixpyrroles embedded in partially hydrophilic polyurethane matrices allow for observation of analyte-specific changes in color when the anions are administered in the form of their aqueous solutions and in the presence of weakly competing anions.

Columnar Self-Assembled Ureido Crown Ethers: An Example of Ion-Channel Organization in Lipid Bilayers

The self-assembly of ureido crown-ether derivatives has been examined in homogeneous solution, in the solid state, and in planar bilayer membranes. The self-assembly is driven by head-to-tail hydrogen bonding between the urea functional groups. Dimers and higher oligomers are formed in CDCl3 solution as assessed by the change in the ureido NH chemical shift as a function of concentration. Single-crystal X-ray diffraction shows that an antiparallel association of the ureas produces columnar channels composed of face-to-face crown ethers. Powder X-ray diffraction studies also show the presence of a minor phase based upon a parallel urea association leading to an alternative columnar arrangement of the crown ethers. In bilayer membranes at low concentration of ureido crown ether added, membrane disruption is observed together with rare single-channel openings, but at higher concentration, a rich array of interconverting channel conductance states is observed. The channel results are interpreted as arising from discreet stacks of ureido crown ethers where the transport of cations would occur via the macrocycles, admixed with larger pores formed by association of the crown ether headgroups around a central large pore.

Tunable DNA Cleavage by Intercalating Peptidoconjugates

The properties of a novel family of peptide-based DNA-cleavage agents are described. Examination of the DNA-cleavage activities of a systematic series of peptide-intercalator conjugates revealed trends that show a strong dependence on peptide sequence. Conjugates differing by a single residue displayed reactivities that varied over a wide range. The cleavage activity was modulated by the electrostatic or steric qualities of individual amino acids. Isomeric conjugates that differed in the position of the tether also exhibited different reactivities. The mechanism of DNA cleavage for these compounds was also probed and was determined to involve hydrogen-atom abstraction from the DNA backbone. Previous studies of these compounds indicated that amino acid peroxides were the active agents in the cleavage reaction; in this report, the chemistry underlying the reaction is characterized. The results reported provide insight into how peptide sequences can be manipulated to produce biomimetic compounds.

Optical detection of singlet oxygen from single cells

The lowest excited electronic state of molecular oxygen, singlet molecular oxygen, O(2)(a (1)Delta(g)), is a reactive species involved in many chemical and biological processes. To better understand the roles played by singlet oxygen in biological systems, particularly at the sub-cellular level, optical tools have been developed to create and directly detect this transient state in time- and spatially-resolved experiments from single cells. Data obtained indicate that, contrary to common perception, this reactive species can be quite long-lived in a cell and, as such, can diffuse over appreciable distances including across the cell membrane into the extracellular environment. On one hand, these results demonstrate that the behavior of singlet oxygen in an intact cell can be significantly different from that inferred from model bulk studies. More generally, these results provide a new perspective for mechanistic studies of intra- and inter-cellular signaling and events that ultimately lead to photo-induced cell death.