Hybridizing Oligonucleotides with Hydrophobic Peptide Nucleic Acids Assists Their Cellular Uptake through Aggregate Formation.

We applied hybridization between hydrophobic peptide nucleic acids (PNAs) and oligodeoxynucleotides (ODNs) to achieve their cellular uptake without any need for transfection reagents. We employed a pyrenyl unit as a hydrophobic functional group and introduced it at the terminus of the PNA strand. The pyrene-tethered PNA (PyPNA) strongly bound with its complementary ODNs to generate amphiphiles; the resulting hybrids formed aggregates that showed efficient cellular uptake and high biological stability. Aggregates containing a functional DNA aptamer that bound to the PyPNA penetrated the cell membrane smoothly, with the aptamer exerting its original function in living cells. Thus, PyPNA efficiently assisted the additive-free cellular uptake of ODNs.

Modulation of cell membrane functionalization with aggregates of oligodeoxynucleotides containing alkyl chain-modified uridines.

In this study, we prepared oligodeoxynucleotides (ODNs) containing the uridine base modified by an alkyl chain at the 5-position (AU) and characterized their aggregate formation, localization, and functions in cells. These experiments revealed that aggregates of these ODNs were readily transported into cells, but their localization was dependent upon the number of hydrophobic units. ODNs with one modified AU were transported in the cytosol, while ODNs with multiple AU modifications resulted in their accumulation at the cell membrane. We also examined the ability of the AU-modified ODNs to capture small molecules at the cell membrane and their cellular uptake. We positioned a thioflavin-T (ThT)-binding aptamer on the cell membrane by means of hybridization with ODNs with three AUs at the strand end. Treatment with ThT resulted in its efficient uptake into cells, due to the capture of the ThT by the aptamers on the cell membrane. Thus, we demonstrated the functionalization of cell membranes with modified ODNs and the efficient delivery of small molecules into the cells.

Enzymatic activation of indolequinone-substituted 5-fluorodeoxyuridine prodrugs in hypoxic cells.

Among the various enzymes, reductases that catalyze one-electron reduction are involved in the selective activation of functional compounds or materials in hypoxia, which is one of the well-known pathophysiological characteristics of solid tumors. Enzymatic one-electron reduction has been recognized as a useful reaction that can be applied in the design of tumor hypoxia-targeting drugs. In this report, we characterized the enzymatic reaction of 5-fluorodeoxyuridine (FdUrd) prodrug bearing an indolequinone unit (IQ-FdUrd), which is a substrate of reductases. IQ-FdUrd was activated to release FdUrd under hypoxic conditions after treatment with cytochrome NADPH P450 reductase. We also confirmed that IQ-FdUrd showed selective cytotoxicity in hypoxic tumor cells.

Tracking the Oxygen Status in the Cell Nucleus with a Hoechst-Tagged Phosphorescent Ruthenium Complex.

Molecular oxygen in living cells is distributed and consumed inhomogeneously, depending on the activity of each organelle. Therefore, tractable methods that can be used to monitor the oxygen status in each organelle are needed to understand cellular function. Here we report the design of a new oxygen-sensing probe for use in the cell nucleus. We prepared "Ru-Hoechsts", each consisting of a phosphorescent ruthenium complex linked to a Hoechst 33258 moiety, and characterized their properties as oxygen sensors. The Hoechst unit shows strong DNA-binding properties in the nucleus, and the ruthenium complex shows oxygen-dependent phosphorescence. Thus, Ru-Hoechsts accumulated in the cell nucleus and showed oxygen-dependent signals that could be monitored. Of the Ru-Hoechsts prepared in this study, Ru-Hoechst b, in which the ruthenium complex and the Hoechst unit were linked through a hexyl chain, showed the most suitable properties for monitoring the oxygen status. Ru-Hoechsts are probes with high potential for visualizing oxygen fluctuations in the nucleus.

Phosphorescent ruthenium complexes with bromopyrene unit that enhance oxygen sensitivity.

Ruthenium complexes are very useful phosphorescent probes for the visualization of hypoxia. We designed and synthesized three ruthenium complexes possessing bromopyrene, naphthalene, or anthracene units to improve the oxygen response. These ruthenium complexes provided strong phosphorescence under hypoxic conditions, while an increase in oxygen concentration led to a decrease in phosphorescence intensity. Among the ruthenium complexes, that with a bromopyrene unit (Ru-BrPy) had the best properties. This showed good cellular uptake and bright emission in cells, and had the highest sensitivity for molecular oxygen. Thus, Ru-BrPy is a promising candidate as a molecular probe for detecting cellular hypoxia.

Aggregate Formation of Oligonucleotides that Assist Molecular Imaging for Tracking of the Oxygen Status in Tumor Tissue.

The use of DNA aggregates could be a promising strategy for the molecular imaging of biological functions. Herein, phosphorescent oligodeoxynucleotides were designed with the aim of visualizing oxygen fluctuation in tumor cells. DNA-ruthenium conjugates (DRCs) that consisted of oligodeoxynucleotides, a phosphorescent ruthenium complex, a pyrene unit for high oxygen responsiveness, and a nitroimidazole unit as a tumor-targeting unit were prepared. In general, oligonucleotides have low cell permeability because of their own negative charges; however, the DRC formed aggregates in aqueous solution due to the hydrophobic pyrene and nitroimidazole groups, and smoothly penetrated the cellular membrane to accumulate in tumor cells in a hypoxia-selective manner. The oxygen-dependent phosphorescence of DRC in cells was also observed. In vivo experiments revealed that aggregates of DRC accumulated in hypoxic tumor tissue that was transplanted into the left leg of mice, and showed that oxygen fluctuations in tumor tissue could be monitored by tracking of the phosphorescence emission of DRC.

Confined Singlet Oxygen in Mesoporous Silica Nanoparticles: Selective Photochemical Oxidation of Small Molecules in Living Cells.

Chemical conversion of specific bioactive molecules by external stimuli in living cells is a powerful noninvasive tool for clarification of biomolecular interactions and to control cellular functions. However, in chaotic biological environments, it has been difficult to induce arbitrary photochemical reactions on specific molecules because of their poor molecular selectivity. Here we report a selective and nontoxic photochemical reaction system utilizing photoactivated mesoporous silica nanoparticles to control biological functions. Methylene blue modification within nanoparticle pores for photosensitization produced singlet oxygen confined to the pore that could mediate selective oxidation of small molecules without any damage to living cells. This intracellular photochemical system produced bioactive molecules in situ and remotely controlled the cell cycle phase. We also confirmed that this photoreaction could be applied to control cell cycle phase in tumor tissue transplanted in mice. The cell cycle phase in the cells in mice, to which our system was administered, was arrested at the G2/M phase upon photoirradiation. We demonstrate a simple and promising method for the exogenous conversion of an intracellular biomolecule to another functional compound.

Preparation of alkyne-labeled 2-nitroimidazoles for identification of tumor hypoxia by Raman spectroscopy.

Hypoxia is a characteristic feature of solid tumors. Herein, we have developed novel hypoxia-sensitive probes (IM-ACs) for Raman spectroscopic analysis, consisting of nitroimidazole as a hypoxia-targeting unit and acetylene group as the signal-emitting unit. Among IM-ACs synthesized in this study, IM-AC possessing a diacetylene group (IM-AC 3), showed suitable properties as a hypoxia indicator. When administered to A549 cells, we observed a strong signal of IM-AC 3 around 2200cm-1 in the Raman spectra from hypoxic cells. Ex vivo experiments suggest that IM-AC 3 remained in hypoxic tumor tissue and emitted a strong signal.

Cationic porphyrin-quinoxaline conjugate as a photochemically triggered novel cytotoxic agent.

A novel cationic porphyrin-quinoxaline conjugate 8 was prepared in good yield by the coupling of activated quinoxaline carboxylic acid 5 with an appropriate aminoporphyrin. The UV-vis spectra of conjugate 8 with the addition of ctDNA shows substantial hypochromicity (39%) and a red shift (12 nm) in the Soret band indicating intercalation and self stacking along the surface. The binding constant of conjugate 8 with ctDNA was determined to be 1.26×10(6) M(-1). The porphyrin-quinoxaline conjugate 8 displayed enhanced photocytotoxicity (IC50=0.06 µM) when compared to TMPyP against A549 cancer cells.

Novel porphyrin-psoralen conjugates: synthesis, DNA interaction and cytotoxicity studies.

A Cu(i)-catalyzed azide-alkyne cycloaddition reaction (CuAAC) has been utilized to prepare novel triazole-linked cationic porphyrin-psoralen conjugates that exhibited significant photocytotoxicity against A549 cancer cells (IC50 = 84 nM).

Preparation of Glycan Arrays Using Glycopeptides Derived From Biomaterials.

In general, viruses recognize host cell surface glycans, but the measurement of virus-host cell glycan interaction is not widely operated. This is not only because commercially available, structure-defined glycans are limited, but also because such interactions, if any, between viruses and isolated glycans are relatively weak, and thus, difficult to detect by conventional methods, e.g., enzyme-linked immune-sorbent assay. We describe a practical method to detect virus binding to glycans; for this, preparation of glycan arrays using glycopeptides derived from biomaterials is necessary. In this context, neoglycoprotein is produced using bovine serum albumin (BSA) and commercially available glycopeptides, with which influenza viruses are detected using an evanescent-field-activated fluorescence scanner. It is clearly shown that H1N1 strains of influenza virus recognize BSA, to which DiNeuα2-6bianntena-peptide (SGP) is covalently linked, while on the other hand H5N1 strains recognize BSA linked to DiNeuα2-3bianntena-peptide (α2,3SGP).

Changes of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides.

Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (PC) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in PC in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.

NFkappaB decoy delivery using dendritic poly(l-lysine) for treatment of endotoxin-induced hepatitis in mice.

Mono-dispersed, 6th generation dendritic poly(l-lysine) (KG6) forms a stable complex with plasmid DNA and this complex can circulate in vivo for extended times before the DNA finally accumulates in the liver. In this study, we attempted to use KG6 as a carrier of NFkappaB decoy oligonucleotide to the liver to treat hepatitis, induced by lipopolysaccharide and d-galactosamine. KG6 formed a complex with the NFkappaB decoy. Serum aspartate aminotransferase and alanine aminotransferase were dramatically suppressed in the hepatitis mouse model after intravenous injection of KG6/NFkappaB decoy complexes. Expression levels of several cytokines and proteins related to the inflammatory reaction were also suppressed by intravenous administration of KG6/NFkappaB decoy complexes. Because [(32)P] NFkappaB decoy was found in non-parenchymal cells after intravenous injection, KG6 has been shown to be a promising carrier molecule of various oligonucleotides to non-parenchymal liver cells, including Kupffer cells.

Aggregate Formation of BODIPY-Tethered Oligonucleotides That Led to Efficient Intracellular Penetration and Gene Regulation.

Exogenous nucleic acids showed low efficiency regarding cellular uptake and low stability in biological conditions; therefore, a number of techniques have been developed to improve their basic properties. One of the best solutions is the application of nanosized particles consisting of oligonucleotides that penetrate the cell membrane without any additives and exhibit high stability in cells. In this report, we employed a simple approach to address the basic properties of nanoparticles of oligonucleotides in biological systems. We prepared BODIPY-labeled oligonucleotides that carried an exclusive modification at the strand end. BODIPY shows high hydrophobicity and fluorescent emission; therefore, the oligonucleotides formed nanosized aggregates in aqueous solution and their behaviors in cells or tissues were easily tracked. Detailed experiments revealed that aggregate formation was indispensable for the high cellular uptake of the oligonucleotides via scavenger-receptor-mediated endocytosis. In addition, the aggregates provided an efficient gene regulation in living cells and tumor tissues transplanted into mice.

A novel interleukin-13 receptor alpha 2-targeted hybrid peptide for effective glioblastoma therapy.

We previously designed and reported a novel class of drugs, namely hybrid peptides, which are chemically synthesized and composed of a targeted binding peptide and a lytic-type peptide containing cationic amino acid residues that cause cancer cell death. In the present study, we screened for peptides that bind to interleukin-13 receptor alpha 2 (IL-13Rα2) by using a T7 random peptide phage display library system and isolated several positive phage clones. The A2b11 peptide, which was one of the positive clones, was shown to bind to IL-13Rα2 protein by Biacore analysis and a binding assay using glioblastoma (GB) cell lines. This peptide was linked with a lytic peptide containing a linker sequence to form the IL-13Rα2-lytic hybrid peptide. The IL-13Rα2-lytic hybrid peptide showed cytotoxic activity against GB cell lines in vitro. The IL-13Rα2-lytic hybrid peptide also affected Akt and Erk1/2 activation following treatment with interleukin-13 and induced rapid ATP dynamics in GB cells. Anti-tumor activity of the IL-13Rα2-lytic hybrid peptide was observed in vivo after intratumoral injection in a mouse xenograft model of human GB cells. These results suggest that the IL-13Rα2-lytic hybrid peptide might be a potent therapeutic option for patients with GB.

Controlling Localization and Excretion of Nanoparticles by Click Modification of the Surface Chemical Structures inside Living Cells.

Invited for this month's cover is the group of Drs. Takeo Ito and Kazuhito Tanabe from Kyoto University, Japan. The cover image shows accumulation of silica nanoparticles on the plasma membrane by click modification of the surface in living cells. Read the full text of the article at 10.1002/cplu.201402436.

Controlling Localization and Excretion of Nanoparticles by Click Modification of the Surface Chemical Structures inside Living Cells.

Surface modification of silica nanoparticles (SiNPs) inside living cells was conducted by using the copper-free bioorthogonal click reaction to evaluate the effects of surface chemical structures on dynamic behavior and excretion of SiNPs. The results demonstrated the spatial translocation of intracellular SiNPs to the plasma membrane upon surface modification in situ with phospholipids. Moreover, the extent and kinetics of excretion of the SiNPs from inside the cell were enhanced by modification.

Electron transport through 5-substituted pyrimidines in DNA: electron affinities of uracil and cytosine derivatives differently affect the apparent efficiencies.

We investigated excess electron transport (EET) in DNA containing cytosine derivatives. By arranging the derivatives according to their electron affinities, the apparent EET efficiency was successfully regulated. Unexpectedly, however, providing gradients of electron affinity by inserting 5-fluorocytosine did not always enhance EET.

Biodistribution and Tumor Localization of PEG-Modified Dendritic Poly(L-Lysine) Oligonucleotide Complexes.

A poly(ethylene glycol) (PEG)-modified dendritic poly(L-lysine) (PEG-WeKG6) containing tryptophan residues in its core was synthesized as an oligonucleotide carrier to tumors after systemic injection. PEG- WeKG6 formed a stable complex with double-stranded deoxyoligonucleotide (ODN). The size and the zeta-potential of the complex were smaller than those of a dendritic poly(L-lysine) without PEG (WeKG6). To study the biodistribution of the complexes in tumor-bearing mice after intravenous injection, the den- drimers and the oligonucleotide were labeled with gadolinium and Cy5, respectively. Our results show that PEG modification of the dendrimer improved the stability of ODN in blood circulation. Effective accumulation of the PEG-WeKG6/ODN complex in the tumor tissue was found 24 h after the injection. These results indicate that PEG-WeKG6 is suitable for forming a complex with any genetic or therapeutic material for efficient delivery to tumors.