Water-Soluble Rotaxane-Type Porphyrin Dyes as a Highly Membrane-Permeable and Durable Photosensitizer Suitable for Photodynamic Therapy.

Porphyrins have emerged as highly effective photosensitizers in the field of photodynamic therapy (PDT) because of their high singlet oxygen generation efficiency. However, most porphyrin derivatives do not have adequate water solubility and cell membrane permeability suitable for use in PDT. In addition, they frequently suffer from low durability under photoirradiation.

2-Aminopyridine as a Nucleobase Substitute for Adenine in DNA-like Architectures: Synthesis of Alkynyl -Nucleotides and Their Hybridization Characteristics.

Halogenated 2-aminopyridine was attached to the acetylene terminal of ethynyl -2-deoxy-β-d-ribofuranoside as a nucleobase substitute, and then, the -nucleoside was incorporated into natural DNAs. The resulting chimeric DNA constructed double helical structures with the complementary chimeric DNA. In the duplex, 2-aminopyridine functioned as an adenine analogue that formed a base pair with a non-natural thymine isostere.

Additive-Free Enzymatic Phosphorylation and Ligation of Artificial Oligonucleotides with C-Nucleosides at the Reaction Points.

We report enzymatic phosphorylation and additive-free ligation of DNAs containing unnatural C-nucleotide residues through the action of T4 polynucleotide kinase and T4 DNA ligase. The artificial units are each made up of an alkynyl deoxyribose component and one of the unnatural nucleobases D*, T*, G*, and C*, corresponding-from a viewpoint of hydrogen-bonding patterns-to natural A, T, G, and C, respectively. Phosphorylation progressed quantitatively at the 5'-end in the cases of all of the artificial units in the chimeric DNAs.

Photoinduced Electron Transfer-Regulated Protein Labeling With a Coumarin-Based Multifunctional Photocrosslinker.

We developed a novel diazirine-based photolabeling agent having a (coumarin-4-yl)methyl ester scaffold, which exhibited multiple photochemical properties of crosslinking, fluorogenicity and cleavage. These properties can be kinetically regulated via photoinduced electron transfer between diazirine and coumarin moieties. The C-O bond of (coumarin-4-yl)methyl ester can be cleaved via photochemical excitation of coumarin moiety, that function has been initially quenched by the diazirine moiety.

Syndecan-4 Is a Receptor for Clathrin-Mediated Endocytosis of Arginine-Rich Cell-Penetrating Peptides.

Arginine-rich cell-penetrating peptides (CPPs) such as Tat and oligoarginine peptides have been widely used as carriers for intracellular delivery of bioactive molecules. Despite accumulating evidence for involvement of endocytosis in the cellular uptake of arginine-rich CPPs, the primary cell-surface receptors for these peptide carriers that would initiate endocytic processes leading to intracellular delivery of bioactive cargoes have remained poorly understood. Our previous attempt to identify membrane receptors for octa-arginine (R8) peptide, one of the representative arginine-rich CPPs, using the photo-cross-linking probe bearing a photoreactive diazirine was not successful due to considerable amounts of cellular proteins nonspecifically bound to the affinity beads.

Synthesis of Nonnatural Oligonucleotides Made Exclusively of Alkynyl C-Nucleosides with Nonnatural Bases.

This unit describes detailed procedures for the preparation of nonnatural C-nucleosides comprising seven types of nonnatural nucleobases attached to 1'-position of 2'-deoxyribose through an acetylene bond with the β-configuration. In addition, derivatization of these alkynyl C-nucleosides into the corresponding phosphoramidites and the subsequent oligonucleotide synthesis are also presented. The processes are depicted in three parts.

A firmly hybridizable, DNA-like architecture with DAD/ADA- and ADD/DAA-type nonnatural base pairs as an extracellular genetic candidate.

We describe artificial DNA molecules exclusively consisting of four types of alkynyl C-nucleotides with nonnatural bases. The artificial DNA exhibited almost the same characteristics as natural DNA, such as in regard to the stepwise duplex and triplex formation and the right-handed higher-order structure with an antiparallel alignment fashion.

An isotope-coded fluorogenic cross-linker for high-performance target identification based on photoaffinity labeling.

A photoaffinity labeling (PAL)-based method for the rapid identification of target proteins is presented in which a high-performance chemical tag, an isotope-coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage.

Coupling reaction of thioamides with sulfonyl azides: an efficient catalyst-free click-type ligation under mild conditions.

We report a coupling reaction of thioamides and sulfonyl azides to generate sulfonyl amidines in the absence of any activation additives. The reaction progresses in various solvents under mild conditions. Water exhibits the highest performance with respect to efficiency.

A supramolecular DNA self-assembly based on β-cyclodextrin-adamantane complexation as a bioorthogonal sticky end motif.

We propose linear end-to-end assemblies of short DNA duplexes based on β-cyclodextrin-adamantane complexation. The assembled duplexes exhibited increased Tm values compared with those of the corresponding natural hybrids. Competition experiments with external guest molecules showed a substantial decrease in Tm of the terminal modified duplexes, suggesting the viability of inter-duplex complexation.

Identification of cellular proteins interacting with octaarginine (R8) cell-penetrating peptide by photo-crosslinking.

Octaarginine (R8) is a representative cell-penetrating peptide. Lanthionine synthetase component C-like protein 1 (LanCL1) was identified as a potential intracellular target of R8 by using a photo-crosslinking assay that utilized a phenyl-trifluoromethyl diazirine moiety and peptide mass fingerprinting. Increased cellular uptake of R8 by LanCL1-overexpressing cells was observed.

Electrochemical direct detection of DNA deamination catalyzed by APOBEC3G.

APOBEC3G catalyzes deamination of cytosines in HIV-1 genome, and restricts the HIV-1 infection. Here, we propose a picomole-scale assay for the detection of DNA deamination catalyzed by APOBEC3G. Our results show the suitability of the developed method for a time course analysis of enzyme-catalyzed DNA modifications.

Electrochemical detection of insertion/deletion mutations based on enhanced flexibility of bulge-containing duplexes on electrodes.

Ferrocene-modified DNA probes formed fully matched duplexes and bulge-containing ones with wild-type and insertion/deletion-type complements of clinical importance, respectively. Cyclic voltammetry measurements revealed that the bulge-containing duplexes showed an increased flexibility compared to the fully matched duplexes. The difference in the bending elasticity could be read out electrochemically by square wave voltammetry.

Specific induced circular dichroism and enhanced B to z transitions of duplexes stabilized by chromophore-linked alkynylnucleoside residues.

We have developed an induced circular dichroism (ICD) probe with a chromophore-linked alkynyldeoxyribose skeleton for analyzing higher-order structures of DNA duplexes in the visible-light region. When CG-repeated oligonucleotides (ODNs) with the probe at their 5' ends adopted Z-form duplexes at a high NaCl concentration, strong ICD signals were observed at the absorptive region of the chromophore. On the other hand, their B-form duplexes, formed at a low NaCl concentration, produced a faint ICD signal.

Detection of mismatched duplexes by synchronizing the pulse potential frequency with the dynamics of ferrocene/isoquinoline conjugate-connected DNA probes immobilized onto electrodes.

Cyclic voltammetry was performed at various scan rates for the duplexes from ferrocene/isoquinoline conjugate-connected DNA probes on gold electrodes. The relationship between the observed currents and the scan rates disclosed the enhanced bending elasticity of the mismatched duplexes compared with the fully matched duplexes. The difference of the dynamics was easily detected through the currents from the conjugate by adjusting the pulse potential frequency in square-wave voltammetry.

Artificial DNA made exclusively of nonnatural C-nucleosides with four types of nonnatural bases.

We describe a new class of DNA-like oligomers made exclusively of nonnatural, stable C-nucleosides. The nucleosides comprise four types of nonnatural bases attached to a deoxyribose through an acetylene bond with the beta-configuration. The artificial DNA forms right-handed duplexes and triplexes with the complementary artificial DNA.

Photooxygenation of alkynylperylenes. Formation of dibenzo[jk,mn]phenanthrene-4,5-diones.

3-(1-Alkynyl)perylenes undergo oxygenation when subjected to irradiation with visible light under aerated conditions. The structures of novel oxygenated products formed in this manner are assigned as regioisomeric dibenzo[jk,mn]phenanthrene-4,5-diones.

Artificial DNAs based on alkynyl C-nucleosides as a superior scaffold for homo- and heteroexcimer emissions.

DNA-like fluorescent oligomers composed of alkynyl beta-D-ribofuranosides bearing pyrene, perylene, and anthracene as a fluorophore were synthesized by solid-phase DNA synthesis. The fluorescent oligomers possess the defined number and order of the fluorophores. In these oligomers, the adjacent fluorophores efficiently interact with each other by hydrophobic interactions in their electronic ground states in a face-to-face fashion.

Single-nucleotide polymorphism detection with "wire-like" DNA probes that display quasi "on-off" digital action.

Establishing a reliable genotyping protocol is a critical matter in post-sequence genetics. In this article, we describe a highly sensitive electrochemical detection of complementary DNAs (up to 43-mer) based on hole transport with molecular-scale, "wire-like" DNA probes. The presence of a single-base mismatch in the DNA duplexes caused a dramatic decrease in the electrochemical response.

Artificial nucleosides possessing metal binding sites at the 3'- and 5'-positions of the deoxyribose moieties.

This paper describes a convenient synthetic procedure for nucleoside mimics, 1-6, in which the 3',5'-hydroxy groups of natural 2'-deoxythymidine or 2'-deoxyadenosine are replaced by thiol, amine, or alkylthiol groups. Such nucleosides would be built up into a single DNA strand with cooperative participation of metal coordination, where internucleoside linkages are replaced by metal complexation motifs. The X-ray crystal structure and complexation behaviors of 3',5'-dithiothymidine, 1, with Au(I) are also reported.

Glucopyranoside Recognition by Polypyridine-Macrocyclic Receptors Possessing a Wide Cavity with a Flexible Linkage.

New polypyridine-macrocyclic receptors for glucopyranosides were designed and synthesized. The artificial receptors possess a terpyridine skeleton as a hydrogen-bonding site and a flexible polyoxyethylene chain as a bridge for the macrocyclic structure, in which the cavity of the receptors is large enough to incorporate pyranosides. The receptors showed high affinities for n-octyl beta-(D)-glucopyranoside, and selective binding of the receptors was observed between epimeric pyranosides.