Pyrene-Modified Guanine Cluster Probes Forming DNA/RNA Hybrid Three-Way Junctions for Imaging of Intracellular MicroRNAs.

MicroRNAs (miRNAs) regulate gene expression in cells; high levels of expression are associated with various cancers. In this paper, we describe PyA-modified nucleic acid probes that can detect intracellular miRNAs by forming DNA/RNA hybrid three-way junction structures containing a fluorescent scaffold-a so-called G-cluster. This G-cluster featured two mismatched strands, four guanine residues, and one fluorescent adenine residue having a pyrene moiety covalently connected at the 8-position through an acetylene linker. The scaffold underwent a dramatic shift in its emission wavelength when two mismatched strands formed a duplex, similar to the behavior of an adenine pentad system (A-cluster). We applied the G-cluster scaffold in a three-way junction system to probe for miRNAs; its red-shifted fluorescence intensity and stability were greater than those reported previously for A-cluster three-way junction probes. Furthermore, confocal microscopy of cancer cell lines revealed bright fluorescence emissions in response to the miRNAs in the cells. Thus, this system can be applied intracellularly as a potential fluorescent probe for the detection of various biologically important nucleic acids.

Design and Properties of Ligand-Conjugated Guanine Oligonucleotides for Recovery of Mutated G-Quadruplexes.

The formation of a guanine quadruplex DNA structure (G4) is known to repress the expression of certain cancer-related genes. Consequently, a mutated G4 sequence can affect quadruplex formation and induce cancer progression. In this study, we developed an oligonucleotide derivative consisting of a ligand-containing guanine tract that replaces the mutated G4 guanine tract at the promoter of the vascular endothelial growth factor (VEGF) gene. A ligand moiety consisting of three types of polyaromatic hydrocarbons, pyrene, anthracene, and perylene, was attached to either the 3' or 5' end of the guanine tract. Each of the ligand-conjugated guanine tracts, with the exception of anthracene derivatives, combined with other intact guanine tracts to form an intermolecular G4 on the mutated VEGF promoter. This intermolecular G4, exhibiting parallel topology and high thermal stability, enabled VEGF G4 formation to be recovered from the mutated sequence. Stability of the intramolecular G4 increased with the size of the conjugated ligand. However, suppression of intermolecular G4 replication was uniquely dependent on whether the ligand was attached to the 3' or 5' end of the guanine tract. These results indicate that binding to either the top or bottom guanine quartet affects unfolding kinetics due to polarization in DNA polymerase processivity. Our findings provide a novel strategy for recovering G4 formation in case of damage, and fine-tuning processes such as replication and transcription.

A novel nucleic acid aptamer tag: a rapid fluorescence strategy using a self-constructing G-quadruplex from AGG trinucleotide repeats.

Herein, we have developed a novel fluorescence labeling strategy for nucleic acid aptamers based on self-assembling between AGG tri-nucleotide repeats and a pyrene-modified oligonucleotide. This strategy could be an effective tool for developing targeting-imaging systems and biosensor systems to detect target molecules.

PyA-cluster system for the detection and imaging of miRNAs in living cells through double-three-way junction formation.

Herein, we describe an extended version of a fluorescence probe for detecting miRNAs through the novel application of a PyA-cluster system. By testing various (CG)n sequences in the middle of the oligonucleotide strand of the probe, we obtained an optimal sequence that formed a double-three-way-junction structure, with two PyA units positioned close together, in the presence of the target miRNA. This system readily detected the locations of target miRNAs in living cells and allowed visualization of structural changes through variations in the color of the fluorescence.

Recovery of the Formation and Function of Oxidized G-Quadruplexes by a Pyrene-Modified Guanine Tract.

Oxidation is one of the frequent causes of DNA damage, especially to guanine bases. Guanine bases in the G-quadruplex (G4) are sensitive to damage by oxidation, resulting in transformation to 8-oxo-7,8-dihydroguanine (8-oxoG). Because the formation of G4 represses the expression of some cancer-related genes, the presence of 8-oxoG in a G4 sequence might affect G4 formation and induce cancer progression. Thus, oxidized-G4 formation must be controlled using a chemical approach. In the present study, we investigated the effect of introduction of 8-oxoG into a G4 sequence on the formation and function of the G4 structure. The 8-oxoG-containing G4 derived from the promoter region of the human vascular endothelial growth factor ( VEGF) gene differed topologically from unoxidized G4. The oxidized VEGF G4 did not act as a replication block and was not stabilized by the G4-binding protein nucleolin. To recover G4 function, we developed an oligonucleotide consisting of a pyrene-modified guanine tract that replaces the oxidized guanine tract and forms stable intermolecular G4s with the other intact guanine tracts. When this oligonucleotide was used, the oxidized G4 stalled replication and was stabilized by nucleolin as with the unmodified G4. This strategy generally enables recovery of the function of any oxidized G4s and therefore has potential for cancer therapy.

Facile conversion of ATP-binding RNA aptamer to quencher-free molecular aptamer beacon.

We have developed RNA-based quencher-free molecular aptamer beacons (RNA-based QF-MABs) for the detection of ATP, taking advantage of the conformational changes associated with ATP binding to the ATP-binding RNA aptamer. The RNA aptamer, with its well-defined structure, was readily converted to the fluorescence sensors by incorporating a fluorophore into the loop region of the hairpin structure. These RNA-based QF-MABs exhibited fluorescence signals in the presence of ATP relative to their low background signals in the absence of ATP. The fluorescence emission intensity increased upon formation of a RNA-based QF-MAB·ATP complex.

Quencher-free molecular aptamer beacons (QF-MABs) for detection of ATP.

We have constructed a simple and efficient system-based on quencher-free molecular aptamer beacons (QF-MABs)-for probing ATP. In the absence of ATP, the fluorescence of a pyrene fluorophore on the loop position (15 nucleotides from the 5' end) of the optimal QF-MAB was quenched by the neighboring nucleobases; in its presence, fluorescence was recovered, due to a conformational change in the secondary structure of the QF-MAB.

Cancer-specific gene silencing through therapeutic siRNA delivery with B vitamin-based nanoassembled low-molecular-weight hydrogelators.

This paper describes the synthesis, characterization, and in vitro and in vivo siRNA transfection ability of B vitamin-based cationic clickable bolaamphiphiles (VBs). Our VBs derived from vitamins B2, B3, B5, B6, and B7 formed nanoassembled low-molecular-weight hydrogelators (LMWGs, vitagels). The vitagels VB2, VB6, and VB7 (derived from vitamins B2, B6, and B7, respectively) facilitated delivery of small interfering RNAs (siRNA), efficiently silencing gene expression specifically into cancer cell lines; in addition, the LMWGs derived from vitamins B3, B5, and B6 were biocompatible. An ex vivo study in a mouse model revealed that the siRNA delivered by the vitagel VB7 was located primarily at the site of the tumor. The gene silencing efficiency of vascular endothelial growth factor siRNA delivered by vitagels was dependent on the nature of the vitamin headgroup, the N/P ratio, and, interestingly, the hydrogelation properties of the VBs.

Fluorescence modification of the AAAA (4A) loop: toward a probe of the structural dynamics of the i-motif of the retinoblastoma gene.

Systematic modification of the 4A loop region of the Rb gene with (Py)A fluorophore units allows discrimination of the fluorescence signals corresponding to structural dynamics from single-stranded to i-motif structures.

Tissue specific delivery of estrone-conjugated siRNAs.

An estrone phosphoramidite, synthesized in a single step, was directly incorporated at the 5' ends of small interfering RNAs (siRNAs). The resulting estrone-conjugated siRNAs readily pass through cellular membranes and down-regulate the target protein, and show specific distributions in vivo.

Fluorescent peptide indicator displacement assay for monitoring interactions between RNA and RNA binding proteins.

This paper describes a sensitive, non-destructive displacement assay, using a fluorescent peptide indicator, for real-time monitoring of the interactions between RNA and RNA binding proteins (RBPs). The developed fluorescent peptide indicators, each containing a mid-sequence fluorophore unit, allowed sensing of target RNA and RNA-RBP interactions through changes in fluorescence intensity. We anticipate that this assay will open up new possibilities for meaningful studies of RNA-RBP interactions.

A low-molecular-weight supramolecular hydrogel of riboflavin bolaamphiphile for VEGF-siRNA delivery.

A low-molecular-weight hydrogel derived from riboflavin (vitamin B(2)) that self-assembles to provide supramolecular nanofibers, biocompatible material, can be used to deliver VEGF-siRNA efficiently into human cells by the endocytosis pathway, where the siRNA is functionalized.

Delivery of floxuridine derivatives to cancer cells by water-soluble organometallic cages.

The self-assembly of 2,4,6-tris(pyridin-4-yl)-1,3,5-triazine (tpt) triangular panels with p-cymene (pPr(i)C(6)H(4)Me) ruthenium building blocks and 2,5-dioxydo-1,4-benzoquinonato (dobq) or 5,8-dioxydo-1,4-naphthoquinonato (donq) bridges, in the presence of a pyrenyl-nucleoside derivatives (pyreneR), affords the triangular prismatic host-guest compounds [(pyrene-R)⊂Ru(6)(pPr(i)C(6)H(4)Me)(6)(tpt)(2)(dobq)(3)](6+) ([(pyrene-R)⊂1](6+)) and [(pyrene-R)⊂Ru(6)(pPr(i)C(6)H(4)Me)(6)(tpt)(2)(donq)(3)](6+) ([(pyrene-R)⊂2](6+)), respectively. The inclusion of six monosubstitutedpyrenyl-nucleosides (pyrene-R1 = 5'-(1-pyrenyl butanoate)-2'-deoxyuridine, pyrene-R2 = 5-fluoro-5'-(1-pyrenyl butanoate)-2'-deoxyuridine, pyrene-R3 = 5'-{N-[1-oxo-4-(1-pyrenyl)butyl]-glycyl}-2'-deoxyuridine, pyrene-R4 = 5-fluoro-5'-{N-[1-oxo-4-(1-pyrenyl)butyl]-glycyl}-2'-deoxyuridine, pyrene-R5 = 5-fluoro-5'-{N-[1-oxo-4-(1-pyrenyl)butyl]-phenylalanyl}-2'-deoxyvuridine, pyrene-R6 = 5-fluoro-5'-{N-[1-oxo-4-(1-pyrenyl)butyl]-phenylalanyl}-2'-deoxyuridine) has been accomplished. The carceplex nature of [(pyrene-R)⊂1](6+) with the pyrenyl moiety firmly encapsulated in the hydrophobic cavity of the cage with the nucleoside groups pointing outward was confirmed by NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS), while the host-guest nature of [(pyrene-R)⊂2](6+) was studied in solution by NMR techniques. In contrast to the floxuridine compounds used in the clinic, the host-guest complexes are highly water-soluble. Consequently, the cytotoxicities of these water-soluble compounds have been established using human ovarian A2780 and A2780cisR cancer cells. All the host-guest systems are more cytotoxic than the empty cages alone [1][CF(3)SO(3)](6) (IC(50) = 23 µM) and [2][CF(3)SO(3)](6) (IC(50) = 10 µM), the most active compound [pyrene-R4⊂1][CF(3)SO(3)](6)being 2 orders of magnitude more cytotoxic (IC(50) = 0.3 µM) on these human ovarian cancer cell lines (A2780 and A2780cisR).

Complexation and conjugation approaches to evaluate siRNA delivery using cationic, hydrophobic and amphiphilic peptides.

In this study, we used solid phase synthesis to prepare three kinds of peptides and then formulated their peptide-siRNA complexes and peptide-siRNA conjugates. Both the complexation and conjugation systems were nontoxic and allowed the delivery of siRNA into the cytoplasm without the need for any transfection agents and with subsequent inhibition of gene expression.

5'-Triphosphate-RNA-independent activation of RIG-I via RNA aptamer with enhanced antiviral activity.

RIG-I is a cytosolic receptor for non-self RNA that mediates immune responses against viral infections through IFNα/ß production. In an attempt to identify novel tools that modulate IFNα/ß production, we used SELEX technology to screen RNA aptamers that specifically target RIG-I protein. Most of the selected RIG-I aptamers contained polyU motifs in the second half regions that played critical roles in the activation of RIG-I-mediated IFNß production. Unlike other known ligands, RIG-I aptamer bound and activated RIG-I in a 5'-triphosphate-independent manner. The helicase and RD domain of RIG-I were used for aptamer binding, but intact RIG-I protein was required to exert aptamer-mediated signaling activation. Furthermore, replication of NDV, VSV and influenza virus in infected host cells was efficiently blocked by pre- or post-treatment with RIG-I aptamer. Based on these data, we propose that RIG-I aptamer has strong potential to be an antiviral agent that specifically boosts the RIG-I-dependent signaling cascade.

Design, synthesis, and anticancer activities of novel perfluoroalkyltriazole-appended 2'-deoxyuridines.

We have focused on the C5-modification of 2'-deoxyuridine with substituted heterocycles for bioactivity, such as antiviral or anticancer activity. Herein, we report a novel class of nucleoside analogues with perfluoroalkyltriazole moiety as an anticancer drug candidate.

Synthesis of AZT-based cationic lipids and in vitro evaluation of siRNA delivery.

New types of cationic lipids based on AZT were evaluated for their biological effects in terms of their cytotoxicity and their cellular delivery of siRNA.

C5-Modified nucleosides exhibiting anticancer activity.

We describe (i) a simple method for the synthesis of C5-modified nucleosides from 5-iodo-2'-deoxyuridine and (ii) their activity against six types of human cancer cell lines (HCT15, MM231, NCI-H23, NUGC-3, PC-3, ACHN). We generated nitrile oxides in situ from oximes using a commercial bleaching agent; their cycloadditions with 5-ethynyl-2'-deoxyuridine yielded isoxazole derivatives possessing activity against the cancer cell lines. We synthesized several azides from benzylic bromides and their click reactions with 5-ethynyl-2'-deoxyuridine provided triazole derivatives.

Label-free electrochemical detection of the p53 core domain protein on its antibody immobilized electrode.

We report quantitative results on interactions between a tumor suppressor protein, p53, also known as a prognostic cancer marker, and its antibody. The p53 antibody molecules immobilized on an (R)-lipo-diaza-18-crown-6 self-assembled monolayer (SAM)-modified gold disk electrode were shown to effectively capture the p53 protein by Western blot, quartz crystal microbalance, and electrochemical impedance experiments. The p53 protein thus captured modulated the ability of the electrode for charge transfer to and from a redox probe in the solution in a p53 concentration range of approximately 0.1-30 microg/mL. The same interaction was also observed in the human embryonic kidney cell lysate, demonstrating that the SAM-modified electrode can serve as a selective platform for electrochemically monitoring the cellular p53 concentration.

Homoadenine signalling system for SNP typing.

We report a homoadenine-based fluorescent probing system containing two pyrene-modified deoxyadenosine units for SNP typing in homoadenine and homothymine.