On-Demand Ligand-Base DNA Sensor with Electrochemical Impedance Spectroscopy.

We have developed a DNA sensor that can be finalized to detect a specific target on demand. The electrode surface was modified with 2,7-diamino-1,8-naphthyridine (DANP), a small molecule with nanomolar affinity for the cytosine bulge structure. The electrode was immersed in a solution of synthetic probe-DNA that had a cytosine bulge structure at one end and a complementary sequence to the target DNA at the other end.

Ameliorating Role of Hydrogen-Rich Water Against NSAID-Induced Enteropathy via Reduction of ROS and Production of Short-Chain Fatty Acids.

Background: Nonsteroidal anti-inflammatory drug (NSAID)-induced enteropathy, the mechanism of which is involved in oxidative stress, can be lethal due to hemorrhage. Thus, we aimed to investigate the effect of hydrogen-rich water (HRW), in terms of oxidative stress, on intestinal mucosal damage as well as changes in the gut microbiome and the short-chain fatty acids (SCFAs) content in feces.

Methods: Hydrogen-rich water was orally administered for 5 days to investigate the effectiveness of indomethacin-induced enteropathy in mice.

Electrochemical Impedimetric Real-Time Polymerase Chain Reactions Using Anomalous Charge Transfer Enhancement.

We developed a new electrochemical impedimetric method for the real-time detection of polymerase chain reactions (PCR) based on our recent discovery that the DNA intercalator, [Ru(bpy)DPPZ], anomalously enhances charge transfer between redox mediators, K[Fe(CN)]/K[Fe(CN)], and a carbon electrode. Three mM [Fe(CN)] and 5 μM [Ru(bpy)DPPZ] were added to the PCR solution, and electrochemical impedance spectroscopy (EIS) measurements were performed at each elongation heat cycle. The charge transfer resistance (Rct) was initially low due to the presence of [Ru(bpy)DPPZ] in the solution.

High allele discrimination in the typing of single nucleotide polymorphisms of miRNA.

MicroRNAs (miRNAs) belonging to the same family have similar sequences and are difficult to identify. Herein, we report the reverse transcription-hairpin-probe-polymerase chain reaction (RT-Hpro-PCR) technique, which utilises a reverse transcription (RT) primer containing a 5'-end deoxyribonucleic acid (DNA) tag, to detect miRNAs with similar sequences. This strategy follows a two-step RT-PCR method using 6-7-mer RT-primers with a ~ 10-mer tag sequence at the 5'-end and a probe with a hairpin structure (Hpro), including two C-bulges, attached.

Protective Effect of Luminal Uric Acid Against Indomethacin-Induced Enteropathy: Role of Antioxidant Effect and Gut Microbiota.

Background: Uric acid (UA) has anti- and pro-inflammatory properties. We previously revealed that elevated serum UA levels provide protection against murine small intestinal injury probably via luminal UA secreted in the small intestine. Luminal UA may act as an antioxidant, preventing microbiota vulnerability to oxidative stress.

RT-Hpro-PCR: A MicroRNA Detection System Using a Primer with a DNA Tag.

MicroRNAs (miRNAs) are short RNAs that regulate the expression of complementary messenger RNAs and are involved in numerous human diseases. However, current detection techniques lack the sensitivity to detect miRNAs of low abundance. Moreover, at a length of 20-25 bases, miRNAs are too short for the reverse transcription (RT) polymerase chain reaction (PCR).

Development of 2, 7-Diamino-1, 8-Naphthyridine (DANP) Anchored Hairpin Primers for RT-PCR Detection of Chikungunya Virus Infection.

A molecular diagnostic platform with DANP-anchored hairpin primer was developed and evaluated for the rapid and cost-effective detection of Chikungunya virus (CHIKV) with high sensitivity and specificity. The molecule 2, 7-diamino-1, 8-naphthyridine (DANP) binds to a cytosine-bulge and emits fluorescence at 450 nm when it is excited by 400 nm light. Thus, by measuring the decline in fluorescence emitted from DANP-primer complexes after PCR reaction, we could monitor the PCR progress.

Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA.

A fluorescent molecule DANP that binds to cytosine bulge DNA and emits characteristic fluorescence was conjugated to pyrene to give a new fluorescence probe PyDANP. Temperature- and solvent-dependent absorption changes showed that DANP and pyrene chromophores stacked at room temperature in an aqueous buffer solution and quenched fluorescence. Upon binding of DANP moiety in PyDANP to cytosine bulge DNA, the fluorescence from DANP bound to C-bulge increased by ∼12-fold, showing that PyDANP is a turn-ON probe for the detection of C-bulge DNA.

Detection of hepatitis C virus by single-step hairpin primer RT-PCR.

We developed a novel single-step virus detection system using the fluorescent molecule with a hairpin primer on the reverse transcription (RT)-polymerase chain reaction (PCR). Primers that are specific to Hepatitis C virus (HCV) having a hairpin tag at the 5'-end were used for RT and PCR. The HCV-RNA template was reverse transcribed by reverse transcriptase with the hairpin primer (HP), and the resulting cDNA was amplified directly by HP-PCR (RT-HP-PCR).

A novel DANP-coupled hairpin RT-PCR for rapid detection of Chikungunya virus.

Chikungunya has re-emerged as an important arboviral infection of global health significance. Because of lack of a vaccine and effective treatment, rapid diagnosis plays an important role in early clinical management of patients. In this study, we have developed a novel molecular diagnostic platform that ensures a rapid and cost-effective one-step RT-PCR assay, with high sensitivity and specificity, for the early detection of the Chikungunya virus (CHIKV).

Transformation of cytosine to uracil in single-stranded DNA via their oxime sulfonates.

The novel transformation of cytosine oxime sulfonate (C*) to uracil sulfonate (U*) proceeded by a Co(II)-assisted benzoyl peroxide reaction, eventually leading to the conversion of cytosine to uracil.

Reaction of cytosine with bisulfite and hydroxylamine.

The synthesis of DNA oligomer containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate by the simultaneous addition of bisulfite and hydroxylamine under mild conditions is reported. To the best of our knowledge, the reaction of the oxime into the ketone, N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate into 5,6-dihydrouracil-6-sulfonate or uracil has not been reported. Moreover, this issue contains the difficulty in specific reactivity of oxime derivative from DNA bases include (5m)C toward reagent; for example, T also reacts to potassium permanganate known as a reagent for oxime into ketone.

Synthesis and reaction of DNA oligomers containing modified cytosines related to bisulfite sequencing.

The synthesis of DNA oligomers containing N(4)-hydroxy-5,6-dihydrocytosine-6-sulfonate by using ligand-induced base flipping of cytosine followed by the simultaneous addition of bisulfite and hydroxylamine is reported. In contrast to C, the flipped-out 5-methylcytosine was selectively oxidized over thymines and cytosines in the duplex by potassium permanganate. Ligand-induced base flipping is a convenient and powerful strategy for the synthesis of modified cytosines and 5-methylcytosines related to bisulfite sequencing at the predetermined site of DNA.

The reaction of cytosine with bisulfite by base flipping from the duplex.

Methylation of cytosine at the C5-position in DNA plays a major role in epigenetic gene control. The detection of 5-methylcytosine was designed with the base flipping from the duplex using NC and CGG/CGG triad. Using bisulfite and hydroxylamine, the reaction of cytosine in 11-mer duplex produced the adduct of bisulfite and hydroxylamine, which was isolated by HPLC and identified by MALDI-TOF MS.

Emission of characteristic fluorescence from the ligand-cytosine complex in U_A/ACU bulged RNA duplex.

Here we show that N,N-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine (DANP) binds to the single cytosine bulge in RNA duplexes. When the base pairs flanking the C-bulge were A-U base pairs, a characteristic fluorescence was emitted from the DANP-C-bulge complex. The fluorescence would be useful for detecting the C-bulge in RNA secondary structures.

Allele specific C-bulge probes with one unique fluorescent molecule discriminate the single nucleotide polymorphism in DNA.

A combination of an allele specific C-bulge probe and the fluorescent molecule N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine (DANP) that binds specifically to the C-bulge provides a method for single nucleotide polymorphism (SNP) typing with only one fluorescent molecule without covalent modification of the DNA probe. The allele specific C-bulge probe contains one additional cytosine and produces a C-bulge directly flanking the SNP site upon hybridization to the target DNA. The C-bulge is a scaffold to recruit and retain DANP directly neighboring the SNP site.

Synthesis and redox properties of trinuclear ruthenium-acetylide complexes with tri(ethynylphenyl)amine bridge.

Novel trinuclear ruthenium complexes have been prepared by using tri(4-ethynylphenyl)amine as a bridging ligand. Cyclic voltammetry of the trinuclear ruthenium complexes revealed stepwise quasi-reversible redox behavior of three ruthenium-acetylide species and the central triphenylamine unit, whereas the mononuclear analog showed two sequential quasi-reversible redox waves. The spectroelectrochemical UV-VIS spectral studies suggested that the 1e- oxidized triruthenium species was stable and showed a characteristic absorption at lambda(max) = 505 nm.

Convergent synthesis of platinum-acetylide dendrimers.

An efficient convergent route to the main chain type of organometallic dendrimers, in which platinum moieties are linked by 1,3,5-triethynylbenzene, has been developed. The synthesis of platinum-acetylide dendrons involved the use of two types of trialkylsilyl groups for protection of the terminal acetylene. The platinum-acetylide dendrimers were prepared up to the third generation by reacting dendrons with a triplatinum core and a tetraplatinum core.

Quasi-octahedral complexes of pentamethylcyclopentadienyliridium(III) bearing bis(diphenylphosphinomethyl)phenylphosphine (dpmp).

Reaction of [Cp*IrCl2]2 (1) with dpmp in the presence of KPF6 afforded a binuclear complex [Cp*IrCl(dpmp-P1,P2;P3)IrCl2Cp*](PF6) (2) (dpmp =(Ph2PCH2)2PPh). The mononuclear complex [Cp*IrCl(dpmp-P1,P2)](PF6) (4) was generated by the reaction of [Cp*IrCl2(BDMPP)](BDMPP =PPh[2,6-(MeO)2C6H3]2) with dpmp in the presence of KPF6. These mono- and binuclear complexes have four-membered ring structures with a terminal and a central P atom of the dpmp ligand coordinated to an iridium atom as a bidentate ligand.

Helical Chiral Polyisocyanides Possessing Porphyrin Pendants: Determination of Helicity by Exciton-Coupled Circular Dichroism.

Exciton-coupled circular dichroism of the porphyrin Soret band of triblock copolymers prepared from chiral isocyanide monomers and an achiral tetraphenylporphyrin derivative (TPP) provides a novel method for determining the helical sense of poly(aryl isocyanide)s (see the schematic representation of the structure).