DNA-binding small-ligand-immobilized surface plasmon resonance biosensor for detecting thymine-related single-nucleotide polymorphisms

A surface plasmon resonance (SPR) biosensor that carries DNA-binding small ligands has been developed for the detection of single-nucleotide polymorphisms (SNPs). 3,5-Diaminopyrazine derivatives, with a hydrogen-bonding profile fully complementary to the thymine base, were utilized as recognition elements on the sensor surface, and a target single-stranded DNA sequence was hybridized with a DNA probe containing an abasic site to place this site opposite a nucleobase to be detected. In a continuous flow of sample solutions buffered to pH 6.4 (0.25 M NaCl), the 3,5-diaminopyrazine-based SPR sensor can detect an orphan nucleobase in the duplex with a clear selectivity for thymine over cytosine, guanine, and adenine (5'-GTT GGA GCT GXG GGC GTA GGC-3'/3'-CAA CCT CGA CNC CCG CAT CCG-5'; X=abasic site, N=target nucleobase G, C, A, or T). The SPR response was linear in the concentration range 10-100 nM. Allele discrimination is possible based on the combination of different binding surfaces in a flow cell of the SPR system, which is demonstrated for the analysis of the thymine/cytosine mutation present in 63-meric polymerase chain reaction (PCR) amplification products (Ha-ras gene, codon 12, antisense strand). Comparison with a bulk assay based on 3,5-diaminopyrazine/DNA binding shows that the immobilization of 3,5-diaminopyrazine derivatives on the SPR sensor allows more sensitive detection of the target DNA sequence, and binding selectivity can be tuned by controlling the salt concentration of sample solutions. These features of the DNA-binding small-molecule-immobilized SPR sensor are discussed as a basis for the design of SPR biosensors for SNP genotyping.     

Soft-sputtering of insulin films in argon-cluster secondary ion mass spectrometry

In secondary ion mass spectrometry (SIMS) of organic substances, the dissociation of the sample molecules is crucial. We have developed SIMS equipment capable of bombardment, where the primary ions are argon cluster ions with kinetic energy per atom controllable down to 1 eV. We previously reported the detection of intact ions of insulin and cytochrome C using this equipment. In this paper, we present a detailed characterization of the emission of secondary ions from insulin, focusing on the difference in secondary ion yield between intact ions and fragment ions by varying the incident angle of the cluster ions. The emission intensity of the intact ions was changed drastically due to the exposed dosage and incident angle of the cluster ions in contrast to the fragment ions. We discuss these results based on the manner in which the argon-cluster ions collide with the organic solid.     

Label-free molecular beacon system based on DNAs containing abasic sites and fluorescent ligands that bind abasic sites

A new class of label-free molecular beacon (MB) system based on DNA strands that contain abasic (AP) sites (AP-DNA) and adopt stem-loop structures, in combination with fluorescent ligands that bind these AP sites, has been developed. Unlike a conventional MB, which requires covalent labeling of the MB with a fluorophore and a quencher, the developed system (APMB) does not require covalent attachment of signal transduction units. Detailed sensing functions of a series of APMB systems were examined with the aid of the fluorescent ligand named ATMND to provide insight into the design strategy for APMB systems. The effects of the stem length and the position of the AP site in the stem moiety on the fluorescence response of the APMB system were examined. Genotyping of a G/C SNP of PCR amplification products was successfully demonstrated with the APMB system and blue-fluorescent ATMND as a ligand. The APMB system was further extended to a system that utilized green-fluorescent lumiflavin.     

Functionalization of mesoporous silica membrane with a Schiff base fluorophore for Cu(II) ion sensing

A Schiff base (SB) immobilized hybrid mesoporous silica membrane (SB-HMM) was prepared by immobilizing a Schiff base onto the pore surface of mesoporous silica (pore size=3.1 nm) embedded in the pores of a porous anodic alumina membrane. In contrast to the non-fluorescent analogous SB molecule in homogeneous solutions, SB-HMM exhibited intense fluorescence due to emission enhancement caused by aggregation of SB groups on the pore surface. The high quantum efficiency of the surface SB groups allows SB-HMM to function as a fluorescent sensor for Cu(II) ions in an aqueous solution with good sensitivity, selectivity and reproducibility. Under the optimal conditions described, the linear ranges of fluorescence intensity for Cu(II) are 1.2-13.8(M (R(2)=0.993) and 19.4-60 (R(2)=0.992) (M. The limit of detection for Cu(II) is 0.8 μM on basis of the definition by IUPAC (C(LOD)=3.3S(b)/m).     

Synthesis of indole and biindolyl triflones: trifluoromethanesulfonylation of indoles with Tf2O/TTBP (2,4,6-tri-tert-butylpyridine) system

A convenient synthesis of indole triflones is reported. N-Alkyl, aryl and N-H indole triflones were obtained in 82-96% yields by the Tf(2)O/TTBP System. Biindolyl triflones were accessed in 51-81% yields for the first time by simple treatment of the resulting indole triflones with a base and without any use of organometallic chemistry. An environmentally friendly solvent, Solkane 365/227, can be substituted for this process without any loss of efficiency.     

Selective photoinduced energy transfer from a thiophene rotaxane to acceptor

An energy transfer process was investigated using cyclodextrin-oligothiophene rotaxanes (2T-[2]rotaxane). The excited energy of 2T-[2]rotaxane is transferred to the sexithiophene derivative which is included in the cavity of β-CD stoppers of 2T-[2]rotaxane.     

Highly luminescent SiO(2) beads with multiple QDs: Preparation conditions and size distributions

Multiple CdTe quantum dots (QDs) were incorporated in SiO(2) beads using a reverse micelle route (i.e., a water-in-oil emulsion) and a precursor solution of SiO(2)-coated CdTe QDs as the water phase. The QDs in the beads retained their initial photoluminescence efficiency (56%) because they had a thin SiO(2) shell that prevented removal of the ligands from their surface during incorporation. Because of the SiO(2) sol in the precursor solution, the size of the water pools in water-in-oil emulsion increased to 700±320nm compared to 25±5nm when an aqueous CdTe QD solution was used. The size of the beads prepared in the water pools depended strongly on the preparation parameters (water phase injection speed, tetraethyl orthosilicate concentration, reaction time). The beads were easily separated into three size ranges (60±23, 160±40, and 650±200nm) by filtering for further application.     

Fluorescent trimethyl-substituted naphthyridine as a ligand for C-C mismatch detection in CCG trinucleotide repeats

We report on the selective binding of 2-amino-5,6,7-trimethyl-1,8-naphthyridine (ATMND) to C-C mismatch present in the hairpin structures of (CCG)(n) trinucleotide repeats that are associated with neurological diseases; this binding is accompanied by significant fluorescence quenching of ATMND.     

Localization of the Grover Walks on Spidernets and Free Meixner Laws

In the first part, we have constructed several families of interacting wedge-local nets of von Neumann algebras. In particular, we discovered a family of models based on the endomorphisms of the U(1)-current algebra ${\mathcal{A} ^{(0)}}$ of Longo-Witten. In this second part, we further investigate endomorphisms and interacting models. The key ingredient is the free massless fermionic net, which contains the U(1)-current net as the fixed point subnet with respect to the U(1) gauge action. Through the restriction to the subnet, we construct a new family of Longo-Witten endomorphisms on ${\mathcal{A} ^{(0)}}$ and accordingly interacting wedge-local nets in two-dimensional spacetime. The U(1)-current net admits the structure of particle numbers and the S-matrices of the models constructed here do mix the spaces with different particle numbers of the bosonic Fock space.