Unambiguous detection of target DNAs by excimer-monomer switching molecular beacons

A new class of molecular beacons were developed in which pyrene fluorophores were connected both at 3' and 5' ends of a single-stranded oligonucleotide. The two pyrene-based fluorophores were synthesized from the same starting material, so that the preparation of the beacons was simplified. The detection strategy of the beacons for target DNAs is based on "excimer-monomer emission switching" of the pyrene fluorophores: excimer emission of the pyrene moieties changed to monomer one when the beacons hybridized with the targets. This type of two-state mode of fluorescence allows unambiguous detection of the target DNAs because strict 1:1 correlation between the nonhybridized and the hybridized beacons can be monitored by the presence of isoemissive points of the fluorescence changes. The beacons can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones.     

Phonon density of states and compression behavior in iron sulfide under pressure

We report the partial phonon densities of states (DOS) of iron sulfide, a possible component of the rocky planet's core, measured by the 57Fe nuclear resonant inelastic x-ray scattering and calculate the total phonon DOS under pressure. From the phonon DOS, we drive thermodynamic parameters. A comparison of the observed and estimated compressibilities makes it clear that there is a large pure electronic contribution in the observed compressibility in the metallic state. Our results present the observation of thermodynamic parameters of iron sulfide with the low-spin state of an Fe2+ ion at the high density, which is similar to the condition of the Martian core.     

Anomalous behavior of the coefficient of normal restitution in oblique impact

The coefficient of normal restitution in an oblique impact is theoretically studied. Using a two-dimensional lattice model for an elastic disk and an elastic wall, we demonstrate that the coefficient of normal restitution can exceed unity and has a peak against the incident angle in our simulation. We also explain this behavior based upon a phenomenological theory.     

A new plane type sensor for concentration measurement in liquid

In this paper, we propose a new plane type sensor for measurement of the liquid. In the proposed sensor, the PVDF films with the transparent conductive electrodes are respectively arranged on the surface of a LED and a photodiode. The optical properties of the liquid are measured using the LED and the photodiode, and the electrical and ultrasonic properties are measured using the PVDF films on the surface of the LED and photodiode. Therefore, the optical, electrical and ultrasonic properties at same space are measured by the proposed sensor. Three parameters in the sample liquid were estimated by the proposed sensor.     

Biological identification of peptides that specifically bind to poly(phenylene vinylene) surfaces: recognition of the branched or linear structure of the conjugated polymer

Peptides that bind to poly(phenylene vinylene) (PPV) were identified by the phage display method. Aromatic amino acids were enriched in these peptide sequences, suggesting that a π-π interaction is the key interaction between the peptides and PPV. The surface plasmon resonance (SPR) experiments using chemically synthesized peptides demonstrated that the Hyp01 peptide, with the sequence His-Thr-Asp-Trp-Arg-Leu-Gly-Thr-Trp-His-His-Ser, showed an affinity constant (7.7 × 10(5) M(-1)) for the target, hyperbranched PPV (hypPPV) film. This value is 15-fold greater than its affinity for linear PPV (linPPV). In contrast, the peptide screened for linPPV (Lin01) showed the reverse specificity for linPPV. These results suggested that the Hyp01 and Lin01 peptides selectively recognized the linear or branched structure of PPVs. The Ala-scanning experiment, circular dichroism (CD) spectrometry, and molecular modeling of the Hyp01 peptide indicated that adequate location of two Trp residues by forming the polyproline type II (P(II)) helical conformation allowed the peptide to specifically interact with hypPPV.     

Synthesis and characterization of A4[Re6Q8L6]@SiO2 red-emitting silica nanoparticles based on Re6 metal atom clusters (A = Cs or K, Q = S or Se, and L = OH or CN)

Metal atom clusters constitute very promising candidates as luminophores for applications in biotechnology because they are nanosized entities offering robust luminescence in the near-infrared field (NIR). However, they cannot be used as prepared for biological applications because of potential toxic effects and quenching of the clusters' luminescence in aqueous media, and they therefore need to be dispersed in a biocompatible matrix. We describe herein the encapsulation of octahedral rhenium clusters, denoted as A(4)[Re(6)Q(8)L(6)] (A = Cs or K, Q = S or Se, and L = OH or CN), in silica nanoparticles by a water-in-oil microemulsion process, paying particular attention to the clusters' stability. The obtained A(4)[Re(6)Q(8)L(6)]@SiO(2) nanoparticles are 30 nm in size with good monodispersity and a perfectly spherical shape, as shown by scanning electron microscopy (SEM). The presence of cluster units inside the silica matrix was evidenced by scanning transmission electron microscopy in annular dark-field mode (ADF-STEM). From the point of view of their optical properties, the A(4)[Re(6)Q(8)L(6)]@SiO(2) nanoparticles show red and NIR emission under UV excitation, even when dispersed in water. The evolution of the structural and luminescence properties of clusters before and after encapsulation was followed by Raman and photoluminescence spectroscopy.     

Optical and electronic properties of siloxane-bridged cyclic dimers with naphthylene or pyrenylene moieties

The optical and electronic properties of novel siloxane-bridged cyclic dimers with naphthylene (CD1) or pyrenylene (CD2) moieties are described. CD1 and CD2 were obtained by the cyclic dimerization of 1,4-bis(dimethylhydroxysilyl)naphthalene (M1) and 1,6-bis(dimethylhydroxysilyl)pyrene (M2), respectively. CD1 and CD2 mainly exhibited the emission from their excimers owing to their short distances between aryl moieties in CD1 and CD2, which were determined to be 3.44 Å and 3.41 Å by the X-ray crystallographic analysis, respectively. The absorption spectra of CD2 in the presence of 7,7,8,8-tetracyanoquinodimethane (TCNQ) revealed that CD2 has the ability to form 1:1 charge-transfer complex with TCNQ, indicating the existence of the transannular π-π interaction between closely located pyrene components in CD2.