Site-specific binding of chelerythrine and sanguinarine to single pyrimidine bulges in hairpin DNA

Spectrofluorometric titration, electrospray ionization time-of-flight mass spectrometric and UV melting methods were employed to study the binding of chelerythrine and sanguinarine to bulged DNA. The results showed that both alkaloids bind specifically to single pyrimidine (C, T) bulge sites. The ability of sanguinarine to bind to both regular and bulged hairpins was found to be stronger than that of chelerythrine, but the binding selectivity of chelerythrine toward single-base bulges was much larger than that of sanguinarine. Figure Association constants for chelerythrine and sanguinarine toward regular and single-base bulged hairpins obtained from fluorometric analysis     

Photoinduced tandem three-component coupling of propanedinitrile, 2,5-dimethylhexa-2,4-diene, and cyanoarenes

A tandem three-component coupling photoreaction proceeds upon photoirradiation of MeCN/H2O solutions containing propanedinitrile (1, malononitrile), 2,5-dimethylhexa-2,4-diene (2), and polycyanoarenes in the presence of phenanthrene and carbonate, leading to selective alpha-monoalkylation of 1. The reaction proceeds via photo-NOCAS (Nucleophile-Olefin Combination, Aromatic Substitution) type mechanism: nucleophilic attack of the anion of 1 to photogenerated 2(*+) is followed by ipso-substitution on the radical anion of the polycyanoarene. It advances under mild, safe, and environmentally friendly conditions such as proceeding at ambient temperature without metals and halogens, and in the presence of weak base. The reaction also represents a novel and metal-free cross-coupling reaction that leads to ipso-substitution on polycyanoarene via aryl-cyano bond cleavage. In addition, the reaction is a rare example of introducing carbon nucleophile in the photoinduced electron transfer reaction, except that of cyanide ion.     

Estimation of dye configuration from conventional chiroptical spectra of porphyrin integrates: combination of exciton theory with Monte Carlo molecular structural simulation

Dye integrates (arrays and aggregates) are the subject of current interest in photochemical devices. However, they are in general not suitable for X-ray crystallography because of their poor crystallinity. Here, we improved a simple method of estimating dye configurations in porphyrin integrates from their visible absorption (AB) and circular dichroism (CD) spectra. For this purpose, we calculate the dipolar and optical rotatory strengths of an integrate on the basis of the exciton theory for a given porphyrin configuration, generate the theoretical AB and CD spectra of the dye integrate using a phenomenological line shape function, a Voigt function with an adjustable line width, and optimize the configuration by minimizing the square sum (S) of the difference between the observed and calculated spectra. We adopted two optimization methods to achieve a least-squares fit between the calculated and observed spectra: the Metropolis Monte Carlo (MC) method, which incorporates S into the molecular force-field energy as a constraint, and the quasi-Newton (QN) method, which numerically minimizes S and uses no molecular force field. To check the feasibility of these methods, we simulated the AB and CD spectra of Tr?ger's base and meso-meso-linked porphyrins using the QN program, then compared the dye configurations with their X-ray structures. The calculated dye configuration of Tr?ger's base porphyrin is sufficiently in agreement with that of the X-ray structure (RMSD=0.21 A for the ZnS4 center), whereas that of meso-meso-linked porphyrin was not. These results were discussed in terms of charge transfer between two porphyrins. Finally, we applied the QN and MC methods to the structural estimation of a newly prepared peptide-linked bis(porphyrin) Boc-(PorZn,S)2-OBut. The best configurations estimated by these two methods were sufficiently in agreement with each other.     

Mass transfer of weak acid in nanometer-sized pores of octadecylsilyl-silica gel

The sorption of bromophenol blue or anthracene-9-carboxylic acid as a weak acid into single octadecylsilyl (ODS)-silica gel microparticles in a solution was analyzed by microcapillary injection-manipulation and absorption microspectroscopy. The distribution ratio and the sorption rate were highly dependent on the pH of the solution. These results are discussed in terms of the acid dissociation/association, distribution between the ODS and solution phases, and intraparticle diffusion of the weak acid in the nanometer-sized pores of the ODS-silica gel.     

Concise total synthesis of (-)-spongotine A

The first asymmetric total synthesis of spongotine A is described. The oxidative synthesis of the imidazoline/ketone unit from keto aldehyde and diamine is a key step in this synthesis. The absolute stereochemistry of the asymmetric center of natural spongotine A is revealed as the (S)-configuration.     

Echo-intensity compensation in echolocating bats (Pipistrellus abramus) during flight measured by a telemetry microphone

An onboard microphone (Telemike) was developed to examine changes in the basic characteristics of echolocation sounds of small frequency-modulated echolocating bats, Pipistrellus abramus. Using a dual high-speed video camera system, spatiotemporal observations of echolocation characteristics were conducted on bats during a landing flight task in the laboratory. The Telemike allowed us to observe emitted pulses and returning echoes to which the flying bats listened during flight, and the acoustic parameters could be precisely measured without traditional problems such as the directional properties of the recording microphone and the emitted pulse, or traveling loss of the sound in the air. Pulse intensity in bats intending to land exhibited a marked decrease by 30 dB within 2 m of the target wall, and the reduction rate was approximately 6.5 dB per halving of distance. The intensity of echoes returning from the target wall indicated a nearly constant intensity (-42.6 +/- 5.5 dB weaker than the pulse emitted in search phase) within a target distance of 2 m. These findings provide direct evidence that bats adjust pulse intensity to compensate for changes in echo intensity to maintain a constant intensity of the echo returned from the approaching target at an optimal range.     

Heterodyne Interferometers Using Orthogonally Polarized and Two-Frequency Shifted Light Sources with Super-high Extinction Ratio

This paper describes heterodyne interferometers using orthogonally polarized and two-frequency shifted light sources of two types with super-high extinction ratio to reduce non-linearity of the interferometer due to polarization cross-talk. The acousto-optic modulators are used to shift light frequency. In the first interferometer the light source with Glan-Thomson prisms of very high extinction ratio (50 dB) is used to make the polarization cross-talk very small. In the second interferometer the light source of two-frequency shifted beams with small crossing angle (2.5 rnrad-10 mrad) is used to completely exclude non-linearity of the interferometer due to polarization cross-talk. By measuring the thickness of vacuum evaporation film, it was demonstrated that the interferometers are useful to measure thickness of a thin film in nanometer order.     

A protocol for searching the most probable phase‐retrieved maps in coherent X‐ray diffraction imaging by exploiting the relationship between convergence of the retrieved phase and success of calculation

Coherent X‐ray diffraction imaging (CXDI) is a technique for visualizing the structures of non‐crystalline particles with size in the submicrometer to micrometer range in material sciences and biology. In the structural analysis of CXDI, the electron density map of a specimen particle projected along the direction of the incident X‐rays can be reconstructed only from the diffraction pattern by using phase‐retrieval (PR) algorithms. However, in practice, the reconstruction, relying entirely on the computational procedure, sometimes fails because diffraction patterns miss the data in small‐angle regions owing to the beam stop and saturation of the detector pixels, and are modified by Poisson noise in X‐ray detection. To date, X‐ray free‐electron lasers have allowed us to collect a large number of diffraction patterns within a short period of time. Therefore, the reconstruction of correct electron density maps is the bottleneck for efficiently conducting structure analyses of non‐crystalline particles. To automatically address the correctness of retrieved electron density maps, a data analysis protocol to extract the most probable electron density maps from a set of maps retrieved from 1000 different random seeds for a single diffraction pattern is proposed. Through monitoring the variations of the phase values during PR calculations, the tendency for the PR calculations to succeed when the retrieved phase sets converged on a certain value was found. On the other hand, if the phase set was in persistent variation, the PR calculation tended to fail to yield the correct electron density map. To quantify this tendency, here a figure of merit for the variation of the phase values during PR calculation is introduced. In addition, a PR protocol to evaluate the similarity between a map of the highest figure of merit and other independently reconstructed maps is proposed. The protocol is implemented and practically examined in the structure analyses for diffraction patterns from aggregates of gold colloidal particles. Furthermore, the feasibility of the protocol in the structure analysis of organelles from biological cells is examined.     

RNA Aptamers That Reversibly Bind Photoresponsive Azobenzene‐Containing Peptides

Modulation of biological networks assembled by diverse interactions among biologically active molecules has provided a platform for innovative biotechnologies. Here, we report RNA aptamers that bind to a photoresponsive peptide (KRAzR; Lys‐Arg‐azobenzene‐Arg) containing azobenzene chromophore, which can change its structure by photoirradiation. Aptamers were identified after 10 cycles of an in vitro selection procedure starting with a DNA library containing a 70 nt random region. Surface plasmon resonance (SPR) analysis demonstrated that interactions between aptamers and KRAzR were fully controlled by appropriate photoirradiation to the SPR sensor chip. Upon irradiation of 360 nm on the KRAzR‐immobilized surface, the binding of each aptamer to the surface was significantly decreased. Subsequent photoirradiation of the same surface with 430 nm restored the aptamer binding to the surface. We also observed that direct photoirradiation of the aptamer–peptide complex on a gold surface actively promoted dissociation of the complex. Furthermore, a doped reselection method was applied to acquire structural and sequence information of aptamer 66. From a data analysis of the conserved region and the mutation frequency, we were able to select a plausible secondary structure among three candidates predicted by computational folding simulation.