NMR study on the photoresponsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form

Two diastereomers of a photoresponsive oligodeoxyribonucleotide tethering a trans-azobenzene, based on the chirality of the central carbon of a diol linker, were separated by reversed-phase HPLC. On the basis of 2D NMR analysis, absolute configurations of the diastereomers alpha and beta (tentatively designated from differences in their retention time) were determined as R- and S-forms, respectively. For both diastereomers, their NMR-determined duplex structure showed that trans-azobenzene intercalates between base pairs, because distinct NOEs were observed between the protons of azobenzene and those of the adjacent base pairs, such as with the imino protons and methyl protons of thymine. The melting temperatures of both duplexes were higher than that of the corresponding native duplex, which contained no azobenzene residue, due to the intercalated trans-azobenzene stabilizing the duplex by a stacking interaction. Between these two diastereomers, differences in T(m) were also found: the melting temperature of the R-form duplex (alpha-isomer) was higher than that of the S-form (beta-isomer). On the basis of the NMR-determined structure, this difference was attributed to the fact that the S-form (beta isomer) causes more stress forming the duplex than does the R-form (alpha isomer) due to disturbances of the right-hand helix.     

Accurate fluorescent polymeric thermometers containing an ionic component

Fluorescent polymeric thermometers consisting of only N-alkylacrylamide and fluorescent components show rather low temperature resolution in their functional ranges (ca. 15-50 degrees C) because of the occurrence of intermolecular aggregation, which causes hysteresis in their fluorescence response to changes in temperature. By adding an ionic component to prevent such intermolecular aggregation, we obtained four fluorescent polymeric thermometers that offer high temperature resolution (<0.2 degrees C). Each new fluorescent polymeric thermometer covered the temperature range, 9-33 degrees C, 30-51 degrees C, 49-66 degrees C or 4-38 degrees C.     

Solution structure of S-DNA formed by covalent base pairing involving a disulfide bond

Here, we present the solution structure of a DNA duplex containing a disulfide base pair (S-DNA). The unnatural nucleoside "S" possessing a thiophenyl group as base was incorporated into a self-complementary singled-stranded oligonucleotide. Crosslinking of the disulfide base pair was analyzed by non-denaturing polyacrylamide gel electrophoresis. Under oxidizing conditions a high molecular weight band as 18 mer, corresponding to the double-stranded molecule (5'-GCGASTCGC: 3'-CGCTSAGCG), was found, whereas single-stranded self-complementary 9 mer oligonucleotide GCGASTCGC was detected in the presence of a reducing agent. These results suggest that the oligonucleotide is covalently linked by disulfide bonding under oxidizing conditions, which can be reversibly reduced to two thiol groups under reducing conditions. CD spectrum of S-DNA (CGASTCG) under oxidizing conditions suggested that the duplex had a right-handed double-stranded structure similar to that of natural DNA (B-form, CGATCG). NMR studies confirmed that this CGASTCG resembled natural B-DNA and that the two phenyl rings derived from the disulfide base pairing intercalated into the duplex. However, these two phenyl rings were not positioned in the same plane as the other base pairs. Specifically, NOEs suggest that although CGASTCG adopts a structure similar to B-type DNA, the S-DNA duplex is bent at the point of disulfide base pairing to face the major groove.     

An arrayed-window microfluidic device for observation of mixed nanoparticles with an X-ray free-electron laser

Optical Review - A microfluidic device was developed for coherent diffraction imaging using an X-ray free-electron laser (XFEL-CDI). Liquid samples, which are separately packed in reservoirs of the...     

Environment‐Sensitive Fluorophores with Benzothiadiazole and Benzoselenadiazole Structures as Candidate Components of a Fluorescent Polymeric Thermometer

An environment‐sensitive fluorophore can change its maximum emission wavelength (λ_em), fluorescence quantum yield (Φ_f), and fluorescence lifetime in response to the surrounding environment. We have developed two new intramolecular charge‐transfer‐type environment‐sensitive fluorophores, DBThD‐IA and DBSeD‐IA, in which the oxygen atom of a well‐established 2,1,3‐benzoxadiazole environment‐sensitive fluorophore, DBD‐IA, has been replaced by a sulfur and selenium atom, respectively. DBThD‐IA is highly fluorescent in n‐hexane (Φ_f=0.81, λ_em=537 nm) with excitation at 449 nm, but is almost nonfluorescent in water (Φ_f=0.037, λ_em=616 nm), similarly to DBD‐IA (Φ_f=0.91, λ_em=520 nm in n‐hexane; Φ_f=0.027, λ_em=616 nm in water). A similar variation in fluorescence properties was also observed for DBSeD‐IA (Φ_f=0.24, λ_em=591 nm in n‐hexane; Φ_f=0.0046, λ_em=672 nm in water). An intensive study of the solvent effects on the fluorescence properties of these fluorophores revealed that both the polarity of the environment and hydrogen bonding with solvent molecules accelerate the nonradiative relaxation of the excited fluorophores. Time‐resolved optoacoustic and phosphorescence measurements clarified that both intersystem crossing and internal conversion are involved in the nonradiative relaxation processes of DBThD‐IA and DBSeD‐IA. In addition, DBThD‐IA exhibits a 10‐fold higher photostability in aqueous solution than the original fluorophore DBD‐IA, which allowed us to create a new robust molecular nanogel thermometer for intracellular thermometry.     

Enhancing solution-phase supramolecular interactions between monomeric porphyrins and [60]fullerene by simple chemical modification

The supramolecular interactions of N-methylporphyrin and iridium porphyrin with C₆₀ in toluene solution were investigated using NMR spectroscopy and absorption spectroscopy. Our results demonstrate that both the N-methylation and iridium metalation of porphyrin are effective means to enhance the binding affinity to C₆₀, resulting in 1:1 complexation for N-methylporphyrin/C₆₀ and 2:1 complexation for iridium porphyrin/C₆₀.     

Paramagnetic Inversion of the Sign of the Interference Contribution to the Transverse Relaxation of the Imido Protons of the Coordinated Imidazoles in the UniformlyN-Labeled Cytochromec3

In the spectrum of uniformly¹⁵N-labeled cytochromec₃, the relative linewidths of the doublet peaks of the¹⁵N-coupled imido proton of the coordinated imidazole group were reversed on oxidation. This inversion was explained by the interference relaxation process between the electron–proton dipolar and¹⁵N–¹H dipolar interactions. The inversion can be used to assign the imido protons of the coordinated imidazole groups in heme proteins.