Topologically-Interlocked Minicircles as Probes of DNA Topology and DNA-Protein Interactions

DNA minicircles exist in biological contexts, such as kinetoplast DNA, and are promising components for creating functional nanodevices. They have been used to mimic the topological features of nucleosomal DNA and to probe DNA-protein interactions such as HIV-1 and PFV integrases, and DNA gyrase. Here, we synthesized the topologically-interlocked minicircle rotaxane and catenane inside a frame-shaped DNA origami. These minicircles are 183 bp in length, constitute six individual single-stranded DNAs that are ligated to realize duplex interlocking, and adopt temporary base pairing of single strands for interlocking. To probe the DNA-protein interactions, restriction reactions were carried out on DNAs with different topologies such as free linear duplex or duplex constrained inside origami and free or topologically-interlocked minicircles. Except the free linear duplex, all tested structures were resistant to restriction digestion, indicating that the topological features of DNA, such as flexibility, curvature, and groove orientation, play a major role in DNA-protein interactions.     

Oblique interactions of weakly nonlinear long waves in dispersive systems

Studies on the oblique interactions of weakly nonlinear long waves in dispersive systems are surveyed. We focus mainly our concentration on the two-dimensional interaction between solitary waves. Two-dimensional Benjamin–Ono (2DBO) equation, modified Kadomtsev–Petviashvili (MKP) equation and extended Kadomtsev–Petviashvili (EKP) equation as well as the Kadomtsev–Petviashvili (KP) equation are treated. It turns out that a large-amplitude wave can be generated due to the oblique interaction of two identical solitary waves in the 2DBO and the MKP equations as well as in the KP-II equation. Recent studies on exact solutions of the KP equation are also surveyed briefly.     

Tuning the Reactivity of a Substrate for SNAP-Tag Expands Its Application for Recognition-Driven DNA-Protein Conjugation

Recognition-driven modification has been emerging as a novel approach to modifying biomolecular targets of interest site-specifically and efficiently. To this end, protein modular adaptors (MAs) are the ideal reaction model for recognition-driven modification of DNA as they consist of both a sequence-specific DNA-binding domain (DBD) and a self-ligating protein-tag. Coupling DNA recognition by DBD and the chemoselective reaction of the protein tag could provide a highly efficient sequence-specific reaction. However, combining an MA consisting of a reactive protein-tag and its substrate, for example, SNAP-tag and benzyl guanine (BG), revealed rather nonselective reaction with DNA. Therefore new substrates of SNAP-tag have been designed to realize sequence-selective rapid crosslinking reactions of MAs with SNAP-tag. The reactions of substrates with SNAP-tag were verified by kinetic analyses to enable the sequence-selective crosslinking reaction of MA. The new substrate enables the distinctive orthogonality of SNAP-tag against CLIP-tag to achieve orthogonal DNA-protein crosslinking by six unique MAs.     

Multiple gamma functions,multiple sine functions,and Appell’s <Emphasis Type="Italic">O</Emphasis>-functions

Kurokawa introduced q-multiple gamma functions and q-multiple sine functions. We show that the Appell’s O-function is expressed via the q-multiple gamma function. We also give some applications of this result. For example, we obtain a formula for the “Stirling modular form” and calculate special values of the q-multiple sine function. Moreover, we give some formulas of Eisenstein series and double cotangent functions and its generalization. Then the former gives an infinite product expression of the double sine function explicitly and a result of Kurokawa.     

Synthesis of core-shell structured Au@Bi2S3 nanorod and its application as DNA immobilization matrix for electrochemical biosensor construction

The core-shell structured Au@Bi2S3 nanorods have been prepared through direct in-situ growth of Bi2S3 at the surface of pre-synthesized gold nanorods.The product was characterized by X-ray diffraction,transmission electron microscopy and energy-dispersive X-ray spectroscopy.Then the obtained Au@Bi2S3 nanorods were coated onto glassy carbon electrode to act as a scaffold for fabrication of electrochemical DNA biosensor on the basis of the coordination of-NH2 modified on 5’-end of probe DNA and Au@Bi2S3.Electrochemical characterization assays demonstrate that the Au@Bi2S3 nanorods behave as an excellent electronic transport channel to promote the electron transfer kinetics and increase the effective surface area by their nanosize effect.The hybridization experiments reveal that the Au@Bi2S3 matrix-based DNA biosensor is capable of recognizing complementary DNA over a wide concentration ranging from 10 fmol/L to 1 nmol/L.The limit of detection was estimated to be 2 fmol/L(S/N=3).The biosensor also presents remarkable selectivity to distinguish fully complementa ry sequences from basemismatched and non-complementary ones,showing great promising in practical application.     

Novel superconducting phases in copper oxides and iron-oxypnictides: NMR studies

We reexamine the novel phase diagrams of antiferromagnetism (AFM) and high-T_c superconductivity (HTSC) for a disorder-free CuO₂ plane based on an evaluation of local hole density (p) by site-selective Cu-NMR studies on multilayered copper oxides. Multilayered systems provide us with the opportunity to research the characteristics of the disorder-free CuO₂ plane. The site-selective NMR is the best and the only tool used to extract layer-dependent characteristics. Consequently, we have concluded that the uniform mixing of AFM and SC is a general property inherent to a single CuO₂ plane in an underdoped regime of HTSC. The T=0 phase diagram of AFM constructed here is in quantitative agreement with the theories in a strong correlation regime which is unchanged even with mobile holes. This Mott physics plays a vital role for mediating the Cooper pairs to make T_c of HTSC very high. By contrast, we address from extensive NMR studies on electron-doped iron-oxypnictides La1111 compounds that the increase in T_c is not due to the development of AFM spin fluctuations, but because the structural parameters, such as the bond angle α of the FeAs₄ tetrahedron and the a-axis length, approach each optimum value. Based on these results, we propose that a stronger correlation in HTSC than in FeAs-based superconductors may make T_c higher significantly.     

Tris(porphyrinyl-oxinato)Ga Complexes as a Photosynthetic Antenna Miniature

Two oxinylporphyrins, 5-(8-hydroxy-5-quinolinyl)-10,15,20-( p -tolyl)- porphyrin ( 1 ) and 5,15-bis(8-hydroxy-5-quinolinyl)-10,20-bis( n -heptyl)-porphyrin ( 2 ), were prepared and coordinated with Ga(III) to afford tris(oxinato) complex 3 and poly(oxinato) complex 4 , respectively. The structure of 3 was analyzed by variable temperature NMR study with referring to tris(8-hydroxy-5-quinolinyl)Ga(III) complex 5 to be in a meridional form. Oxinato ligands of 3 and 5 were exchanged with one another, with keeping the meridional structure. UV-Vis and fluorescence spectra of tris(oxinato)complex 3 and poly(oxinato)complex 4 were compared with each monomeric compound 1 and 2 . The absorption spectra showed only a slight broadening of the Soret band, suggesting trivial electronic and excitonic interactions. The fluorescence intensity was increased significantly compared with each monomeric compound 1 and 2 . At the same time, efficient excitation energy transfer among three porphyrins has been observed.     

A novel anthracene-based fluorescent colorimetric sensor for the simple naked-eye diagnosis of methylmalonic aciduria

A novel molecular sensor using anthracene bearing two amidopyridines emits blue fluorescence in the presence of succinic acid and green fluorescence in the presence of malonic acid, and its fluorescence intensity increased upon binding. Using this molecular sensor, we succeeded in detecting the difference of one carbon atom between succinic acid and malonic acid with the naked-eye. Furthermore, when methylmalonic acid was dissolved in urine to provide a model system for methylmalonic aciduria, the fluorescence changed from blue to green, and methylmalonic acid was successfully detected with the naked-eye.