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.     

Investigation of Molecular Diffusion at Block Copolymer Thin Films Using Maximum Entropy Method-Based Fluorescence Correlation Spectroscopy and Single Molecule Tracking

Fluorescence correlation spectroscopy (FCS) has been widely used to investigate molecular diffusion behavior in various samples. The use of the maximum entropy method (MEM) for FCS data analysis provides a unique means to determine multiple distinct diffusion coefficients without a priori assumption of their number. Comparison of the MEM-based FCS method (MEM-FCS) with another method will reveal its utility and advantage as an analytical tool to investigate diffusion dynamics. Herein, we measured diffusion of fluorescent probes doped into nanostructured thin films using MEM-FCS, and validated the results with single molecule tracking (SMT) data. The efficacy of the MEM code employed was first demonstrated by analyzing simulated FCS data for systems incorporating one and two diffusion modes with broadly distributed diffusion coefficients. The MEM analysis accurately afforded the number of distinct diffusion modes and their mean diffusion coefficients. These results contrasted with those obtained by fitting the simulated data to conventional two-component and anomalous diffusion models, which yielded inaccurate estimates of the diffusion coefficients. Subsequently, the MEM analysis was applied to FCS data acquired from hydrophilic dye molecules incorporated into microphase-separated polystyrene-block-poly(ethylene oxide) (PS-b-PEO) thin films characterized under a water-saturated N₂ atmosphere. The MEM analysis revealed distinct fast and slow diffusion components attributable to molecules diffusing on the film surface and inside the film, respectively. SMT studies of the same materials yielded trajectories for mobile molecules that appear to follow the curved PEO microdomains. Diffusion coefficients obtained from the SMT data were consistent with those obtained for the slow diffusion component detected by MEM-FCS. These results highlight the utility of MEM-FCS and SMT for gaining complementary information on molecular diffusion processes in heterogeneous material systems.

Graphical Abstract

     

Photoinduced Pyramidal Inversion Behavior of Phosphanes Involved with Aggregation-Induced Emission Behavior

Aggregation-induced emission (AIE) is a fascinating phenomenon because of the applications of luminescent materials in the aggregated state, which exploit the large structural changes of the molecules in the excited state. Recently, it was reported that triphenylphosphane derivatives show AIE behavior in which they undergo potentially large structural changes in the excited state. Inspired by this report, photoinduced pyramidal inversion behavior of phosphanes was investigated. In photochemical experiments, the prepared P-stereogenic phosphanes exhibited photoracemization in dilute solution, and a negative correlation was observed between the photoracemization and the AIE phenomenon. Theoretical computations revealed that the inversion barrier in the excited state was much smaller than that in the ground state. This is the first report on the photoinduced pyramidal inversion behavior of phosphanes, which will provide new and unexplored applications.     

12-Epi-9-deacetoxyxenicin,new cytotoxic diterpenoid from a Bornean soft coral,Xenia sp.

One new compound, 12-epi-9-deacetoxyxenicin (1) along with a hydroperoxide product, 12-epi-9-deacetoxy-8-hydroperoxyxenicin (2) and two known sesquiterpenoids (3–4) were isolated from a population of Bornean soft coral Xenia sp. The structures of these secondary metabolites were elucidated based on their spectroscopic data. Compounds 1 and 2 showed cytotoxic activity against ATL cell line, S1T. In addition, compound 3 exhibited hyphal inhibition of Lagenidium thermophilum.     

Control of chain ends of polyesters in polycondensation of AA and BB monomers by use of solid‐phase reagent

For selective synthesis of linear polyester having a functional group at one end, polycondensation between 1,4‐butanediol ( 1a ) and sebacoyl chloride ( 2a ) and between 1,12‐dodecanediol ( 1b ) and isophthaloyl chloride ( 2b ) was conducted in the presence of oxime resin or oxime silica gel, followed by cleavage of the formed polyester from the solid‐phase support with aniline. Matrix‐assisted laser desorption ionization time‐of‐flight mass spectra and ¹H NMR spectra of the cleaved polyester showed that the products contained not only polyester with anilide at one end ( poly 1 ), but also polyester with anilides at both ends ( poly 2 ). The product ratio of poly 1 to poly 2 ( poly 1 / poly 2 ) was dependent on monomers, monomer concentration, feed ratio of monomer to oxime moiety in the support, oxime content in the support, reaction solvent, and the nature of the support. Polyester with a high poly 1 / poly 2 ratio of 81/21 and moderate molecular weight (M_n = 1430 g/mol) was obtained by polycondensation of 1b and 2b in the presence of oxime silica gel in dichloromethane. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 1379–1386     

Constraints in the variational principle for stationary states

Constraints in the variational principle for stationary states (VPSS) are classified in accordance with Dirac’s constrained classical mechanics and the time-dependent variational principle (TDVP). All of the VPSS constraints are required to belong to the first-class TDVP as constants of motion to ensure the real-valuedness of the Lagrange multipliers. The VPSS constraints are further classified as either first-class or second-class. The first-class VPSS constraints are constants of variation with symmetry-adapted wave functions. If the representation basis for the constraint operators is incomplete, however, the first-class VPSS constraints lead to broken-symmetry solutions. The nondegenerate energies of \({}^2E'\) at the \(D_{3h}\) geometry in the Jahn–Teller distortion of H\(_3\) are presented as an example of a problem with broken-symmetry. An ad hoc adjustment is suggested by considering the second-class pseudo-VPSS constraints with new adiabatic parameters.     

Single-step preparation of topological gels using vinyl-modified β-cyclodextrin as a figure-of-six cross-linker

Herein, we have proposed a single-step preparation of topological gels using vinyl-modified β-cyclodextrin (V-β-CyD) and isoprene. Copolymerization of V-β-CyD and isoprene in an aqueous solution resulted in gelation due to V-β-CyD acting as a novel type of copolymer chain cross-linker. The vinyl moiety of V-β-CyD becomes a part of the copolymer, while the β-CyD moiety of V-β-CyD simultaneously incorporates the isoprene component of the copolymer. V-β-CyD is capable of two different modes of cross-linking at each end, i.e., chemically bonding and mechanically interlocking. Due to the shape of the cross-linking point, we refer to it as figure-of-six cross-linking. Nuclear magnetic resonance analysis showed that the gel contained V-β-CyD and isoprene in an approximately 1:0.3 stoichiometry. The relatively high content of β-CyD was reflected in the character of the gel; the gel swelled in dimethylformamide which is a good solvent of β-CyD. A fluorometric analysis using 6-(p-toluidino)-2-naphthalenesulfonic acid showed that the appended β-CyD was able to accommodate guest molecules. Introduction of an additional vinyl monomer into the gel was also successful. Addition of 4-vinylphenylboronic acid to the preparation procedure yielded a sugar-responsive gel that swelled in the presence of d-fructose.     

Crystalline‐Sponge‐Based Structural Analysis of Crude Natural Product Extracts

Characterization of complex natural product mixtures to the absolute structural level of their components often requires significant amounts of starting materials and lengthy purification process, followed by arduous structure elucidation efforts. The crystalline sponge (CS) method has demonstrated utility in the absolute structure elucidation of isolated organic compounds at miniscule quantities compared to conventional methods. In this work, we developed a new CS‐based workflow that greatly expedites the in‐depth structural analysis of crude natural product extracts. Using a crude extract of the red alga Laurencia pacifica, we showed that CS affinity screening prior to compound isolation enables prioritization of analytes present in the extract, and we subsequently resolved the molecular structures of six sesquiterpenes with stereochemical clarity from around 10 mg crude extract. This study demonstrates a new chemotyping workflow that can greatly accelerate natural product discovery from complex samples.     

DNA Origami Scaffolds as Templates for Functional Tetrameric Kir3 K+ Channels

In native systems, scaffolding proteins play important roles in assembling proteins into complexes to transduce signals. This concept is yet to be applied to the assembly of functional transmembrane protein complexes in artificial systems. To address this issue, DNA origami has the potential to serve as scaffolds that arrange proteins at specific positions in complexes. Herein, we report that Kir3 K⁺ channel proteins are assembled through zinc‐finger protein (ZFP)‐adaptors at specific locations on DNA origami scaffolds. Specific binding of the ZFP‐fused Kir3 channels and ZFP‐based adaptors on DNA origami were confirmed by atomic force microscopy and gel electrophoresis. Furthermore, the DNA origami with ZFP binding sites nearly tripled the K⁺ channel current activity elicited by heterotetrameric Kir3 channels in HEK293T cells. Thus, our method provides a useful template to control the oligomerization states of membrane protein complexes in vitro and in living cells.     

The second-generation synthesis of BICMAP analogues

We previously reported the synthesis of BICMAP (1a) via 6-diphenylphosphino-2,3-dihydrobenzofuran as a key intermediate. However, we did not successfully synthesize BICMAP analogues via a similar synthetic route. Herein we report the second-generation synthesis of BICMAP and its derivatives via diethylphosphonate as a key intermediate.