Helix-Sense-Selective Permeation of Racemic Helical Oligoacetylenes through One-Handed Helical Channels in Polymer Membranes.

Helix-sense-selective permeation (HSSPerm) of racemic helical oligoacetylenes through one-handed helical channels has been realized. The one-handed helical channels were created in the one-handed helical polyacetylene membranes by the helix-sense-selective decomposition (HSS-SCAT) of the corresponding racemic helical polyacetylene membranes, followed by removing the formed oligomers. Since the HSS-SCAT reaction proceeds with just circularly polarized visible light with no reagents, no catalysts, no solvent, and high selectivity, the chiral channel-containing membrane with high purity was obtained easily. This membrane could separate racemic helical oligoacetylenes enantioselectively in up to 30%ee. To our knowledge, this is the first example of HSSPerm.

Synthesis and Direct Observation of Chiral Supramolecular Polymer of Porphyrin Having Cholesteryl Groups.

We report the synthesis and microscopic investigations of two chiral helical porphyrin supramolecular polymers with different coordinating metals that are expected to be capable of serving as synthetic macromolecular motors driven by thermal fluctuations. Furthermore, based on their microscopic images, we propose a stepwise process for the formation of higher-order structures. These porphyrins formed completely different association states, and this was reflected in the marked differences in the shapes of the supramolecular polymers. The Cu-TChOAlaCPP supramolecular polymers formed H-aggregate rods in diisopropyl ether, then grew into superhelices and then into ribbons. On the other hand, Zn-TChOAlaCPP supramolecular polymers formed aggregates based on van der Waals interactions in diethyl ether, then grew into fibers and then grew into multiple-helices and ribbons. In addition, we imaged the interaction between long and short chains of the Cu-TChOAlaCPP supramolecular polymer by fast-scanning atomic force microscopy, and we indicated the availability as a macromolecular motor driven by thermal fluctuations.

Synthesis and Direct Observation of Molecules of 2D Polymers: With High Molecular Weights, Large Areas, Small Micropores, Solubility, Membrane Forming Ability, and High Oxygen Permselectivity.

If ideal 2D polymer (2DP) macromolecules with small pores that are similar in size to gas molecules, large areas, small thickness, and excellent membrane-forming ability are synthesized, ultimate gas separation membranes would be obtained. However, as far it is known, such ideal well-characterized 2DP macromolecules are not isolated. In this study, an ideal 2DP macromolecule is synthesized by using the successive three reactions (Glaser coupling, SCAT reaction, and the introduction of octyl groups), in which the conjugated framework structure is maintained, from a fully conjugated 1D polymer. Because this exfoliated 2DP is soluble, the macromolecular structure can be fully characterized by 1 H-NMR, GPC, SEM, AFM, and its dense membrane with no defects can be fabricated by the solvent cast method. This soluble 2DP macromolecule has very small micropores (6.0 Å) inside the macromolecule, a large area (30 × 68 nm by SEM and AFM), high molecular weight (Mn = 2.80 × 105 by GPC), and a small thickness (4.4 Å by AFM). This membrane shows the highest oxygen permselectivity exceeding Robeson's upper line because of the high molecular sieving effect of the controlled small micropores.

Single-Molecule Unidirectional Processive Movement along a Helical Polymer Chain in Non-aqueous Medium.

In this work, a molecule "walking" along a single chain of a synthetic helical polymer, which is used as a rail on a substrate in an organic solvent at room temperature, is observed. The walking comprises the unidirectional processive movement of a short-chain molecule along a chiral helical chain in 3 nm steps, driven by Brownian motion and a tapping effect of the atomic force microscopy tip based on a flash ratchet mechanism. Furthermore, the rail consists of a long-chain substituted phenylacetylene polymer with pendant cholesteryl groups, along which the short-chain molecule can walk as a result of van der Waals interactions. The macromolecular motion is videoed using a fast-scanning atomic force microscope, and additionally, this phenomenon is also simulated by all-atom molecular dynamics calculations. On the basis of these results, we propose the principle of a polymer molecular motor. This is the first report of a synthetic walking machine of a chiral helical polymer driven by thermal fluctuation as an artificial life function.

Identification of AR-V7 downstream genes commonly targeted by AR/AR-V7 and specifically targeted by AR-V7 in castration resistant prostate cancer.

Primary prostate cancer (PC) progresses to castration-resistant PC (CRPC) under androgen deprivation therapy, by mechanisms e.g. expression of androgen receptor (AR) splice variant-7 (AR-V7). Here we conducted comprehensive epigenome and transcriptome analyses comparing LNCaP, primary PC cells, and LNCaP95, AR-V7-expressing CRPC cells derived from LNCaP. Of 399 AR-V7 target regions identified through ChIP-seq analysis, 377 could be commonly targeted by hormone-stimulated AR, and 22 were specifically targeted by AR-V7. Among genes neighboring to these AR-V7 target regions, 78 genes were highly expressed in LNCaP95, while AR-V7 knockdown led to significant repression of these genes and suppression of growth of LNCaP95. Of the 78 AR-V7 target genes, 74 were common AR/AR-V7 target genes and 4 were specific AR-V7 target genes; their most suppressed genes by AR-V7 knockdown were NUP210 and SLC3A2, respectively, and underwent subsequent analyses. NUP210 and SLC3A2 were significantly upregulated in clinical CRPC tissues, and their knockdown resulted in significant suppression of cellular growth of LNCaP95 through apoptosis and growth arrest. Collectively, AR-V7 contributes to CRPC proliferation by activating both common AR/AR-V7 target and specific AR-V7 target, e.g. NUP210 and SLC3A2.

Differential gene analysis during the development of obliterative bronchiolitis in a murine orthotopic lung transplantation model: A comprehensive transcriptome-based analysis.

BACKGROUND: Obliterative bronchiolitis (OB) is a known issue during minor histocompatibility antigen (mHA) disparity during lung transplantation. This study evaluated gene expression in a murine orthotropic lung transplantation model using microarray analysis. METHODS: Left lungs from C57BL/10(H-2b) donor mice were transplanted into mHA-mismatched C57BL/6(H-2b) recipient mice. Three groups (OB, non-OB, and sham controls) were confirmed pathologically and analyzed. Gene expression changes in the lung grafts were determined by microarray and immunohistochemical staining, and genes were verified by quantitative PCR in the lungs and mediastinal lymph nodes (LNs). RESULTS: A total of 1343 genes were upregulated in the OB lungs compared to the sham group. Significant upregulation was observed for genes related to innate, e.g. Tlr2 and CCL3 and adaptive immunity, e.g. H2-ab1 and Il-21. Positive labeling for MHC class II antigen was observed in the bronchial epithelium of OB accompanied with B cells. We found increased Tlr2, Ccl3, H2-ab1, Il-21, Ighg3, Ifng, and Pdcd1 mRNA expression in the OB lung, and increased Il-21, Ighg3, and Pdcd1 expression in the OB LNs. CONCLUSIONS: Adaptive and innate immune reactions were involved in OB after lung transplantation, and genetic examination of related genes could be used for detection of OB.

Optically active triptycenes containing hexa-peri-hexabenzocoronene units.

A pair of novel optically active triptycene-based molecules ((R,R)-1 and (S,S)-1) containing two hexabenzocoronene moieties were synthesized and their optical and chiroptical properties were investigated. Optically active 1 emitted preferred-handed circularly polarized light upon UV irradiation, with the luminescence dissymmetry factors found to be approximately 1.0 × 10-3. Based on a comparative study using the analogous triptycene derivative with two hexaphenylbenzene units (2), which was the key precursor of 1, the ladder-type rigid structure with an asymmetrically bent geometry was important for optically active 1 to exhibit circularly polarized luminescence (CPL). We also showed that rac-1 undergoes conglomerate crystallization, which allowed CPL to be produced by a random selection of crystals prepared from rac-1.

One-Step Synthesis of One-Dimensional Supramolecular Assemblies Composed of Helical Macromolecular Building Blocks.

Living systems achieve sophisticated functions using supramolecular protein assemblies, in which the protein building blocks possess a specific secondary structure and are noncovalently arranged in a preprogrammed manner. Herein, we demonstrate the one-step synthesis of one-dimensional macromolecular assemblies by simply mixing a glycine-based isocyanide with a nickel catalyst, in which helical constituent polymers are linked end-to-end through multiple hydrogen bonds. The applicable scope of this approach is not confined to a particular monomer bearing a specially designed pendant, but covers a wide range of glycine-based isocyanides with or without aromatic and other functional groups. Surprisingly, copolymerization with an analogous chiral isocyanide (1 mol %) afforded an almost perfect one-handed helical supramolecular fiber owing to intramolecular/intermolecular dual chiral amplifications. The simplicity and broad applicability of this approach, which can also afford exquisite chiral amplification, enable the creation of a wide variety of functional supramolecular assemblies and provide access to new supramolecular materials.

Direct Observation of Long-Chain Branches in a Low-Density Polyethylene.

Low-density polyethylene (LDPE) has short-chain branch (SCB) and long-chain branch (LCB). In particular, the influence of the structure of LCBs on polymer properties is remarkable; however, it has been difficult to precisely analyze LCB structures. In this study, we measured the chain length of LCBs and the distance between branch points of LDPE by atomic force microscopy. Consequently, three LCBs were confirmed in a main chain of 162 nm, and their length were measured as 10, 31, and 18 nm. The positions of the LCBs were 33, 70, and 78 nm from the main-chain end.

Synthesis of a one-handed helical polythiophene: a new approach using an axially chiral bithiophene with a fixed syn-conformation.

We report an optically active polythiophene capable of forming a one-handed helically folded conformation without needing aggregate formation, poor solvent conditions, hydrogen-bonded ion-pair formation or guest addition. The target polythiophene (poly-TR) with a static axial chirality in the main chain was synthesized via Stille coupling copolymerization of a glucose-linked chiral 5,5'-dibromobithiophene with 2,5-bis(stannyl)thiophene. Poly-TR showed a characteristic circular dichroism and circularly polarized luminescence, which were completely different to those observed for an analogous polymer (poly-PhR) and the corresponding unimer/dimer model compounds. This chiroptical study, combined with the results of all-atom molecular dynamics simulations, revealed that poly-TR can fold into a left-handed helical conformation under good solvent conditions. Partial conformational regulation derived from the fixed syn-conformation of the chiral bithiophene unit was considered a key factor in producing the one-handed helical polythiophene.

Triptycene-Based Ladder Polymers with One-Handed Helical Geometry.

Here we report an efficient synthesis of optically active ladder-type molecules and polymers through intramolecular cyclization of chiral triptycenes containing bis[2-(4-alkoxyphenyl)ethynyl]phenylene units. The electrophile-induced cyclization reactions are directed away from the bridgehead carbon atoms of triptycene by steric factors, thereby producing one-handed twisted ladder units without any detectable byproducts. Moreover, the quantitative and regioselective nature of this intramolecular cyclization allowed us to synthesize optically active ladder polymers with a well-defined one-handed helical geometry in which homoconjugated dibenzo[ a, h]anthracene units are helically arranged along the main chain. This synthesis route enables the construction of a variety of nanoscale helical ladder architectures and provides an entry into new chiroptical materials.

Direct observation of dynamic interaction between a functional group in a single SBR chain and an inorganic matter surface.

As a composite of hybrid organic-inorganic materials, blending hydrophilic silica microparticles with oil-extended rubber can improve vehicle tire performance but the nanometer scale effects of microparticle inclusion have not been thoroughly studied. Here, we used atomic force microscopy (AFM) video imaging to closely investigate the behavior of functionalized and unmodified styrene-butadiene rubber (SBR), as models for tire rubber, on mica surfaces. The hydrophilic silica microparticle surface could be simulated by a mica substrate because both have silanol groups on their surface. Using AFM video imaging, we tracked the behavior of individual SBR polymer chains on mica surfaces to reveal how polymer modification affects the interaction of SBR with mica surfaces. We measured the diffusion coefficients and spring constants of single SBR polymer chains for the first time, demonstrating that it is possible to parameterize the relationship between the molecular dynamic structure of a polymer and rubber properties of the vulcanized compound.

Region-specific alteration of histone modification by LSD1 inhibitor conjugated with pyrrole-imidazole polyamide.

Epigenome regulates gene expression to determine cell fate, and accumulation of epigenomic aberrations leads to diseases, including cancer. NCD38 inhibits lysine-specific demethylase-1 (LSD1), a histone demethylase targeting H3K4me1 and H3K4me2, but not H3K4me3. In this study, we conjugated NCD38 with a potent small molecule called pyrrole (Py) imidazole (Im) polyamide, to analyze whether targets of the inhibitor could be regulated in a sequence-specific manner. We synthesized two conjugates using ß-Ala (ß) as a linker, i.e., NCD38-ß-ß-Py-Py-Py-Py (NCD38-ß2P4) recognizing WWWWWW sequence, and NCD38-ß-ß-Py-Im-Py-Py (NCD38-ß2PIPP) recognizing WWCGWW sequence. When RKO cells were treated with NCD38, H3K4me2 levels increased in 103 regions with significant activation of nearby genes (P = 0.03), whereas H3K4me3 levels were not obviously increased. H3K27ac levels were also increased in 458 regions with significant activation of nearby genes (P = 3 × 10-10), and these activated regions frequently included GC-rich sequences, but less frequently included AT-rich sequences (P < 1 × 10-15) or WWCGWW sequences (P = 2 × 10-13). When treated with NCD38-ß2P4, 234 regions showed increased H3K27ac levels with significant activation of nearby genes (P = 2 × 10-11), including significantly fewer GC-rich sequences (P < 1 × 10-15) and significantly more AT-rich sequences (P < 1 × 10-15) compared with NCD38 treatment. When treated with NCD38-ß2PIPP, 82 regions showed increased H3K27ac levels, including significantly fewer GC-rich sequences (P = 1 × 10-11) and fewer AT-rich sequences (P = 0.005), but significantly more WWCGWW sequences (P = 0.0001) compared with NCD38 treatment. These indicated that target regions of epigenomic inhibitors could be modified in a sequence-specific manner and that conjugation of Py-Im polyamides may be useful for this purpose.

Synthesis of Two Well-Defined Quadruple-Stranded Copolymers having Two Kinds of Backbones by Postpolymerization of a Helical Template Polymer.

A brand new, soluble quadruple-stranded copolymer is synthesized by using a self-template polymer from a new monomer. In addition, another very unique quadruple-stranded copolymer having a π-π stacking supramolecular polymer main chain is synthesized by selective photocyclic aromatization of the quadruple-stranded copolymer. The two quadruple-stranded copolymers gave self-standing membranes.

Frequent promoter hypermethylation associated with human papillomavirus infection in pharyngeal cancer.

Oropharyngeal squamous cell carcinoma (OPSCC) incidence has increased dramatically due to human papillomavirus (HPV); however, associated epigenetic alterations are not well studied. We performed genome-wide DNA methylation analysis using an Infinium 450k BeadArray for clinical OPSCC and non-cancerous samples and cancer cell lines with/without 5-aza-2'-deoxycytidine and/or trichostatin A treatment. Frequent promoter hypermethylation and methylation-associated silencing were detected in 144 genes, which included those involved in cell-cell signaling and neuron differentiation. The methylation of nine genes (GHSR, ITGA4, RXRG, UTF1, CDH8, FAN19A4, CTNNA2, NEFH, and CASR) was quantitatively validated in 70 pharyngeal SCC cases by pyrosequencing. Hypermethylation significantly correlated with HPV-L1 positivity, but not with age or smoking status. p16INK4A was generally activated in HPV-L1(+) tumors, and p16-positive cases significantly associated with better prognosis. RXRG hypermethylation strongly correlated with positivity of HPV-L1 and p16 (P = 3 × 10-5 and P = 5 × 10-4, respectively). RXRG-methylation(+) significantly associated with better prognosis when analyzing all tumor cases (P = 0.04), and when analyzing the p16-negative poorer-outcome group (P = 0.03). Thus, aberrant DNA methylation might be involved in HPV-associated OPSCC; in addition, DNA methylation could serve as a marker to classify subgroups based on outcome.

Synthesis of pyrrole-imidazole polyamide oligomers based on a copper-catalyzed cross-coupling strategy.

Pyrrole-imidazole (Py-Im) polyamides are useful tools for chemical biology and medicinal chemistry studies due to their unique binding properties to the minor groove of DNA. We developed a novel method of synthesizing Py-Im polyamide oligomers based on a Cu-catalyzed cross-coupling strategy. All four patterns of dimer fragments could be synthesized using a Cu-catalyzed Ullmann-type cross-coupling with easily prepared monomer units. Moreover, we demonstrated that pyrrole dimer, trimer, and tetramer building blocks for Py-Im polyamide synthesis were accessible by combining site selective iodination of the pyrrole/pyrrole coupling adduct.

Platinum-Catalyzed Friedel-Crafts-Type C-H Coupling-Allylic Amination Cascade to Synthesize 3,4-Fused Tricyclic Indoles.

A novel platinum-catalyzed cascade cyclization reaction was developed by intramolecular Friedel-Crafts-type C-H coupling of aniline derivatives with a propargyl carbonate unit-allylic amination sequence. Treatment of various propargyl carbonates tethered to meta-aniline derivatives with a Pt(dba)3/DPEphos catalyst system afforded the corresponding 3,4-fused tricyclic 3-alkylidene indolines in 42-99% yield, which were transformed into 3,4-fused indole derivatives by reaction with trifluoroacetic acid. The reaction products exhibited antiproliferative activities against cancer cells, but not normal cells, revealing the potential usefulness of this reaction for medicinal chemistry.

Inhibition of DNA Methylation at the MLH1 Promoter Region Using Pyrrole-Imidazole Polyamide.

Aberrant DNA methylation causes major epigenetic changes and has been implicated in cancer following the inactivation of tumor suppressor genes by hypermethylation of promoter CpG islands. Although methylated DNA regions can be randomly demethylated by 5-azacytidine and 5-aza-2'-deoxycytidine, site-specific inhibition of DNA methylation, for example, in the promoter region of a specific gene, has yet to be technically achieved. Hairpin pyrrole (Py)-imidazole (Im) polyamides are small molecules that can be designed to recognize and bind to particular DNA sequences. In this study, we synthesized the hairpin polyamide MLH1_-16 (Py-Im-ß-Im-Im-Py-γ-Im-Py-ß-Im-Py-Py) to target a CpG site 16 bp upstream of the transcription start site of the human MLH1 gene. MLH1 is known to be frequently silenced by promoter hypermethylation, causing microsatellite instability and a hypermutation phenotype in cancer. We show that MLH1_-16 binds to the target site and that CpG methylation around the binding site is selectively inhibited in vitro. MLH1_non, which does not have a recognition site in the MLH1 promoter, neither binds to the sequence nor inhibits DNA methylation in the region. When MLH1_-16 was used to treat RKO human colorectal cancer cells in a remethylating system involving the MLH1 promoter under hypoxic conditions (1% O2), methylation of the MLH1 promoter was inhibited in the region surrounding the compound binding site. Silencing of the MLH1 expression was also inhibited. Promoter methylation and silencing of MLH1 were not inhibited when MLH1_non was added. These results indicate that Py-Im polyamides can act as sequence-specific antagonists of CpG methylation in living cells.

Modulation of the EMT/MET process by pyrrole-imidazole polyamide targeting human transforming growth factor-ß1.

Transforming growth factor-ß1 (TGF-ß1) is a potent induction factor for epithelial-mesenchymal transition (EMT). Mesenchymal-epithelial transition (MET), as the inverse process of EMT, has recently been reported to promote the induction of induced pluripotent stem cells (iPSCs). We have developed pyrrole-imidazole (PI) polyamide, a novel gene regulator that targets human TGF-ß1, and investigated its effects on the EMT/MET process. PI polyamide targeted to TGF-ß1 significantly inhibited the mRNA expression of TGF-ß1 and SNAI1 as an EMT marker and increased mRNA and protein expression of E-cadherin in human epithelial cells. To enhance the induction of iPSCs by the MET process, PI polyamide targeted to TGF-ß1 was applied to human fibroblasts transfected with exogenous reprogramming factors by Sendai virus vector and grown in human iPSCs. The PI polyamide significantly increased the number of alkaline phosphatase-positive colonies. The expression of undifferentiated markers was also observed in these colonies. These results suggest that PI polyamide targeted to human TGF-ß is a novel compound that can control the EMT/MET process of human epithelial cells and enhance the induction of human fibroblasts to iPSCs.

Inhibition of KRAS codon 12 mutants using a novel DNA-alkylating pyrrole-imidazole polyamide conjugate.

Despite extensive efforts to target mutated RAS proteins, anticancer agents capable of selectively killing tumour cells harbouring KRAS mutations have remained unavailable. Here we demonstrate the direct targeting of KRAS mutant DNA using a synthetic alkylating agent (pyrrole-imidazole polyamide indole-seco-CBI conjugate; KR12) that selectively recognizes oncogenic codon 12 KRAS mutations. KR12 alkylates adenine N3 at the target sequence, causing strand cleavage and growth suppression in human colon cancer cells with G12D or G12V mutations, thus inducing senescence and apoptosis. In xenograft models, KR12 infusions induce significant tumour growth suppression, with low host toxicity in KRAS-mutated but not wild-type tumours. This newly developed approach may be applicable to the targeting of other mutant driver oncogenes in human tumours.