Conformation Dynamics of Single Polymer Strands in Solution.

Conformational changes in macromolecules significantly affect their functions and assembly into high-level structures. Despite advances in theoretical and experimental studies, investigations into the intrinsic conformational variations and dynamic motions of single macromolecules remain challenging. Here, liquid-phase transmission electron microscopy enables the real-time tracking of single-chain polymers. Imaging linear polymers, synthetically dendronized with conjugated aromatic groups, in organic solvent confined within graphene liquid cells, directly exhibits chain-resolved conformational dynamics of individual semiflexible polymers. These experimental and theoretical analyses reveal that the dynamic conformational transitions of the single-chain polymer originate from the degree of intrachain interactions. In situ observations also show that such dynamics of the single-chain polymer are significantly affected by environmental factors, including surfaces and interfaces.

Synchronous Preparation of Length-Controllable 1D Nanoparticles via Crystallization-Driven In Situ Nanoparticlization of Conjugated Polymers.

Precise size control of semiconducting nanomaterials from polymers is crucial for optoelectronic applications, but the low solubility of conjugated polymers makes this challenging. Herein, we prepared length-controlled semiconducting one-dimensional (1D) nanoparticles by synchronous self-assembly during polymerization. First, we succeeded in unprecedented living polymerization of highly soluble conjugated poly(3,4-dihexylthiophene). Then, block copolymerization of poly(3,4-dihexylthiophene)-block-polythiophene spontaneously produced narrow-dispersed 1D nanoparticles with lengths from 15 to 282 nm according to the size of a crystalline polythiophene core. The key factors for high efficiency and length control are a highly solubilizing shell and slow polymerization of the core, thereby favoring nucleation elongation over isodesmic growth. Combining kinetics and high-resolution imaging analyses, we propose a unique mechanism called crystallization-driven in situ nanoparticlization of conjugated polymers (CD-INCP) where spontaneous nucleation creates seeds, followed by seeded growth in units of micelles. Also, we achieved "living" CD-INCP through a chain-extension experiment. We further simplified CD-INCP by adding both monomers together in one-shot copolymerization but still producing length-controlled nanoparticles.

Semi-conducting 2D rectangles with tunable length via uniaxial living crystallization-driven self-assembly of homopolymer.

Semi-conducting two-dimensional (2D) nanoobjects, prepared by self-assembly of conjugated polymers, are promising materials for optoelectronic applications. However, no examples of self-assembled semi-conducting 2D nanosheets whose lengths and aspect ratios are controlled at the same time have been reported. Herein, we successfully prepared uniform semi-conducting 2D sheets using a conjugated poly(cyclopentenylene vinylene) homopolymer and its block copolymer by blending and heating. Using these as 2D seeds, living crystallization-driven self-assembly (CDSA) was achieved by adding the homopolymer as a unimer. Interestingly, unlike typical 2D CDSA examples showing radial growth, this homopolymer assembled only in one direction. Owing to this uniaxial growth, the lengths of the 2D nanosheets could be precisely tuned from 1.5 to 8.8 µm with narrow dispersity according to the unimer-to-seed ratio. We also studied the growth kinetics of the living 2D CDSA and confirmed first-order kinetics. Subsequently, we prepared several 2D block comicelles (BCMs), including penta-BCMs in a one-shot method.

Morphologically Tunable Square and Rectangular Nanosheets of a Simple Conjugated Homopolymer by Changing Solvents.

Two-dimensional (2D) polymer nanosheets have been attracting immense attention owing to their potential applications in optical devices, membranes, and catalysis. However, creating uniform monolayered 2D nanosheets through polymer self-assembly is very challenging, especially when using homopolymers. In this work, we designed a new crystalline polyacetylene that contains fluorenes and triisopropylsilyl side chains, which could self-assemble into sharp-edged 5-nm-thick square nanosheets with a narrow length dispersity of 1.01, by simple heating and aging in dichloromethane (DCM). Interestingly, the addition of tetrahydrofuran (THF) or chloroform to the heated polymer solution in DCM changed the morphology from square to rectangle. The aspect ratios increased linearly, from 1.0 to 10.6, according to the amount of THF or chloroform added, while maintaining narrow length dispersities less than 1.06. These unique fluorescent semiconducting nanosheets with tunable shapes exhibit high potential for optoelectronic applications.

Conformation of Tunable Nanocylinders: Up to Sixth-Generation Dendronized Polymers via Graft-Through Approach by ROMP.

Well-defined dendronized polymers (denpols) bearing high-generation dendron are attractive nano-objects as high persistency provides distinct properties, contrast to the random coiled linear polymers However, their syntheses via graft-through approach have been very challenging due to their structural complexity and steric hindrance retarding polymerization. Here, we report the first example of the synthesis of poly(norbornene) (PNB) containing ester dendrons up to the sixth generation (G6) by ring-opening metathesis polymerization. This is the highest generation ever polymerized among dendronized polymers prepared by graft-through approach, producing denpols with molecular weight up to 1960 kg/mol. Combination of size-exclusion chromatography, light scattering, and neutron scattering allowed a thorough structural study of these large denpols in dilute solution. A semiflexible cylinder model was successfully applied to represent both the static and dynamic experimental quantities yielding persistent length (l p), cross-sectional radius (R cs), and contour length (L). The denpol persistency seemed to increase with generation, with l p reaching 27 nm (Kuhn length 54 nm) for PNB-G6, demonstrating a rod-like conformation. Poly(endo-tricycle[4.2.2.0]deca-3,9-diene) (PTD) denpols exhibited larger persistency than the PNB analogues of the same generation presumably due to the higher grafting density of the PTD denpols. As the dendritic side chains introduce shape anisotropy into the denpol backbone, future work will entail a study of these systems in the concentrated solutions and melts.

BioVyon Protein A, an alternative solid-phase affinity matrix for chromatin immunoprecipitation.

Chromatin immunoprecipitation (ChIP) is an important technique in the study of DNA/protein interactions. The ChIP procedure, however, has limitations in that it is lengthy, can be inconsistent, and is prone to nonspecific binding of DNA and proteins to the bead-based solid-phase matrices that are often used for the immunoprecipitation step. In this investigation, we examined the utility of a new matrix for ChIP assays, BioVyon Protein A, a solid support based on porous polyethylene. In ChIP experiments carried out using two antibodies and seven DNA loci, the performance of BioVyon Protein A was significantly better, with a greater percentage of DNA pull-down in all of the assays tested compared with bead-based matrices, Protein A Sepharose, and Dynabeads Protein A. Furthermore, the rigid porous disc format within a column made the BioVyon matrix much easier to use with fewer steps and less equipment requirements, resulting in a significant reduction in the time taken to process the ChIP samples. In summary, BioVyon Protein A provides a column-based assay method for ChIP and other immunoprecipitation-based procedures; the rigid porous structure of BioVyon enables a fast and robust protocol with higher ChIP enrichment ratios.

Probing the roles of active site residues in the 3'-5' exonuclease of the Werner syndrome protein.

Werner syndrome is a premature aging disease caused by mutations in the WS gene and a deficiency in the function of Werner protein (WRN). The lack of WRN results in a cellular phenotype of genomic instability. WRN belongs to the RecQ DNA helicase family, but unlike other RecQ family members it possesses a functional exonuclease domain. We determined the crystal structure of mWRNexo (residues 31-238) bound to Zn(2+) and the sulfate ion. Compared with the structure of human WRNexo (hWRNexo), notable conformational changes were observed in several active site residues in an H5-H6 loop and in helices H6 and H7 of mWRNexo, presumably because of the presence of sulfate, which mimics the phosphate of substrate DNA. In particular, the side chains of Lys(185) and Tyr(206) were reoriented toward the Zn(2+) ion, whereas the side chain of Arg(190) pointed away from the active site center. Mutational analysis of these conserved residues abolished WRN exonuclease activity, suggesting that these residues play a critical role in the WRNexo activity. Based on substrate modeling and mutational analyses, we propose a mechanism by which WRNexo becomes activated upon substrate DNA binding. We also describe the low resolution trimeric structure of mouse WRNexoL (mWRNexoL, residues 31-330), as elucidated by small angle x-ray scattering (SAXS) analyses.

CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide.

CTCF is a transcription factor with highly versatile functions ranging from gene activation and repression to the regulation of insulator function and imprinting. Although many of these functions rely on CTCF-DNA interactions, it is an emerging realization that CTCF-dependent molecular processes involve CTCF interactions with other proteins. In this study, we report the association of a subpopulation of CTCF with the RNA polymerase II (Pol II) protein complex. We identified the largest subunit of Pol II (LS Pol II) as a protein significantly colocalizing with CTCF in the nucleus and specifically interacting with CTCF in vivo and in vitro. The role of CTCF as a link between DNA and LS Pol II has been reinforced by the observation that the association of LS Pol II with CTCF target sites in vivo depends on intact CTCF binding sequences. "Serial" chromatin immunoprecipitation (ChIP) analysis revealed that both CTCF and LS Pol II were present at the beta-globin insulator in proliferating HD3 cells but not in differentiated globin synthesizing HD3 cells. Further, a single wild-type CTCF target site (N-Myc-CTCF), but not the mutant site deficient for CTCF binding, was sufficient to activate the transcription from the promoterless reporter gene in stably transfected cells. Finally, a ChIP-on-ChIP hybridization assay using microarrays of a library of CTCF target sites revealed that many intergenic CTCF target sequences interacted with both CTCF and LS Pol II. We discuss the possible implications of our observations with respect to plausible mechanisms of transcriptional regulation via a CTCF-mediated direct link of LS Pol II to the DNA.