DNA-Grafted Supramolecular Polymers: Helical Ribbon Structures Formed by Self-Assembly of Pyrene-DNA Chimeric Oligomers

The controlled arraying of DNA strands on adaptive polymeric platforms remains a challenge. Here, the noncovalent synthesis of DNA-grafted supramolecular polymers from short chimeric oligomers is presented. The oligomers are composed of an oligopyrenotide strand attached to the 5′-end of an oligodeoxynucleotide. The supramolecular polymerization of these oligomers in an aqueous medium leads to the formation of one-dimensional (1D) helical ribbon structures. Atomic force and transmission electron microscopy show rod-like polymers of several hundred nanometers in length. DNA-grafted polymers of the type described herein will serve as models for the development of structurally and functionally diverse supramolecular platforms with applications in materials science and diagnostics.

Valle d’Aosta section of the Sesia Zone: multi-stage HP metamorphism and assembly of a rifted continental margin

The spectrum characteristic of the EMC ranges from eclogites (containing omphacite and/or jadeite, garnet, phengite, glaucophane, zoisite, chloritoid, rutile) to phengite schists, calcschists, and marbles, as well as a variety of orthogneisses. Despite the intense polyphase deformation and HP-metamorphic recrystallization, it is possible in some locations to recognize pre-Alpine characteristics in some of the protoliths. For instance, two types of felsic orthogneiss can be distinguished in the Aosta Valley, one derived from Permian granitoids (with local preservation of intrusive contacts, magmatic inclusions, leucocratic veins and other magmatic structures; Stop 3), the other derived from pre-Variscan leuco-monzogranite, such as the building stone mined at the “Argentera” quarry near Settimo Vittone / Montestrutto (Stop 2; so-called “Verde Argento” contains jadeite, phengite, K-feldspar, quartz). Polycyclic and more rarely monocyclic metasediments contain evidence of a complex Alpine PTDt-evolution, locally including relics of their prograde history from blueschist, one or more stages at eclogite facies. Recent petrochronological studies have dated this HP-evolution of the Sesia Zone in some detail. In the area visited, clear evidence of HP-cycling has been identified in one km-size tectonic slice (Stop 1), but not in adjacent parts of the EMC, indicating “yo-yo tectonics”. Partial retrogression and attendant ductile to brittle deformation of the HP-rocks is evident in one of the outcrops (Stop 4). Apart from the four localities in the Sesia Zone, a final outcrop introduces HP-rocks of the adjacent Piemonte oceanic unit, specifically calc-schists and ophiolite members of the “Zermatt-Saas” zone. The hilltop outcrop (Stop 5) displays foliated antigorite schist with peridotite relics (clinopyroxene, spinel) containing lenses derived from doleritic dykes. These fine-grained metarodingites and the folded veins containing Mg-chlorite and titanoclinohumite within serpentinite once again indicate equilibration under low-temperature eclogite facies conditions. However, these units reached that HP stage more than 20 Ma after the youngest eclogite facies imprint recognized in the Sesia Zone. Despite nearly half a century of intense study in the Sesia Zone, the complex assembly of its HP-terranes and their relation to more external parts of the Western Alps remains incompletely understood. This field guide merely introduces a few of the classic outcrops and discusses some of the critical evidence they contain, but it could not incorporate details on each stage of the evolution recognized so far.

Coordination-directed self-assembly of a simple benzothiadiazole-fused tetrathiafulvalene to low-bandgap metallogels

Coordination-driven gelation of a benzothiadiazole-fused tetrathiafulvalene (TTF) is demonstrated. This is the first work reporting highly stable metallogels based on a donor-acceptor conjugate with such a simple structure for the construction of new low-bandgap materials with various functional properties and novel nanostructures.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Hierarchical self-assembly of the DNA-grafted supramolecular polymers

Conjugation of functional entities with a specific set of optical, mechanical or biological properties to DNA strands allows engineering of sophisticated DNA-containing architectures. Among various hybrid systems, DNA-grafted polymers occupy an important place in modern materials science. In this contribution we present the non-covalent synthesis and properties of DNA-grafted linear supramolecular polymers (SPs), which are assembled in a controllable manner from short chimeric DNA-pyrene oligomers. The synthetic oligomers consist of two parts: a 10 nucleotides long DNA chain and a covalently attached segment of variable number of phosphodiester-linked pyrenes. The temperature-dependent formation of DNA-grafted SPs is described by a nucleation-elongation mechanism. The high tendency of pyrenes to aggregate in water, leads to the rapid formation of SPs. The core of the assemblies consists of stacked pyrenes. They form a 1D platform, to which the DNA chains are attached. Combined spectroscopic and microscopic studies reveal that the major driving forces of the polymerization are π-stacking of pyrenes and hydrophobic interactions, and DNA pairing contributes to a lesser extent. AFM and TEM experiments demonstrate that the 1D SPs appear as elongated ribbons with a length of several hundred nanometers. They exhibit an apparent helical structure with a pitch-to-pitch distance of 50±15 nm. Since DNA pairing is a highly selective process, the ongoing studies are aimed to utilize DNA-grafted SPs for the programmable arrangement of functional entities. For example, the addition of non-modified complementary DNA strands to the DNA-grafted SPs leads to the cooperative formation of higher-order assemblies. Also, our experiments suggest that the fluorescent pyrene core of 1D ribbons serves as an efficient donor platform for energy transfer applications.

Revealing Assembly of a Pore-Forming Complex Using Single-Cell Kinetic Analysis and Modeling

Many biological processes depend on the sequential assembly of protein complexes. However, studying the kinetics of such processes by direct methods is often not feasible. As an important class of such protein complexes, pore-forming toxins start their journey as soluble monomeric proteins, and oligomerize into transmembrane complexes to eventually form pores in the target cell membrane. Here, we monitored pore formation kinetics for the well-characterized bacterial pore-forming toxin aerolysin in single cells in real time to determine the lag times leading to the formation of the first functional pores per cell. Probabilistic modeling of these lag times revealed that one slow and seven equally fast rate-limiting reactions best explain the overall pore formation kinetics. The model predicted that monomer activation is the rate-limiting step for the entire pore formation process. We hypothesized that this could be through release of a propeptide and indeed found that peptide removal abolished these steps. This study illustrates how stochasticity in the kinetics of a complex process can be exploited to identify rate-limiting mechanisms underlying multistep biomolecular assembly pathways.

STUDIES ON THE MECHANISM OF ASSEMBLY OF MURINE LEUKEMIA VIRUS

The purpose of this research was to elucidate the mechanism of assembly of retroviruses, specifically of murine leukemia virus, as studied through the treatment of virus-infected cells with interferon and through the use of temperature sensitive (ts) mutants. Our studies have shown a rapid and specific association of Rauscher murine leukemia virus (R-MuLV) precursor polyprotein Pr65('gag) with cytoskeletal elements in infected mouse fibroblasts. The Pr65('gag) associated with Nonidet P-40 (NP40)-insoluble cytoskeletal structures appeared to be subphosphorylated in comparison to NP40-soluble Pr65('gag). The association of Pr65('gag) with skeletal elements could be disrupted by extraction of the cytoskeleton with sodium deoxycholate, an ionic detergent. Both the skeleton-associated Pr65('gag) and its NP40-soluble counterpart were labeled with {('3)H}-palmitate, indicating their probable association with lipids presumably in the plasma membrane. Pr65('gag) molecules bound to skeletal elements in the infected cell appeared to be more stable to proteolytic processing than NP40-soluble Pr65('gag). Our studies with certain ts mutants of murine leukemia virus, defective in virus assembly, including Mo-MuLV ts3 and R-MuLV ts17, ts24, ts25 and ts26, have shown that virions released at 39(DEGREES)C (nonpermissive temperature) had high levels of uncleaved Pr65('gag) relative to that seen in virions released at 33(DEGREES)C (permissive temperature). Examination of cell extracts revealed that Pr54('gag) was more stable to processing at 39(DEGREES)C than at 33(DEGREES)C, whereas the 'env' and glycosylated 'gag' proteins were processed to the same extent at both temperatures. Detergent extraction of pulse-labeled cells to generate an NP40-insoluble cytoskeleton-enriched fraction showed that in ts3-, ts17- and ts24-infected cells, Pr65('gag) accumulated in the cytoskeleton-enriched fraction. In contrast, cells infected with ts25 or ts26 showed no preferential localization of Pr65('gag) in the cytoskeleton in a short pulse, but instead, Pr65('gag) accumulated in both the NP40-soluble and -insoluble fractions during a chase-incubation. The association of Pr65('gag) with cytoskeletal elements in the cell was neither increased nor decreased by blocking virus assembly and release with interferon. Based on these and other results, we have proposed a model for the active role of cytoskeleton-associated Pr65('gag) in retrovirus assembly.^

Role of phosphatidylethanolamine in the function and assembly of phenylalanine-specific permease of Escherichia coli

Transmembrane segments of polytopic membrane proteins once inserted are generally considered stably oriented due to the large free energy barrier for topological reorientation of adjacent extra-membrane domains. However, proper topology and function of the polytopic membrane protein lactose permease (LacY) of Escherichia coli is dependent on the membrane phospholipid composition revealing topological dynamics of transmembrane domains (Bogdanov, M., Heacock, P. N., and Dowhan, W. (2002) EMBO J. 21, 2107–2116). The high affinity phenylalanine permease PheP shares many topological similarities with LacY. In this study, mutant E. coli cells lacking phosphatidylethanolamine (PE) as a membrane component were used to evaluate the role of PE in the function and assembly of PheP. Active transport of phenylalanine by cells lacking PE was severely inhibited (both Vmax and Km were altered), whereas the PheP protein level in membranes was unaffected. Cysteine residues were introduced into predicted periplasmic or cytoplasmic segments of cysteine-less PheP, and the topology of the protein was explored using a membrane-impermeable thiol-specific biotinylated probe. Based on the biotinylation patterns of PheP in whole cells, the N-terminus and adjoining transmembrane hairpin of PheP adopted an inverted topological orientation in PE-lacking cells. Introduction of PE following the assembly of PheP triggered a reorientation of the N-terminus and adjacent hairpin to their native orientation associated with regain of wild type transport function. These results coupled with the results for LacY support a specific role for membrane lipid composition in determining topological organization and function of membrane proteins. Several other secondary symporters are compromised for activity in PE-lacking cells suggesting that lipid-assisted topogenesis is a general property of such transporters. The reversible orientation of these secondary transport proteins in response to a change of phospholipid composition might be a result of inherent conformational flexibility necessary for transport function or during protein assembly. ^

An eco-friendly way to fire retardant flexible polyurethane foam: layer-by-layer assembly of fully bio-based substances

The objective of the present study is to develop fully renewable and environmentally benign techniques for improving the fire safety of flexible polyurethane foams (PUFs). A multilayered coating made from cationic chitosan (CS) and anionic alginate (AL) was deposited on PUFs through layer-by-layer assembly. This coating system exhibits a slight influence on the thermal stability of PUF, but significantly improves the char formation during combustion. Cone calorimetry reveals that 10 CS-AL bilayers (only 5.7% of the foams weight) lead to a 66% and 11% reduction in peak heat release rate and total heat release, respectively, compared with those of the uncoated control. The notable decreased fire hazards of PUF are attributed to the CS-AL coatings being beneficial to form an insulating protective layer on the surface of burning materials that inhibits the oxygen and heat permeation and slows down the flammable gases in the vapor phase, and thereby improves the flame resistance. This water-based, environmentally benign natural coating will stimulate further efforts in improving fire safety for a variety of polymer substrates.

Assembly of a catalytic unit for RNA microhelix aminoacylation using nonspecific RNA binding domains

An assembly of a catalytic unit for aminoacylation of an RNA microhelix is demonstrated here. This assembly may recapitulate a step in the historical development of tRNA synthetases. The class-defining domain of a tRNA synthetase is closely related to the primordial enzyme that catalyzed synthesis of aminoacyl adenylate. RNA binding elements are imagined to have been added so that early RNA substrates could be docked proximal to the activated amino acid. RNA microhelices that recapitulate the acceptor stem of modern tRNAs are potential examples of early substrates. In this work, we examined a fragment of Escherichia coli alanyl-tRNA synthetase, which catalyzes aminoacyl adenylate formation but is virtually inactive for catalysis of RNA microhelix aminoacylation. Fusion to the fragment of either of two unrelated nonspecific RNA binding domains activated microhelix aminoacylation. Although the fusion proteins lacked the RNA sequence specificity of the natural enzyme, their activity was within 1–2 kcal⋅mol−1 of a truncated alanyl-tRNA synthetase that has aminoacylation activity sufficient to sustain cell growth. These results show that, starting with an activity for adenylate synthesis, barriers are relatively low for building catalytic units for aminoacylation of RNA helices.

Self-assembly of fibronectin into fibrillar networks underneath dipalmitoyl phosphatidylcholine monolayers: Role of lipid matrix and tensile forces

The cell-mediated assembly of fibronectin (Fn) into fibrillar matrices is a complex multistep process that is incompletely understood because of the chemical complexity of the extracellular matrix and a lack of experimental control over molecular interactions and dynamic events. We have identified conditions under which Fn assembles into extended fibrillar networks after adsorption to a dipalmitoyl phosphatidylcholine (DPPC) monolayer in contact with physiological buffer. We propose a sequential model for the Fn assembly pathway, which involves the orientation of Fn underneath the lipid monolayer by insertion into the liquid expanded (LE) phase of DPPC. Attractive interactions between these surface-anchored proteins and the liquid condensed (LC) domains leads to Fn enrichment at domain edges. Spontaneous self-assembly into fibrillar networks, however, occurs only after expansion of the DPPC monolayer from the LC phase though the LC/LE phase coexistence. Upon monolayer expansion, the domain boundaries move apart while attractive interactions among Fn molecules and between Fn and domain edges produce a tensile force on the proteins that initiates fibril assembly. The resulting fibrils have been characterized in situ by using fluorescence and light-scattering microscopy. We have found striking similarities between fibrils produced under DPPC monolayers and those found on cellular surfaces, including their assembly pathways.

Probing the assembly of transcription initiation complexes through changes in σN protease sensitivity

The alternative bacterial σN RNA polymerase holoenzyme binds promoters as a transcriptionally inactive complex that is activated by enhancer-binding proteins. Little is known about how sigma factors respond to their ligands or how the responses lead to transcription. To examine the liganded state of σN, the assembly of end-labeled Klebsiella pneumoniae σN into holoenzyme, closed promoter complexes, and initiated transcription complexes was analyzed by enzymatic protein footprinting. V8 protease-sensitive sites in free σN were identified in the acidic region II and bordering or within the minimal DNA binding domain. Interaction with core RNA polymerase prevented cleavage at noncontiguous sites in region II and at some DNA binding domain sites, probably resulting from conformational changes. Formation of closed complexes resulted in further protections within the DNA binding domain, suggesting close contact to promoter DNA. Interestingly, residue E36 becomes sensitive to proteolysis in initiated transcription complexes, indicating a conformational change in holoenzyme during initiation. Residue E36 is located adjacent to an element involved in nucleating strand separation and in inhibiting polymerase activity in the absence of activation. The sensitivity of E36 may reflect one or both of these functions. Changing patterns of protease sensitivity strongly indicate that σN can adjust conformation upon interaction with ligands, a property likely important in the dynamics of the protein during transcription initiation.

Monitoring the assembly of Ig light-chain amyloid fibrils by atomic force microscopy

Aggregation of Ig light chains to form amyloid fibrils is a characteristic feature of light-chain amyloidosis, a light-chain deposition disease. A recombinant variable domain of the light chain SMA was used to form amyloid fibrils in vitro. Fibril formation was monitored by atomic force microscopy imaging. Single filaments 2.4 nm in diameter were predominant at early times; protofibrils 4.0 nm in diameter were predominant at intermediate times; type I and type II fibrils 8.0 nm and 6.0 nm in diameter, respectively, were predominant at the endpoints. The increase in number of fibrils correlated with increased binding of the fluorescent dye thioflavin T. The fibrils and protofibrils showed a braided structure, suggesting that their formation involves the winding of protofibrils and filaments, respectively. These observations support a model in which two filaments combine to form a protofibril, two protofibrils intertwine to form a type I fibril, and three filaments form a type II fibril.

Functional domains for assembly of histones H3 and H4 into the chromatin of Xenopus embryos

Histones H3 and H4 have a well defined structural role in the nucleosome and an established role in the regulation of transcription. We have made use of a microinjection strategy using Xenopus embryos to define the minimal structural components of H3 and H4 necessary for nucleosome assembly into metazoan chromosomes in vivo. We find that both the N-terminal tail of H4, including all sites of acetylation, and the C-terminal α-helix of the H4 histone fold domain are dispensable for chromatin assembly. The N-terminal tail and an N-terminal α-helix of H3 are also dispensable for chromatin assembly. However, the remainder of the H3 and H4 histone folds are essential for incorporation of these proteins into chromatin. We suggest that elements of the histone fold domain maintain both nucleosomal integrity and have distinct functions essential for cell viability.