Core-shell Au nanoparticle formation with DNA-polymer hybrid coatings using aqueous ATRP

We report here a direct surface-grafting approach to forming DNA-containing polymer shells outside of Au nanoparticles using aqueous atom transfer radical polymerization (ATRP). In this approach, DNA molecules were immobilized on Au particles to introduce ATRP initiators on the surface. The same DNA molecules also acted as particle stabilizers through electrostatic repulsion and allowed particles to stay suspended in water. The immobilized ATRP initiators prompted polymer chain growth under certain conditions to form thick polymer shells outside of the particles. The formation of DNA-polymer hybrids outside of Au nanoparticles was characterized using absorption spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), and gel electrophoresis. The presence of thick polymer shells improved particle stability in high ionic strength media, whereas particles with the DNA coating only aggregated. A visible color difference between these two particle solutions was clearly observed, providing the basis for DNA sensing in homogeneous solutions.     

The template synthesis of dimetallic complexes

The Fe^II ion acts as a template to generate a dinuclear triple-stranded complex, in which two tris-diimine compartments are separated by rigid diphenylurea spacers. The template reaction involves the combination of 11 particles and leads to the formation of a single highly symmetrical product, as shown by X-ray diffraction studies. The diiron(II) complex undergoes reversible oxidation to the Fe^III derivative. On the other hand, the Cu^I centre promotes the template formation of a double stranded dinuclear complex, which shows a total and unique resistance to the oxidation to Cu^II. Such an intriguing feature results (i) from the bulkiness of the substituents, which hinders the planarization of the donor set, and (ii) from the rigidity of the diphenylurea spacers, which prevent disassembling of the double stranded complex and formation of two mononuclear chelated Cu^I species.     

Self-assembly and polymerization of diacetylene-containing peptide amphiphiles in aqueous solution

A systematic study was performed of the fiber forming properties and polymerization characteristics of two peptide amphiphiles containing a diacetylene functionality in the alkyl tail comprising 23 and 25 C atoms, respectively. Both diyne containing peptide amphiphiles were able to form stable beta-sheet fibers of micrometers length in an aqueous solution. However, there was a large difference between the stability of the two amphiphiles. This was shown by a large difference in assembly and disassembly temperature and by different behavior during polymerization. Because the monomers were preorganized with a tight molecular packing, the polymerization could be carried out using wavelengths up to 532 nm. For both amphiphiles, the fiber structure did not change when the polymerization was carried out at an elevated temperature. The degree of polymerization, however, barely decreased for the longer amphiphile (2) but showed a gradual decline for the shorter one (1) when the temperature was raised from room temperature to the melting temperature of the fibers. Furthermore, the pH did not influence the fiber assembly for 2, but hampered it for 1 at alkaline pH. The fiber structure was, for both of the amphiphiles, not dependent on the pH. After polymerization, the molecular packing of the amphiphiles was only slightly influenced by an increase in temperature, as indicated by the small color change of polymerized fibers, which was also reversible. Additionally, pH had no influence on the assembly structure, as indicated by the color of the polymer which was the same at all pH values. Thus, both fibers increased in stability upon polymerization. The large difference in assembly and polymerization behavior of the two similar-looking amphiphiles 1 and 2, with a 23 or 25 carbon tail, is indicative of the subtlety of the assembly and disassembly processes in these fibrous architectures.     

Self-assembly polymerization enhances the immunogenicity of influenza M2e peptide

The extracellular domain of Influenza M2 protein (M2e) was considered as a promising target for universal influenza vaccine development. Several M2e-based influenza vaccines have been developed and many of them used a mutant M2e peptide, in which the two conserved cysteine residues were substituted by serine residues. In this paper, we compared the antigenicity and immunogenicity of wild type and cysteine-mutant M2e peptides. We found that the cysteine substitution slightly affected the antigenicity of M2e epitope, but greatly reduced the immunogenicity of M2e peptide. The cysteine substitution also disabled the M2e peptide from inducing protection against influenza virus challenge in mice. Further analysis revealed that the immunogenicity of M2e peptide was enhanced by the self-assembly of the peptide through inter-peptide disulfide bonds. These results provide new information to improve the design of M2e-based vaccines against potential influenza pandemics.     

Review: Selective ligand-exchange adsorbents prepared by template polymerization

Highly selective ligand-exchange absorbents have been prepared by template polymerization, a process in which the target molecule serves as a template for assembly of specific recognition sites. In an effort to develop materials suitable for chromatographic separations, thin coatings of the selctive templated polymers have been grafted to two reactive macroporous supports, poly(trimethylolpropane trimethacrylate) (TRIM), and propylmethacrylate-derivatized silica beads. The precursor polymer prepared from the trifunctioal TRIM monomer is macroporous and highly crosslinked, providing a stable structure for surface grafting. The TRIM precursor polymer and various surface-grafted copolymers have been characterized by scanning electron microscopy (SEM) and IR, (13)C NMR, and XPS spectroscopic techniques. Composite adsorbents have also been prepared using propylmethacrylate-modified silica particles. While equilibrium rebinding selectivites for both types of surface-templated materials are similar to those reported previously for bulk-polymerized template polymers, the composite materials are far better suited to chromatographic separatios. Highly similar bis-imidazole substrates can be separated by ligand-exchange chromatography on these new templated adsorbents. (c) 1995 John Wiley & Sons, Inc.     

Self-assembly of cationic palladium complexes by redistribution of pyridine ligands

The reaction of [Pd(OAc)₂(py)₂] with [Li((OEt₂)_2.5)][B(C₆F₅)₄] was conducted with intent to generate the cationic palladium complex [Pd(OAc)(py)₃][B(C₆F₅)₄], (2, py = pyridine). A single crystal structure of this material, however, reveals a 1-D polymer structure formed by the self-assembly of alternating dicationic ([Pd(py)₄]²⁺) and neutral ([Pd(OAc)₂(py)₂]) palladium units bridged by acetato linkages to give [Pd(py)₄][Pd(OAc)₂(py)₂][B(C₆F₅)₄]₂ (3). These two palladium sites are produced by disproportionation of the pyridine ligands in [Pd(OAc)(py)₃][B(C₆F₅)₄]. Proton NMR studies confirm the existence of a solvent dependent equilibrium between [Pd(py)₄]²⁺, [Pd(OAc)₂(py)₂] and [Pd(OAc)(py)₃]⁺.     

Self-assembly of Escherichia coli MutL and its complexes with DNA

The Escherichia coli MutL protein regulates the activity of several enzymes, including MutS, MutH, and UvrD, during methyl-directed mismatch repair of DNA. We have investigated the self-association properties of MutL and its binding to DNA using analytical sedimentation velocity and equilibrium. Self-association of MutL is quite sensitive to solution conditions. At 25 °C in Tris at pH 8.3, MutL assembles into a heterogeneous mixture of large multimers. In the presence of potassium phosphate at pH 7.4, MutL forms primarily stable dimers, with the higher-order assembly states suppressed. The weight-average sedimentation coefficient of the MutL dimer in this buffer ( ?s(20,w)) is equal to 5.20 ± 0.08 S, suggesting a highly asymmetric dimer (f/f(o) = 1.58 ± 0.02). Upon binding the nonhydrolyzable ATP analogue, AMPPNP/Mg(2+), the MutL dimer becomes more compact ( ?s(20,w) = 5.71 ± 0.08 S; f/f(o) = 1.45 ± 0.02), probably reflecting reorganization of the N-terminal ATPase domains. A MutL dimer binds to an 18 bp duplex with a 3'-(dT(20)) single-stranded flanking region, with apparent affinity in the micromolar range. AMPPNP binding to MutL increases its affinity for DNA by a factor of ～10. These results indicate that the presence of phosphate minimizes further MutL oligomerization beyond a dimer and that differences in solution conditions likely explain apparent discrepancies in previous studies of MutL assembly.     

The investigation of peptide-oligodeoxythymidylic acid interactions using template chromatography.

Poly(vinyl alcohol) has been substituted with oligodeoxythymidylic acid and the resulting polyanion irreversibly attached to DEAE-cellulose via ionic bonding. Peptide-oligonucleotide interactions have been studied using a column chromatography technique with the PV(pT)n-DEAE-cellulose as stationary phase. Of all the naturally occurring amino acids, only tryptophan and to a lesser extent tyrosine intreact significantly with the immobilized oligodeoxythymidylic acid residues under the conditions for base pairing. The homopolymers of tryptophan and tyrosine undergo greater retardation than the monomers, such that the effect is not additive but multiplicative. Thus Tyr-Tyr-Tyr shows an eightfold and Trp-Trp-Trp an approximately 30-fold larger retardation than tyrosine and tryptophan, respectively. The peptide-oligonucleotide interaction decreases considerably when nonaromatic amino acids are present in the peptide. Consequently, naturally occurring peptides and proteins which contain relatively small amounts of tryptophan and tyrosine compared with the nonaromatic amino acids undergo at the most only slight retardation on the PV(pT)n-DEAE-cellulose. The retention of oligonucleotides and peptides containing these aromatic amino acids is due in both cases mainly to base stacking (roughly 67% of the total interaction) but involves different mechanisms. Thus, the peptides interact preferably with the cellulose matrix whereas the oligonucleotides with the immobilized oligonucleotides. Interaction via hydrogen-bond formation makes up the remaining 33% of the total interaction. The oligonucleotides and peptides of the mobile phase interact with each other also via this mechanism. The strength of the d(pA-A-A) interaction is roughly that of Trp-Trp whereas d(pA-A-A-A) is weaker than Trp-Trp-Trp.     

tRNA maturation: RNA polymerization without a nucleic acid template

The CCA-adding enzyme, which builds and repairs the 3' terminal CCA sequence of tRNA, is the only RNA polymerase that can synthesize a defined nucleotide sequence without using a nucleic acid template. New cocrystal structures tell us how this remarkable enzyme works.     

Solid phase in vitro mutagenesis using plasmid DNA template.

Site-specific mutagenesis was accomplished using a solid support to generate single stranded vector and insert fragments which can be used to form gap-duplex plasmids through flanking, complementary double stranded regions. More than 80% mutants were obtained in both a single and a double primer approach. No special vectors or strains are needed and mismatch repair is avoided as the mutagenesis region is in a single stranded form when transformed into the Escherichia coli host cell. The fragments to be immobilized can be produced either by a polymerase chain reaction using general primers or by a site-specific restriction followed by a fill-in reaction. This novel method is rapid, simple and flexible and well suited for both manual and semi-automated in vitro mutagenesis protocols.     

The effect of antibiotics on the T4 polynucleotide ligase catalyzed template dependent polymerization of oligodeoxythymidylates.

The poly(dA) dependent T4 polynucleotide ligase catalyzed polymerization of oligodeoxythymidylates is dependent upon duplex stability. The antibiotics ethidium bromide, netropsin and Hoechst 33258 stabilize the duplex poly(dA) . P(dT)n (n = 6-10) to thermal denaturation. Ethidium bromide to DNA ratio of 1.25 and netropsin or Hoechst 33258 to DNA ratio of 0.1 the Tm of d(pT) 10 . poly (dA) was increased by 10 degrees and 25 degrees C respectively. The T4 polynucleotide ligase activity was not inhibited under these conditions and temperature optimum of joining of d(pT) 10 . poly(dA) was increased 5 degrees to 10 degrees by the binding of the antibiotics. Duplexes containing shorter oligodeoxythymidylates required lower concentrations of the antibiotics netropsin or Hoechst 33258 to show no inhibition of T4 polynucleotide ligase. The temperature optima of joining the duplexes d(pT)6 . POLY(DA) and d(pT) 8 . poly(dA) were increased by 5 degrees C upon binding of the antibiotics. Polyacrylamide gel analysis of the T4 polynucleotide ligase catalyzed joining of the oligodeoxythymidylates showed that the presence of antibiotics affected the product distribution of the polymerized oligomers.     

Self-assembly of biological macromolecules.

The genetic apparatus of the cell is responsible for the accurate biosynthesis of the primary structure of macromolecules which then spontaneously fold up and, in certain circumstances, aggregate to yield the complex tertiary and quaternary structures of the biologically active molecules. Structures capable of self-assembly in this range from simple monomers through oligomers to complex multimeric structures that may contain more than one type of polypeptide chain and components other than protein. It is becoming clear that even with the simpler monomeric enzymes there is becoming clear that even with the simpler monomeric enzymes there is a kinetically determined pathway for the folding process and that a folded protein must now be regarded as the minimum free energy form of the kinetically accessible conformations. It is argued that the denatured subunits of oligomeric enzymes are likely to fold to something like their final structure before aggregating to give the native quaternary structure and the available evidence would suggest that this is so. The importance of nucleation events and stable intermediates in the self-assembly of more complex structures is clear. Many self-assembling structures contain only identical subunits and symmetry arguments are very successful in accounting for the structures formed. Because proteins are themselves complex molecules and not inelastic geometric objects, the rules of strict symmetry can be bent and quasi-equivalent bonding between subunits permitted. This possibility is frequently employed in biological structures. Conversely, symmetry arguments can offer a reliable means of choosing between alternative models for a given structure. It can be seen that proteins gain stability by growing larger and it is argued in evolutionary terms that aggregation of subunits is the preferred way to increase the size of proteins. The possession of quaternary structure by enzymes allows conferral of other biologically important properties, such as cooperativity between active sites, changes of specificity, substrate channelling and sequential reactions within a multi-enzyme complex. Comparison is made of the invariant subunit compositions of the simpler oligomeric enzymes with the variation evidently open to, say, the 2-oxoacid dehydrogenase complexes of E. coli. With viruses, on the other hand, the function of the quaternary structure is to package nucleic acid and, as an example, the assembly and breakdown of tobacco mosaic virus is discussed. Attention is drawn to the possible ways in which the principles of self-assembly can be extended to make structures more complicated than those that can be formed by simple aggregation of the comonent parts.     

Self-assembly of membrane junctions.

We present a mechanism for the aggregation of mobile intermembrane junctions, such as the connexon dyad of gap junctions. The model demonstrates that intermembrane repulsion provides a powerful self-assembly pressure. If the membrane repulsion is strong enough to prevent membrane adhesion, then the self-assembly pressure is of effective infinite range.     

Increased intestinal chromatin template activity. Influence of 1alpha,25-dihydroxyvitamin D3 and hormone-receptor complexes.

1alpha,25-Dihydroxyvitamin D3 administration to rachitic chicks results in an increase in the chromatin template activity of intestinal target tissue assayed in vitro using Escherichia coli RNA polymerase. The maximum stimulation of template capacity was 12 to 20% over control values and occurred 2 hours after administration of the sterol. This rapid effect preceded the biologic response to 1alpha,25-dihydroxyvitamin D3 in the intestine and was not observed in other tissues such as liver or kidney. The in vivo enhancement of intestinal chromatin template activity was specific for the 1alpha,25-dihydroxyvitamin D3 hormone in that equivalent doses of 25-hydroxyvitamin D3 or vitamin D3 did not elicit a response in 2 to 3 hours. Only 1alpha-hydroxyvitamin D3, a synthetic sterol which is very rapidly metabolized to the 1alpha,25-dihydroxyvitamin D3 form, was able to minic the natural hormone in vivo. To further elucidate the nuclear mechanism of action of 1alpha,25-dihydroxyvitamin D3, the hormone was preincubated at 0 degrees with intestinal cytosol to form hormone-receptor complexes. After addition of the hormone-receptor complexes to purified intestinal mucosa nuclei and incubation for 1 hour at 25 degrees, chromatin isolated from this reconstituted system displayed a significant increase in template activity as compared to chromatin prepared from similar in vitro incubations not containing hormone. This stimulation was 12 to 24% over control values and exhibited an absolute requirement for intestinal cell cytosol. The response was specific for physiologic levels of 1alpha,25-dihydroxyvitamin D3, but occurred with pharmacologic doses of 25-hydroxyvitamin D3. It is concluded that a stimulation of the chromatin template activity of intestinal target tissue by 1alpha,25-dihydroxyvitamin D3 may be an integral part of the ultimate physiologic response of enhanced calcium transport.