Single Template Molecule Research Articles

Encapsulation of silver nanoparticles within double‐cylinder‐type copolymer brushes as templates

AbstractAn encapsulation of silver nanoparticles has been developed based on a template technique. Amphiphilic double‐cylinder‐type copolymer brushes were employed as a single molecule template, utilizing the coordination of Ag+ ions with carboxylate groups in the core of the brush. Subsequently, silver nanoparticles (ca. 7.5 nm in diameter) within the brush template have been prepared by the addition of a chemical reductant, e.g. NaBH4. The solution of the resultant nanocylinder composites was a yellow color due to the surface plasmon resonance. These composites were soluble in organic solvents, because the shell of the copolymer brush protected the fabricated silver nanoparticles from aggregation. Copyright © 2005 John Wiley & Sons, Ltd.

Silver nanoparticles dispersed within amphiphilic star-block copolymers as templates for plasmon band materials

Formation of silver nanoparticles has been developed based on a template technique. Amphiphilic star-block copolymers employed as single molecule template, utilizing the coordination of Ag + ions with carboxyl groups in the core of the star-block copolymer. Silver nanoparticles have been prepared by the addition of chemical reductant, e.g., NaBH 4. The solution of the resultant nanosphere composites showed yellow due to the surface plasmon resonance. These composites were soluble in organic solvents, because hydrophobic corona of the star-block copolymer protected the fabricated silver nanoparticles from aggregation.

Molecular haplotyping by linking emulsion PCR: analysis of paraoxonase 1 haplotypes and phenotypes

Linking emulsion PCR (LE-PCR) enables formation of minichromosomes preserving phase information of two polymorphic loci, hence the haplotype. Emulsion PCR confines two amplicons of two linked polymorphic sites on a single template molecule to one aqueous-phase droplet. Linking PCR uses biotinylated, overlapping linking primers to connect these amplicons in the droplet. After LE-PCR, unlinked amplicons are removed on streptavidin-coated magnetic beads and single-stranded runoff products are capped by primer extension. Quantitative ASPCR can then be used to ascertain the haplotypes of the two polymorphic loci on the minichromosomes. Using LE-PCR, we determined the human paraoxonase-1 [PON1] molecular haplotypes at three loci (−909g>c, L55M, Q192R) in women who were compound heterozygotes for −909g>c/L55M (n = 89), −909g>c/Q192R (n = 77) and L55M/Q192R (n = 68). We observed a strong association between PON1 substrate specificity (paraoxon/phenylacetate substrate activity ratios) and −909g>c/Q192R haplotype. We have demonstrated here a powerful molecular haplotyping technology that can be applied in population studies.

Template-Controlled Synthesis of Wire-Like Cadmium Sulfide Nanoparticle Assemblies within Core−Shell Cylindrical Polymer Brushes

A controlled fabrication of wire-like assemblies of cadmium sulfide (CdS) nanoparticles has been developed based on a template technique. Well-defined amphiphilic core−shell cylindrical polymer brushes were used as single molecule templates, utilizing the coordination of cadmium ions with carboxylate groups in the core of the brush. Formation of CdS nanoparticles inside the polymer brush was carried out via the reaction of the coordinated Cd2+ ions with H2S. This route resulted in wire-like CdS nanoparticle assemblies of about 4−5 nm in diameter and about 170 nm long. After the formation of the CdS nanoparticles, the polymer brush resumes its original chemical structure and morphology and therefore can be used as template again. The obtained polymer−semiconductor nanocomposite is soluble and stable in organic solvents, and potential applications may be found due to the quasi-1D structure of the assembly of CdS nanoparticles. In principle, the present synthetic approach is of general applicability to vario...

On the Nature and Location of Organic Template Molecules and Their Effect on the Stability and Redox Properties of Microporous CoAlPO-34 Catalyst

Small-pore CoAlPO-34 materials were synthesized with a variety of organic template molecules and were characterized in detail, employing microcrystal diffraction, powder diffraction and in situ combined XRD/XAS techniques. We found that, when two template molecules or two nitrogen atoms of a single template molecule are present inside the chabazitic cage, the concentration of cobalt present in the system is ca. 25 at%, which introduces instability in the framework structure during the removal of the organic template. In contrast, when only one template molecule is present, it is possible to control the concentration of Co(II) ions in the framework to ca. 10 at%; these systems show good structural integrity and redox chemistry that was exploited for the regio-selective conversion of linear alkane molecules.

Adsorption isotherms of a molecular imprinted polymer prepared in the presence of a polymerisable template: Indirect evidence of the formation of template clusters in the binding site

The current opinion about molecular imprinted polymers (MIPs) is that their molecular recognition properties are due to the presence of nanocavities formed during a polymerization process developed in the presence of a template molecule. According to this principle, the shape of these nanocavities is complementary to that of the template and non-covalent interactions are established between the binding site and a single template molecule. Nevertheless, there are some experimental indications that the real molecular recognition mechanism involves clusters of template molecules being packed into the binding site. Recently, it has been proposed that template molecules covalently linked to the binding site can act as nucleation points, enhancing the formation of these molecular clusters. We have tested this hypothesis by studying the adsorption isotherms of polymers prepared by imprinting them with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). Three different polymers were considered: P0, prepared without the template, P1, whose template was represented by 2,4,5-T molecules, and P2, whose template was 1/3 constituted by the polymerisable 2-(2,4,5-trichlorophenoxyacetoxy)-ethylmethacrylate (2,4,5-TEMA) and 2/3 by 2,4,5-T. The polymers were prepared by thermoinduced polymerization of template mixtures, 4-vinylpyridine and ethylene dimethacrylate. The crushed polymers were packed into HPLC columns and frontal chromatographic runs were performed by eluting the columns with a mobile phase containing variable amounts of 2,4,5-T. The experimental adsorption isotherms were fitted by using several isotherm models, and the Freundlich–Langmuir model was found to give the best fitting in terms of F-test. All the models considered showed a significant difference between the affinity constant values measured for the polymer P1 and P2, with a higher value for the polymer P2 (for Freundlich–Langmuir model: polymer P1, k=(2.00±0.43)×10 4 M −1; polymer P2, k=(1.93±0.0535)×10 5 M −1; ratio P2/P1, 9.65±2.09). Such experimental results support the hypothesis that a polymer prepared with a limited amount of template covalently attached to the binding site shows an increased affinity for the template itself.

Mineralization of single flexible polyelectrolyte molecules.

Conformation of a single flexible polyelectrolyte molecule with a hydrophobic backbone in aqueous solution is effected by the interplay of the short-range intramolecular attraction and the long-range Coulomb repulsion. The conformation can be frozen if the molecule is trapped by a solid substrate. With this approach, we prepared the range of single molecule templates from poly(2-vinylpyridine) (P2VP) deposited on the surface of Si-wafer or mica in different conformations from an elongated wormlike coil to compact globule. Pd(+2) was coordinated by P2VP via an ion exchange reaction exposing the samples to palladium acetate acidic aqueous solution. In the next step, Pd(+2) was reduced by dimethylamine borane. This route results in wire-shaped metallic nanoparticle assembles of about 2-5 nm in diameter and 50-700 nm in length. The conformation and size of the underlaying polyelectrolyte molecules determine the dimensions of nanoparticles.

DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.

We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, 'jumping PCR', i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than approximately 0.1% even under the unlikely scenario where each amplification starts from a single template molecule.

Facile Sol-gel Synthesis of Porous Silicas Using Poly(propylene)imine Dendrimers as Templates

Commercially available poly(propylene)imine (DAB-Am-32 and DAB-Am-64) dendrimers were used as single-molecule templates to tailor the porosity of silicas via a nonacidic sol-gel method. X-ray diffraction on both the as-prepared (oven-dried at 373 K) and the calcined (833 K) materials revealed that modest contraction took place on template removal and that the cavities created did not achieve three-dimensional ordering under the current synthesis conditions. Transmission electron microscopy of “Pt-stained” samples supported this picture. A modified Horvath–Kawazoe analysis of the argon adsorption isotherms indicated that DAB-Am-64 is a much more effective template than DAB-Am-32. Pyrolysis and oxidation protocols for template removal are also presented.

Use of Polypropyleneimine Tetrahexacontaamine (DAB-Am-64) Dendrimer as a Single-Molecule Template To Produce Mesoporous Silicas

The use of DAB-Am-64 amine dendrimer as a single-molecule template to produce mesoporous cavities in silica sol−gels is reported. The method is meant to afford the synthesis of spheroidal cavities and is likely to enjoy generality, since there are a number of dendritic molecules commercially available today. X-ray diffraction confirms that a coherent distance of ∼25 A is obtained upon calcination, and the modeling of nitrogen adsorption data by a modified Horvath-Kawazoe formalism for spherical cavities reveals that voids of ∼23 A in diameter had been formed.

In situ localized amplification and contact replication of many individual DNA molecules.

We describe a method to clone and amplify DNA by performing the polymerase chain reaction (PCR) in a thin polyacrylamide film poured on a glass microscope slide. The polyacrylamide matrix retards the diffusion of the linear DNA molecules so that the amplification products remain localized near their respective templates. At the end of the reaction, a number of PCR colonies, or 'polonies', have formed, each one grown from a single template molecule. As many as 5 million clones can be amplified in parallel on a single slide. If an Acrydite modification is included at the 5' end of one of the primers, the amplified DNA will be covalently attached to the polyacrylamide matrix, allowing further enzymatic manipulations to be performed on all clones simultaneously. We describe techniques to make replicas of these polony slides, and high throughput sequencing protocols for this technology. Other applications are also discussed.

Evidence for numerous omp1 alleles of porcine Chlamydia trachomatis and novel chlamydial species obtained by PCR.

A nested PCR for genus-specific amplification of the Chlamydia omp1 locus was established. This PCR detected single template molecules in 200-microl specimen aliquots. Amplified chlamydial omp1 alleles were typed by heminested species PCRs and allele PCRs. We applied this method to 407 specimens from several host animals with various clinical conditions, and we detected prevalences of chlamydiae from 6 to 50%. Amplicons from peacock enteritis and equine infertility specimens were not typeable according to present omp1 allelic criteria for the chlamydial species. DNA sequencing revealed novel omp1 alleles which were 29.9 and 47.6% divergent in the deduced peptide sequences from the most closely related chlamydiae. Phylogenetic reconstruction indicated segregation of these alleles from the current four chlamydial species (90 and 97% bootstrap support), thus strongly suggesting the existence of additional chlamydial species. Allele typing of amplicons from swine with intestinal, urogenital, and respiratory infections demonstrated several unique omp1 allelic variants of Chlamydia trachomatis. These novel alleles had deduced peptide sequences which were 11.6 to 19% divergent from porcine C. trachomatis S45. Mutations were clustered in the C-terminal region of variable segment IV of the omp1 locus encoding subspecies and serovar determinants of the chlamydial major outer membrane protein, thus implying that there are numerous serovars of porcine C. trachomatis. These results demonstrate the need for routine application of sensitive genus-specific detection of chlamydiae in animal specimens and suggest a more prominent role than anticipated for chlamydiae in animal diseases.