Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging.
Single-nucleotide polymorphisms (SNPs) are the most frequent type of human genetic variation. Recent work has shown that it is possible to directly analyze SNPs in unamplified human genomic DNA samples using the surface-invasive cleavage reaction followed by rolling circle amplification (RCA) labeling of the cleavage products. The individual RCA amplicon molecules were counted on the surface using fluorescence microscopy. Two principal limitations of such single-molecule counting are the variability in the amplicon size, which results in a large variation in fluorescence signal intensity from the dye-labeled DNA molecules, and a high level of background fluorescence. It is shown here that an excellent alternative to RCA labeling is tagging with gold nanoparticles followed by imaging with a scanning electron microscope. Gold nanoparticles have a uniform diameter (15 +/- 0.5 nm) and provide excellent contrast against the background of the silicon substrate employed. Individual gold nanoparticles are readily counted using publicly available software. The results demonstrate that the labeling efficiency is improved by as much as approximately 15-fold, and the signal-to-noise ratio is improved by approximately 4-fold. Detection of individual cleaved DNA molecules following surface-invasive cleavage was linear and quantitative over 3 orders of magnitude in amount of target DNA (10(-18)-10(-15) mol). (+info)
Calixarene-encapsulated nanoparticles: self-assembly into functional nanomaterials.
Calixarenes are excellent surfactants for enhancing the dispersion and self-assembly of metal nanoparticles into well-defined structures, particularly those with unit length scales in the 10-100 nm size range. Particles within these ensembles are strongly coupled, giving rise to unique collective optical or magnetic properties. The self-assembled nanostructures described in this feature article include 2D arrays of colloidal Au nanoparticles with size-dependent plasmonic responses, and sub-100 nm Co nanoparticle rings with chiral magnetic states. These nanoparticle assemblies may be further developed for applications in chemical sensing based on surface-enhanced Raman scattering (SERS) and as binary elements for nonvolatile memory, respectively. (+info)
A gold nanoparticle based approach for screening triplex DNA binders.
Nanoparticle assemblies interconnected with DNA triple helixes can be used to colorimetrically screen for triplex DNA binding molecules and simultaneously determine their relative binding affinities based on melting temperatures. Nanoparticles assemble only when DNA triple helixes form between DNA from two different particles and a third strand of free DNA. In addition, the triple helix structure is unstable at room temperature and only forms in the presence of triplex DNA binding molecules which stabilize the triple helix. The resulting melting transition of the nanoparticle assembly is much sharper and at a significantly higher Tm than the analogous triplex structure without nanoparticles. Upon nanoparticle assembly, a concomitant red-to-blue color change occurs. The assembly process and color change do not occur in the presence of duplex DNA binders and therefore provide a significantly better screening process for triplex DNA binding molecules compared to standard methods. (+info)
Silica beads with average diameters of 40-600 nm were prepared, and Ru(bpy)3(2+) complexes were incorporated into the beads. These beads were coated by silver layer by layer to generate porous but continuous metal nanoshells. The thicknesses of these metal shells were 5-50 nm. The emission band from the dyes in the silica cores was more narrow and the intensity was enhanced with growth of silver shell thickness due to coupling of the emission light from Ru(bpy)3(2+) in the cores with the metal plasmon from the silver shells. The enhancement of emission intensity was also dependent on the size of the silica core, showing that the enhancement efficiency decreased with an increase in the size of the silica beads. Lifetime measurements support the coupling mechanism between the dye and metal shell. This study can be used to develop novel dye-labeled metal particles with bright and narrow emission bands. (+info)
Asymmetric functionalization of gold nanoparticles with oligonucleotides.
Gold nanoparticles (AuNPs) were anisotropically functionalized with two different oligonucleotide sequences using magnetic microparticles as geometric restriction templates for site-selective enzymatic extension of particle-bound oligonucleotides. The divalent linking capability of the resulting AuNPs allowed for the design and programmable assembly of discrete nanoparticle heterostructures. (+info)
Surface-enhanced fluorescence of fluorescein-labeled oligonucleotides capped on silver nanoparticles.
Tiopronin monolayer-protected silver nanoparticles with different core sizes (average diameter = 2, 5, 20 nm) were prepared by using different mole ratios of silver nitrate/tiopronin. Ligands on the silver particles were partially displaced by fluorescein-labeled thiolate single-stranded oligonucleotides or their complementary unlabeled oligonucleotides through ligand exchange. The fluorophores on silver particles showed a surface-enhanced fluorescence (SEF) dependent on the size of metallic cores. The particles could be coupled through hybridizations of oligonucleotides bound on the particles. The coupled particles were aggregated due to multiple displacements of oligonucleotides on each particle, resulting in stronger SEF. The dye-labeled oligonucleotides were assembled on the silver islands on the solid substrate, and the complementary oligonucleotide-displaced particles were coupled via oligonucleotide hybridization. The couplings between particles and islands resulted in an obvious fluorescence enhancement. (+info)
Enhanced luminescence of phenyl-phenanthridine dye on aggregated small silver nanoparticles.
Tiopronin-coated silver particles (average diameters of core = 1.6 nm) were prepared by a modified Brust method, and the ligands on the metal core were partially displaced by (2-mercapto-propionylamino) acetic acid-2,5-dioxo-pyrrolidin-1-ylester through ligand exchanges. The particles were bound on amine-pendent polymer backbones by condensation to generate compact aggregates of particles. The aggregated particles displayed a plasmon absorbance rising at 440 nm. Luminescence was enhanced to about 2 times with increasing the plasmon rising by the particle aggregation upon excitation at 400 nm when the polymer was labeled by 3,8-diamino-6-phenyl-phenanthridine. (+info)
c-Type cytochrome-dependent formation of U(IV) nanoparticles by Shewanella oneidensis.
Modern approaches for bioremediation of radionuclide contaminated environments are based on the ability of microorganisms to effectively catalyze changes in the oxidation states of metals that in turn influence their solubility. Although microbial metal reduction has been identified as an effective means for immobilizing highly-soluble uranium(VI) complexes in situ, the biomolecular mechanisms of U(VI) reduction are not well understood. Here, we show that c-type cytochromes of a dissimilatory metal-reducing bacterium, Shewanella oneidensis MR-1, are essential for the reduction of U(VI) and formation of extracellular UO(2) nanoparticles. In particular, the outer membrane (OM) decaheme cytochrome MtrC (metal reduction), previously implicated in Mn(IV) and Fe(III) reduction, directly transferred electrons to U(VI). Additionally, deletions of mtrC and/or omcA significantly affected the in vivo U(VI) reduction rate relative to wild-type MR-1. Similar to the wild-type, the mutants accumulated UO(2) nanoparticles extracellularly to high densities in association with an extracellular polymeric substance (EPS). In wild-type cells, this UO(2)-EPS matrix exhibited glycocalyx-like properties and contained multiple elements of the OM, polysaccharide, and heme-containing proteins. Using a novel combination of methods including synchrotron-based X-ray fluorescence microscopy and high-resolution immune-electron microscopy, we demonstrate a close association of the extracellular UO(2) nanoparticles with MtrC and OmcA (outer membrane cytochrome). This is the first study to our knowledge to directly localize the OM-associated cytochromes with EPS, which contains biogenic UO(2) nanoparticles. In the environment, such association of UO(2) nanoparticles with biopolymers may exert a strong influence on subsequent behavior including susceptibility to oxidation by O(2) or transport in soils and sediments. (+info)