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ABSTRACT: A variety of rapid biomolecular assays under development rely on the selective adsorption of single-stranded DNA onto unfunctionalized, negatively charged, citrate-stabilized gold nanoparticles. We investigate the adsorption mechanism with a study of the binding kinetics and find strong evidence for the dominance of hydrophobic effects including linear compensation between the activation energy and the natural log of the Arrhenius prefactor and the correlation of the adsorption rate in the presence of various salts with the Hofmeister series. These results explain the selectivity for single-stranded over double-stranded DNA adsorption and contradict previous work citing an electrostatic DLVO-like mechanism. Our understanding should facilitate improvements to the selective-adsorption-based assays and, more generally, contribute to the understanding of interactions between like-charged species in aqueous solution.
Langmuir 03/2011; 27(5):1770-7. · 4.19 Impact Factor
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ABSTRACT: Dramatic localization of optical fields by interactions with surface plasmons on nanotextured metal surfaces allows us to record Raman spectra of individual chromophores on single chains of a high-molecular-weight model conjugated polymer, poly(2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene. The data are broadly consistent with two configurations of the chromophore that are characteristic of packed and loose conformations of the backbone. Within these types, fluctuations of the chromophore planarity are observed, and we show how they can be analyzed by studying the temporal correlation of successive spectra. Chromophores exhibit some configurational memory on the time scale of minutes. We also observe substantial spectral fluctuations and associate these mostly with thermally induced motions of the chromophore in the "hot spot". However, we also provide instances of data representing irreversible photochemistry as well as charging and discharging of the chromophore. Finally, we show that single chromophores embedded in the polymer reorganize in response to poor solvents.
ACS Nano 12/2007; 1(4):299-306. · 10.77 Impact Factor
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ABSTRACT: We report experiments on dendritic molecules with integrated conjugated chromophores that provide microscopic mechanistic information about their solvation dynamics. The fluorescence of a series of immobilized dendritically organized oligothiophenes is studied as they are exposed to good solvents. Initially, the pi-stacking of the oligothiophene units in the dendrimer is destabilized, but full separation of the oligothiophene dendrons takes a time that is orders of magnitude longer due to barriers to torsional motion of the ester linkages. The metastable state prior to separation of the conjugated segments exhibits solution-like spectroscopy but low fluorescence quantum yield relative to the fully solvated segments. This species may play an important role in the photophysics of conjugated oligomer and polymer films. Unusual non-exponential kinetics for the oligothiophene separation step are observed and can be understood in terms of energy transfer among the dendrons.
The Journal of Physical Chemistry B 12/2007; 111(46):13211-6. · 3.70 Impact Factor
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ABSTRACT: Binding of small oligonucleotides to the periphery of folded RNA can provide insight into the secondary structure of complex RNA in solution. To discriminate between bound and unbound fluorescein-labeled 2'-O-methyl RNA probes, we use ionically coated gold nanoparticles to selectively adsorb unbound probes and quench their fluorescence. The target is the 3' untranslated region of Bombyx mori R2 RNA. Fluorescence indicates that R2 sequences complementary to some of the probes are accessible for binding in the three-dimensional structure. Hybridization occurs under homogeneous conditions in the absence of the gold nanoparticles so that steric issues associated with chip-based assays are avoided. The assay is compatible with well plate formats, takes less than 5 min, and requires only 2 pmol or less of unlabeled target RNA per probe sequence tested.
RNA 12/2007; 13(11):2034-41. · 5.09 Impact Factor
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ABSTRACT: We report an interferometric method to detect chemical binding at an interface. The interference layer consists of the thin native oxide on silicon, and we utilize nearly opposite phase shifts of light at the oxide/water and oxide/silicon interfaces to achieve near-complete destructive interference. We measure selective binding of thrombin in solution to DNA aptamers covalently bound to the oxide. The technique can be used to detect and quantify surface binding of less than 1 A of material, sensitivity similar to that of surface plasmon resonance imaging or arrayed imaging reflectometry. Results are in quantitative agreement with what is predicted theoretically. The method is very convenient to implement since it utilizes unmodified silicon wafers as substrates and is extremely insensitive to both probe light bandwidth and collimation.
Analytical Chemistry 11/2007; 79(20):7589-95. · 5.86 Impact Factor
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ABSTRACT: A new class of semi-flexible dendrimers with oligothiophene (OT) arms up to the third generation have been synthesized and investigated. The synthetic methods employed include a combination of palladium-catalyzed Stille cross-coupling reactions for oligothiophenes, Sonogashira cross-coupling reactions for building blocks, and carbodiimide-mediated esterification for building up the various dendrimers. The optical and electrochemical properties of this series of oligothiophenes-based dendrimers are shown to be strongly influenced by their morphologies as demonstrated by their pronounced solvatochromic and thermochromic responses under different environmental conditions. Introducing rigid oligothiophene arms to shape non-persistent ester-linked dendrimers causes higher generation dendrimers (G2 and G3) to exhibit solvatochromism and thermochromism, while their oligomeric counterpart (3b) and lower generation (G1) analogue do not. Spectroscopic changes due to both intramolecular and intermolecular aggregations are observed.
The Journal of Organic Chemistry 01/2007; 71(25):9475-83. · 4.45 Impact Factor
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ABSTRACT: We use reflectivity changes at an interface functionalized with molecular probes to detect label-free biomolecular binding. Attachment of the target molecules to the surface alters the effective thickness of an antireflective coating formed by thermal oxidation of a silicon wafer to remove destructive interference of the reflected waves. The thermal oxide thickness is adjusted for precise interference using electrostatic layer-by-layer self-assembly of polyelectrolytes to which the molecular probes can be bound covalently. Reflectivity increases of over a factor of 100 are observed for binding of 2.5 nm of streptavidin to biotinylated polyelectrolytes, considerably more sensitive than surface plasmon resonance detection. Theoretical modeling is in agreement with the experimentally observed reflectivity increases and suggests the sensitivity is at present limited by the roughness of the oxide.
Analytical Chemistry 10/2006; 78(18):6622-7. · 5.86 Impact Factor
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ABSTRACT: Deposition of silver nanoparticles directly onto a Rhodamine Red monolayer covalently bound to glass is found to increase the photoluminescence by as much as 20 times depending on excitation wavelength and nanoparticle density. At the same time, the excited state lifetime is reduced by more than a factor of 2, the fluorescence spectrum is blue-shifted, and greater polarization anisotropy in the emission is observed. We attribute these effects to local enhancement of the optical fields near the molecules by interactions with silver plasmons. We approximately separate the relative contributions of increased absorption and increased emissive rate to the observed enhancement of fluorescence. A study of the spatial inhomogeneity of the effect using scanning confocal microscopy demonstrates that average enhancements at least twice as large are possible.
The Journal of Physical Chemistry B 10/2006; 110(35):17383-7. · 3.70 Impact Factor
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ABSTRACT: The study of proteins and the molecules with which they interact on an organismwide scale is critical to understanding basic biology, and understanding and improving human health. New platform technologies allowing label-free, quantitative array-based analysis of proteins are particularly desirable. We have developed an analytical technology, reflective interferometry (RI), which provides specific, rapid, and label-free optical detection of biomolecules in complex mixtures. In order to evaluate the suitability of RI for proteomics, we have prepared a series of arrays bearing the extracellular domain of the secreted enteropathogenic Escherichia coli (EPEC) protein Translocated Intimin Receptor (Tir). These arrays are able to selectively detect the extracellular domain of the protein Intimin, Tir's natural binding partner. Furthermore, we demonstrate the use of RI and Tir-functionalized arrays for the selective detection of EPEC directly from culture.
Biosensors and Bioelectronics 03/2006; 21(8):1659-63. · 5.60 Impact Factor
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ABSTRACT: We observe more than a 200-fold increase in the photoexcited phosphorescent emission of PtOEP (2,3,7,8,12,13,17,18-octaethyl-21H,23H-porphyrin platinum II) in a polystyrene film on nanotextured silver surfaces, coincident with a reduction in the triplet state lifetime by a factor of 5. The large enhancement results in films with apparent luminescence quantum yields much greater than unity and can be understood in terms of increased radiative rates due to interactions between the molecules and the electron plasma in nearby silver nanoparticles. We study the photoluminescence efficiency, excitation spectrum, and decay dynamics as a function of film thickness and silver density. We use a model of the photophysics to decompose the phosphorescent enhancement into contributions from increases in absorption, emissive rate, and quenching. Quenching increases in importance for very thin films, and we conclude that approximately 3 nm spacing between metal and chromophore leads to the largest photoluminescence enhancement.
Journal of the American Chemical Society 05/2005; 127(16):6087-94. · 9.91 Impact Factor
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ABSTRACT: We observe spectral and intensity fluctuations in Raman scattering from single molecules of 4-mercaptopyridine (4-Mpy) adsorbed on textured silver surfaces. We present evidence that the root cause of these fluctuations is thermal. Analysis of the spectra shows that in some cases the spectral changes are associated with molecular reorientation and in others with chemical reactions of the 4-Mpy. Analogous surfaces fully covered with 4-Mpy exhibit similar behavior, indicating that monolayer Raman spectra are dominated by a few molecules at most.
The Journal of Physical Chemistry B 04/2005; 109(8):3387-91. · 3.70 Impact Factor
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ABSTRACT: Simple, fast, economical, and sensitive detection of specific DNA sequences is crucial to pathogen detection and biomedical research. We have designed a novel fluorescent assay for DNA hybridization based on the electrostatic properties of DNA. We exploit the ability to create conditions where single-stranded DNA adsorbs on negatively charged gold nanoparticles while double-stranded DNA does not. Dye-tagged probe sequences have their fluorescence efficiently quenched when they are mixed with gold nanoparticles unless they hybridize with components of the analyte. Subfemtomole amounts of untagged target are detected in minutes using commercially available materials. Target sequences in complex mixtures of DNA and single-base mismatches in DNA sequences are easily detected.
Analytical Chemistry 10/2004; 76(18):5414-7. · 5.86 Impact Factor
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ABSTRACT: We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.
Journal of the American Chemical Society 10/2004; 126(35):10958-61. · 9.91 Impact Factor
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ABSTRACT: New chip-based methods for the detection of unmodified biomolecular targets have significant potential as enabling technology in fundamental biology and biomedical analysis. We report a method based on changes in reflectivity from specially fabricated substrates that is capable of detecting the binding of as little as an average of 0.2 nm (i.e., a fraction of a monolayer) of biomolecules. We demonstrate the method on detection of femtomole quantities of untagged oligonucleotides in an array format, showing that the amount of target bound can be determined quantitatively. The simplicity of the approach promises to make it broadly applicable for any biomolecule for which suitable molecular recognition chemistry is available.
Analytical Chemistry 09/2004; 76(15):4416-20. · 5.86 Impact Factor
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Lewis J. Rothberg
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ABSTRACT: We document the surprising result that single-stranded DNA adsorbs on negatively charged gold nanoparticles (Au-nps) with a rate that depends on sequence length and temperature. After ss-DNA adsorbs on Au-nps, we find that the particles are stabilized against salt-induced aggregation. These observations can be rationalized on the basis of electrostatics and form the basis for a colorimetric assay to identify specific sequences and single nucleotide polymorphisms on polymerase chain reaction (PCR)-amplified DNA. The assay is label-free, requires no covalent modification of the DNA or Au-np surfaces, and takes on the sensitivity of PCR. Most important, binding of target and probe takes place in solution where hybridization occurs in less than 1 min. As an example, we test PCR-amplified genomic DNA from clinical samples for single nucleotide polymorphisms (SNPs) associated with a fatal arrhythmia known as long QT syndrome.
08/2004;
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ABSTRACT: The photoluminescence intensity from a bis (2,2'-bipyridine)-(5-isothiocyanato-phenanthroline) Ruthenium (RuBICP) monolayer covalently bound to a glass substrate is found to be enhanced up to 20 times when silver nanoparticles are deposited on top. The emission spectra are blue shifted by interactions with the silver nanoparticles. Field enhancement is found to be able to enhance the radiative decay rate by over three orders of magnitude but fewer than 2 % of the molecules in the sample experience this large enhancement. Increased absorption rates also increase the luminescence but to a much smaller degree.
MRS Proceedings. 12/2003; 818.
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ABSTRACT: We find that giant surface-enhanced Raman scattering for adsorbates on silver surfaces is present only on surfaces that exhibit self-similar fractal topology as inferred from atomic force microscopy. The fractal character results in localizing the energy of incident photons to volumes of a few nanometers on a side, millions of times smaller than the diffraction limit. Consistent with this finding, we have found an enhancement in spontaneous Raman cross section of >13 orders of magnitude for adsorbates on silver surfaces demonstrated to be fractal. The location of "hot spots" on the fractal surfaces is found to be hypersensitive to incident wavelength and polarization even though the observed Raman scattering is strictly linear in incident intensity. These observations are consistent with localization of the photon energy facilitated by the disordered nature of fractal organization through interference between the incident wave and scattered radiation from silver nanoparticle surface plasmons. We also present a surface preparation method that consistently produces fractal topologies that support single-molecule Raman scattering.
Proceedings of the National Academy of Sciences 07/2003; 100(15):8638-43. · 9.68 Impact Factor
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ABSTRACT: We have demonstrated the feasibility of sensing adsorption of untagged molecular analytes in an electrochemically fabricated porous aluminum oxide template with regular nanometer dimension pores by monitoring reflectivity spectra. Combining this with chemistry to functionalize Al2O3 with DNA oligonucleotides, we are able to sense 2 nmol/cm2 of complementary DNA as a 3.4 nm shift in a spectral minimum. We have modeled the change in reflection spectrum versus uptake of analytes to quantify binding. This technique can achieve subpicomole sensitivity in straightforward fashion with 0.1 mm probe spots.
04/2003;
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ABSTRACT: We report transient and steady state photoluminescence results along with absorption and NMR data to support the existence of two distinct morphological species in MEH−PPV solutions. NMR data provide evidence for the close packing of polymer chains, a consequence of solvent quality reduction. These data are correlated with optical properties of the aggregated species in poor solvents and the isolated chains in good solvents. We infer that steric hindrance of backbone motions increases effective conjugation length and leads to a spectral red shift in absorption and emission. At the same time, interchain excitations with negligible luminescence can be formed, leading to a dramatic reduction in photoluminescence quantum yield. While spectral changes are observed as packing is induced, we show that interchain state formation and its subsequent back-transfer to excitons are particularly sensitive to the interchain registry of the highly packed chains.
02/2001;
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ABSTRACT: We report the design and testing of a versatile biosensor exclusively using silicon. The device structure consists of a microcavity resonator made of various porous silicon layers. Porous silicon contains silicon nanocrystals that can luminesce efficiently in the visible, depending on the size and passivation conditions. When a luminescent porous silicon layer is inserted between two Bragg reflectors (also made of porous silicon), the broad luminescence band is altered and multiple and very narrow peaks are detected. The position of these peaks is extremely sensitive to a small change in refractive index, such as that obtained when a biological object is attached to the large internal surface of porous silicon. We have demonstrated a DNA sensor that displays appropriate sensitivity, selectivity and response speed. The device fabrication procedure and the results of extensive testing are presented. An extension of the DNA biosensor has been made to include the detection of viral DNA. This work will lead to the development of an all-silicon sensor array for the detection of biomacromolecules.
Materials Science and Engineering: C.
