Dual-modality single particle orientation and rotational tracking of intracellular transport of nanocargos

The single particle orientation and rotational tracking (SPORT) technique was introduced recently to follow the rotational motion of plasmonic gold nanorod under a differential interference contrast (DIC) microscope. In biological studies, however, cellular activities usually involve a multiplicity of molecules; thus, tracking the motion of a single molecule/object is insufficient. Fluorescence-based techniques have long been used to follow the spatial and temporal distributions of biomolecules of interest thanks to the availability of multiplexing fluorescent probes. To know the type and number of molecules and the timing of their involvement in a biological process under investigation by SPORT, we constructed a dual-modality DIC/fluorescence microscope to simultaneously image fluorescently tagged biomolecules and plasmonic nanoprobes in living cells. With the dual-modality SPORT technique, the microtubule-based intracellular transport can be unambiguously identified while the dynamic orientation of nanometer-sized cargos can be monitored at video rate. Furthermore, the active transport on the microtubule can be easily separated from the diffusion before the nanocargo docks on the microtubule or after it undocks from the microtubule. The potential of dual-modality SPORT is demonstrated for shedding new light on unresolved questions in intracellular transport.     

Complexation between Amylodextrin Oligomers and Selected Pharmaceuticals Measured through Capillary Electrophoresis

The amylodextrin oligomers, tagged fluorescently at their reducing ends for laser fluorescence detection, were used as model solutes to investigate certain carbohydrate-drug interactions through capillary electrophoresis. The separation patterns of some oligomers were found to be altered significantly by the presence of selected pharmaceuticals used as buffer additives. The selectivity of complexation at a particular size of an oligomer could be judged from alterations in migration times and peak shapes. The formation of complex was influenced substantially by solutes' chemical environment (pH, ionic strength, and the nature and concentration of organic additives). The chemical nature of the guest molecules also played an important role in complexation. Using amylodextrins as chiral selectors, enantiomeric resolution of several pharmaceuticals was achieved electrophoretically. The conclusions drawn from electrophoretic data were found to be in close agreement with the results of a (13)C NMR study.     

DNA-modified nanocrystalline diamond thin-films as stable,biologically active substrates

Diamond, because of its electrical and chemical properties, may be a suitable material for integrated sensing and signal processing. But methods to control chemical or biological modifications on diamond surfaces have not been established. Here, we show that nanocrystalline diamond thin-films covalently modified with DNA oligonucleotides provide an extremely stable, highly selective platform in subsequent surface hybridization processes. We used a photochemical modification scheme to chemically modify clean, H-terminated nanocrystalline diamond surfaces grown on silicon substrates, producing a homogeneous layer of amine groups that serve as sites for DNA attachment. After linking DNA to the amine groups, hybridization reactions with fluorescently tagged complementary and non-complementary oligonucleotides showed no detectable non-specific adsorption, with extremely good selectivity between matched and mismatched sequences. Comparison of DNA-modified ultra-nanocrystalline diamond films with other commonly used surfaces for biological modification, such as gold, silicon, glass and glassy carbon, showed that diamond is unique in its ability to achieve very high stability and sensitivity while also being compatible with microelectronics processing technologies. These results suggest that diamond thin-films may be a nearly ideal substrate for integration of microelectronics with biological modification and sensing.     

Biomolecular screening with encoded porous-silicon photonic crystals

Strategies to encode or label small particles or beads for use in high-throughput screening and bioassay applications focus on either spatially differentiated, on-chip arrays or random distributions of encoded beads. Attempts to encode large numbers of polymeric, metallic or glass beads in random arrays or in fluid suspension have used a variety of entities to provide coded elements (bits)--fluorescent molecules, molecules with specific vibrational signatures, quantum dots, or discrete metallic layers. Here we report a method for optically encoding micrometre-sized nanostructured particles of porous silicon. We generate multilayered porous films in crystalline silicon using a periodic electrochemical etch. This results in photonic crystals with well-resolved and narrow optical reflectivity features, whose wavelengths are determined by the etching parameters. Millions of possible codes can be prepared this way. Micrometre-sized particles are then produced by ultrasonic fracture, mechanical grinding or by lithographic means. A simple antibody-based bioassay using fluorescently tagged proteins demonstrates the encoding strategy in biologically relevant media.     

Fluorescence correlation spectroscopy with patterned photoexcitation for measuring solution diffusion coefficients of robust fluorophores

Patterned fluorescence correlation spectroscopy is developed as a new technique for measuring diffusion coefficients of photostable fluorescent probe molecules. In this method, interference between two intersecting, coherent laser beams creates an excitation fringe pattern from which fluorescence emission is monitored. Spontaneous concentration fluctuations of fluorescent molecules within the excitation volume are detected as excess noise on a fluorescence transient; concentration fluctuations are driven primarily by diffusion of these molecules between interference fringes although contributions from photobleaching and diffusion over the entire pattern dimensions can also be observed. Autocorrelation of the fluorescence transient allows analysis of the temporal characteristics of the fluctuations, which were used to determine solution diffusion coefficients; the method was applied to study the diffusion of Rhodamine 6G (R6G) in water/methanol solutions containing added electrolyte and in pure ethanol. The method can be used to characterize the diffusive transport of fluorescently labeled species, which is an important issue in designing small-volume detection experiments.     

Single-monomer formulation of polymerized polyethylene glycol diacrylate as a nonadsorptive material for microfluidics

Nonspecific adsorption in microfluidic systems can deplete target molecules in solution and prevent analytes, especially those at low concentrations, from reaching the detector. Polydimethylsiloxane (PDMS) is a widely used material for microfluidics, but it is prone to nonspecific adsorption, necessitating complex chemical modification processes to address this issue. An alternative material to PDMS that does not require subsequent chemical modification is presented here. Poly(ethylene glycol) diacrylate (PEGDA) mixed with photoinitiator forms on exposure to ultraviolet (UV) radiation a polymer with inherent resistance to nonspecific adsorption. Optimization of the polymerized PEGDA (poly-PEGDA) formula imbues this material with some of the same properties, including optical clarity, water stability, and low background fluorescence, that make PDMS so popular. Poly-PEGDA demonstrates less nonspecific adsorption than PDMS over a range of concentrations of flowing fluorescently tagged bovine serum albumin solutions, and poly-PEGDA has greater resistance to permeation by small hydrophobic molecules than PDMS. Poly-PEGDA also exhibits long-term (hour scale) resistance to nonspecific adsorption compared to PDMS when exposed to a low (1 μg/mL) concentration of a model adsorptive protein. Electrophoretic separations of amino acids and proteins resulted in symmetrical peaks and theoretical plate counts as high as 4 × 10(5)/m. Poly-PEGDA, which displays resistance to nonspecific adsorption, could have broad use in small volume analysis and biomedical research.     

Increasing the resolution of single pair fluorescence resonance energy transfer measurements in solution via molecular cytometry

We report a method to increase the resolution of single pair fluorescence resonance energy transfer (spFRET) measurements in aqueous solutions. Solution-based spFRET measurements of fluorescently labeled biological molecules (proteins, RNA, DNA) are often used to obtain histograms of molecular conformation without resorting to sample immobilization. However, for solution-phase spFRET studies, the number of photons detected from a single molecule as it diffuses through an open confocal volume element are quite limited. An "average" transit may yield on the order of 40 photons. Shot noise on the number of detected photons substantially limits the resolution of the measurement. The method reported here uses a hydrodynamically focused sample stream to ensure molecules traverse the full width of an excitation laser beam. This substantially increases the average number of photons detected per molecular transit (approximately 85 photons/molecule), which increases measurement precision. In addition, this method minimizes another source of heterogeneity present in diffusive measures of spFRET: the distribution of paths taken through the excitation laser beam. We demonstrate here using a FRET labeled protein sample (a FynSH3 domain) that superior resolution (a factor of approximately 2) can be obtained via molecular cytometry compared to spFRET measurements based upon diffusion through an open confocal volume element.     

Biochips for Cell Biology by Combined Dip‐Pen Nanolithography and DNA‐Directed Protein Immobilization

A general methodology for patterning of multiple protein ligands with lateral dimensions below those of single cells is described. It employs dip pen nanolithography (DPN) patterning of DNA oligonucleotides which are then used as capture strands for DNA‐directed immobilization (DDI) of oligonucleotide‐tagged proteins. This study reports the development and optimization of PEG‐based liquid ink, used as carrier for the immobilization of alkylamino‐labeled DNA oligomers on chemically activated glass surfaces. The resulting DNA arrays have typical spot sizes of 4–5 μm with a pitch of 12 μm micrometer. It is demonstrated that the arrays can be further functionalized with covalent DNA‐streptavidin (DNA‐STV) conjugates bearing ligands recognized by cells. To this end, biotinylated epidermal growth factor (EGF) is coupled to the DNA‐STV conjugates, the resulting constructs are hybridized with the DNA arrays and the resulting surfaces used for the culturing of MCF‐7 (human breast adenocarcinoma) cells. Owing to the lateral diffusion of transmembrane proteins in the cell's plasma membrane, specific recruitment and concentration of EGF receptor can be induced specifically at the sites where the ligands are bound on the solid substrate. This is a clear demonstration that this method is suitable for precise functional manipulations of subcellular areas within living cells.     

Protein capture in silica nanotube membrane 3-D microwell arrays

The microarray format has allowed for rapid and sensitive detection of thousands of analyte DNAs in a single sample, and there is considerable interest in extending this technology to protein biosensing. While glass is the most common substrate for microarrays, its binding capacity is limited because the glass surface is flat. One way to overcome this limitation is to develop arrays based on porous materials. Such "3-D" arrays can provide greater sensitivity because both the capture molecules and the analyte species they bind are immobilized throughout the thickness of the porous material. We describe here 3-D protein microarrays based on nanopore alumina membranes that contain silica nanotubes within the pores. These microarrays are prepared via a plasma-etch method using a TEM grid as the etch mask and consist of individual nanotube-containing microwells imbedded in a Ag film that coats the alumina membrane surface. We show that the microwells can be functionalized with antibodies and that these antibodies can capture their antigen proteins, which serve as prototype analytes. The analyte proteins are fluorescently tagged, which allows for fluorescence microscopy-based imaging of the array. The Ag surrounding the microwells shows very low background fluorescence, thus improving the signal-background ratio obtained from these arrays.     

Aptamer-based detection and quantitative analysis of ricin using affinity probe capillary electrophoresis

The ability to detect sub-nanomolar concentrations of ricin using fluorescently tagged RNA aptamers is demonstrated. Aptamers rival the specificity of antibodies and have the power to simplify immunoassays using capillary electrophoresis. Under nonequilibrium conditions, a dissociation constant, Kd, of 134 nM has been monitored between the RNA aptamer and ricin A-chain. With use of this free-solution assay, the detection of 500 pM (approximately 14 ng/mL) or 7.1 amol of ricin is demonstrated. The presence of interfering proteins such as bovine serum albumin and casein do not inhibit this interaction at sub-nanomolar concentrations. When spiked with RNAse A, ricin can still be detected down to 1 nM concentrations despite severe aptamer degradation. This approach offers a promising method for the rapid, selective, and sensitive detection of biowarfare agents.     

Synchrotron infrared measurements of protein phosphorylation in living single PC12 cells during neuronal differentiation

Protein phosphorylation is a post-translational modification that is essential for the regulation of many important cellular activities, including proliferation and differentiation. Current techniques for detecting protein phosphorylation in single cells often involve the use of fluorescence markers, such as antibodies or genetically expressed proteins. In contrast, infrared spectroscopy is a label-free and noninvasive analytical technique that can monitor the intrinsic vibrational signatures of chemical bonds. Here, we provide direct evidence that protein phosphorylation in individual living mammalian cells can be measured with synchrotron radiation-based Fourier transform-infrared (SR-FT-IR) spectromicroscopy. We show that PC12 cells stimulated with nerve growth factor (NGF) exhibit statistically significant temporal variations in specific spectral features, correlating with changes in protein phosphorylation levels and the subsequent development of neuron-like phenotypes in the cells. The spectral phosphorylation markers were confirmed by bimodal (FT-IR/fluorescence) imaging of fluorescently marked PC12 cells with sustained protein phosphorylation activity. Our results open up new possibilities for the label-free real-time monitoring of protein phosphorylation inside cells. Furthermore, the multimolecule sensitivity of this technique will be useful for unraveling the associated molecular changes during cellular signaling and response processes.     

Subwavelength direct-write nanopatterning using optically trapped microspheres

A number of non-lithographic techniques are now available for processing materials on the nanoscale, including optical techniques capable of producing features that are much smaller than the wavelength of light used. However, these techniques can be limited in speed, ease of use, cost of implementation, or the range of patterns they can write. Here we report how Bessel beam laser trapping of microspheres near surfaces can be used to enable near-field direct-write subwavelength nanopatterning. Using the microsphere as an objective lens to focus the processing laser, we demonstrate arbitrary patterns and individual features with minimum sizes of approximately 100 nm (which is less than one-third the processing wavelength) and a positioning accuracy better than 40 nm in aqueous and chemical environments. Submicron spacing is maintained between the near-field objective and the substrate without active feedback control. If implemented with an array of optical traps, this approach could lead to a high-throughput probe-based method for patterning surfaces with subwavelength features.     

Engineering metal-impurity nanodefects for low-cost solar cells

As the demand for high-quality solar-cell feedstock exceeds supply and drives prices upwards, cheaper but dirtier alternative feedstock materials are being developed. Successful use of these alternative feedstocks requires that one rigorously control the deleterious effects of the more abundant metallic impurities. In this study, we demonstrate how metal nanodefect engineering can be used to reduce the electrical activity of metallic impurities, resulting in dramatic enhancements of performance even in heavily contaminated solar-cell material. Highly sensitive synchrotron-based measurements directly confirm that the spatial and size distributions of metal nanodefects regulate the minority-carrier diffusion length, a key parameter for determining the actual performance of solar-cell devices. By engineering the distributions of metal-impurity nanodefects in a controlled fashion, the minority-carrier diffusion length can be increased by up to a factor of four, indicating that the use of lower-quality feedstocks with proper controls may be a viable alternative to producing cost-effective solar cells.     

Secondary ion MS imaging to relatively quantify cholesterol in the membranes of individual cells from differentially treated populations

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is a well-established bioanalytical method for directly imaging the chemical distribution across single cells. Here we report a protocol for the use of SIMS imaging to comparatively quantify the relative difference in cholesterol level between the plasma membranes of two cells. It should be possible to apply this procedure to the study of other selected lipids. This development enables direct comparison of the chemical effects of different drug treatments and incubation conditions in the plasma membrane at the single-cell level. Relative, quantitative TOF-SIMS imaging has been used here to compare macrophage cells treated to contain elevated levels of cholesterol with respect to control cells. In situ fluorescence microscopy with two different membrane dyes was used to discriminate morphologically similar but differentially treated cells prior to SIMS analysis. SIMS images of fluorescently identified cells reveal that the two populations of cells have distinct outer leaflet membrane compositions with the membranes of the cholesterol-treated macrophages containing more than twice the amount of cholesterol of control macrophages. Relative quantification with SIMS to compare the chemical composition of single cells can provide valuable information about normal biological functions, causative agents of diseases, and possible therapies for diseases.     

Immobilization of DNA hydrogel plugs in microfluidic channels

Acrylamide-modified DNA probes are immobilized in polycarbonate microfluidic channels via photopolymerization in a polyacrylamide matrix. The resulting polymeric, hydrogel plugs are porous under electrophoretic conditions and hybridize with fluorescently tagged complementary DNA. The double-stranded DNA can be chemically denatured, and the chip may be reused with a new analytical sample. Conditions for photopolymerization, hybridization, and denaturation are discussed. We also demonstrate the photopolymerization of plugs containing different DNA probe sequences in one microfluidic channel, thereby enabling the selective detection of multiple DNA targets in one electrophoretic pathway.     

Validity of the diffusion approximation in bio-optical imaging

Accurate numerical simulations based on rigorous radiative transfer theory are used to assess the validity of the diffusion approximation that is frequently used in bio-optical imaging. These simulations show that the error is large for a non-index-matched boundary between air and tissue. This weakness of the diffusion approximation underscores the need to understand how diffusion theory can be used to extract accurate values of tissue optical properties. A validity criterion for the diffusion approximation is established on the basis of the single-scattering albedo a and the asymmetry factor g for a slab with index-matched boundaries.     

Identification of components of protein complexes using a fluorescent photo-cross-linker and mass spectrometry

This study describes a novel method for improving the specific recognition, detection, and identification of proteins involved in multiprotein complexes. The method is based on a combination of coimmunoprecipitation, chemical cross-linking, and specific fluorescent tagging of protein components in close association with one another. Specific fluorescent tagging of the protein complex components was achieved using the cleavable, fluorescent cross-linker sulfosuccinimidyl 2-(7-azido-4-methylcoumarin-3-acetamido) ethyl-1,3'-dithiopropionate (SAED). Following dissociation and separation by SDS-PAGE, the fluorescently tagged proteins are then visualized by UV illumination, excised, and, following in-gel digestion, identified by mass spectrometry. In this study, a complex of the HIV-envelope protein gp120 and its cellular receptor CD4 was used as a model system. The sensitivity of detection of fluorescent SAED-labeled proteins in SDS gels, and the sensitivity of the mass spectrometric identification of fluorescent proteins after in-gel digestion, is in the range of a few hundred femtomoles of protein. This sensitivity is comparable to that achieved with silver-staining techniques, but fluorescence detection is protein independent and no background interference occurs. Furthermore, fluorescence labeling is significantly more compatible with mass spectrometric identification of proteins than is silver staining. The first application of this strategy was in the investigation of the mechanism of spermiation, the process by which mature spermatids separate from Sertoli cells. For the coimmunoprecipitation experiment, an antibody against paxillin, a protein involved in spermatid-Sertoli cell junctional complexes, was used. More components of the paxillin protein complex were visible by fluorescence detection of SAED-labeled proteins than were visible on comparable silver-stained gels. Mass spectrometric analysis of the fluorescently labeled proteins identified integrin alpha6 precursor as a protein associated in a complex with paxillin. The identification of integrin alpha6 precursor was confirmed by Western blot analysis and verifies the applicability of this novel approach for identifying proteins involved in protein complexes.