Design and synthesis of single-nanoparticle optical biosensors for imaging and characterization of single receptor molecules on single living cells

At the cellular level, a small number of protein molecules (receptors) can induce significant cellular responses, emphasizing the importance of molecular detection of trace amounts of protein on single living cells. In this study, we designed and synthesized silver nanoparticle biosensors (AgMMUA-IgG) by functionalizing 11.6 +/- 3.5-nm Ag nanoparticles with a mixed monolayer of 11-mercaptoundecanoic acid (MUA) and 6-mercapto-1-hexanol (1:3 mole ratio) and covalently conjugating IgG with MUA on the nanoparticle surface. We found that the nanoparticle biosensors preserve their biological activity and photostability and can be utilized to quantitatively detect individual receptor molecules (T-ZZ), map the distribution of receptors (0.21-0.37 molecule/microm(2)), and measure their binding affinity and kinetics at concentrations below their dissociation constant on single living cells in real time over hours. The dynamic range of detection is 0-50 molecules per cell. We also found that the binding rate (2-27 molecules/min) is highly dependent upon the coverage of receptors on living cells and their ligand concentration. The binding association and dissociation rate constants and affinity constant are k1 = (9.0 +/- 2.6) x 10(3) M(-1) s(-1), k(-1) = (3.0 +/- 0.4) x 10(-4) s(-1), and KB = (4.3 +/- 1.1) x 10(7) M(-1), respectively.     

Probing specific sequences on single DNA molecules with bioconjugated fluorescent nanoparticles

Nanometer-sized fluorescent particles (latex nanobeads) have been covalently linked to DNA binding proteins to probe specific sequences on stretched single DNA molecules. In comparison with single organic fluorophores, these nanoparticle probes are brighter, are more stable against photobleaching, and do not suffer from intermittent on/off light emission (blinking). Specifically, we demonstrate that the site-specific restriction enzyme EcoRI can be conjugated to 20-nm fluorescent nanoparticles and that the resulting nanoconjugates display DNA binding and cleavage activities of the native enzyme. In the absence of cofactor magnesium ions, the EcoRI conjugates bind to specific sequences on double-stranded DNA but do not initiate enzymatic cutting. For single DNA molecules that are stretched and immobilized on a solid surface, nanoparticles bound at specific sites can be directly visualized by multicolor fluorescence microscopy. Direct observation of site-specific probes on single DNA molecules opens new possibilities in optical gene mapping and in the fundamental study of DNA-protein interactions.     

Probing the radiative transition of single molecules with a tunable microresonator

Using a tunable optical microresonator with subwavelength spacing, we demonstrate controlled modulation of the radiative transition rate of a single molecule, which is measured by monitoring its fluorescence lifetime. Variation of the cavity length changes the local mode structure of the electromagnetic field, which modifies the radiative coupling of an emitting molecule to that field. By comparing the experimental data with a theoretical model, we extract both the pure radiative transition rate as well as the quantum yield of individual molecules. We observe a broad scattering of quantum yield values from molecule to molecule, which reflects the strong variation of the local interaction of the observed molecules with their host environment.     

Tracking individual kinesin motors in living cells using single quantum-dot imaging

We report a simple method using semiconductor quantum dots (QDs) to track the motion of intracellular proteins with a high sensitivity. We characterized the in vivo motion of individual QD-tagged kinesin motors in living HeLa cells. Single-molecule measurements provided important parameters of the motor, such as its velocity and processivity, as well as an estimate of the force necessary to carry a QD. Our measurements demonstrate the importance of single-molecule experiments in the investigation of intracellular transport as well as the potential of single quantum-dot imaging for the study of important processes such as cellular trafficking, cell polarization, and division.     

Real-time monitoring of intracellular mRNA hybridization inside single living cells

A molecular beacon, an oligonucleotide probe with inherent signal transduction mechanisms, is an optimal tool for visualizing real-time mRNA hybridization in single living cells. Each molecular beacon (MB) consists of a single-stranded DNA molecule in a stem-loop conformation with a fluorophore linked to the 5' end and a quencher at the 3' end. In this study, we demonstrate real-time monitoring of mRNA-DNA hybridization inside living cells using molecular beacons. A MB specific for beta-actin mRNA has been designed and synthesized. After microinjection into the cytoplasm of single living kangaroo rat kidney cells (PtK2 cells), the MB hybridizes with beta-actin mRNA as shown by fluorescence measurements over time. Hybridization dynamics have been followed. Strict control experiments have been carried out to confirm that the fluorescence signal increase is indeed due to the hybridization of mRNA inside single living cells. Variation in the MB/mRNA hybridization fluorescent signal has been observed for different PtK2 cells, which indicates the amount of mRNA in different cells is different. We have also monitored the beta-1 andrenergic receptor mRNA inside the PtK2 cells. These studies demonstrate the feasibility of using MBs and the ultrasensitivity achieved in our fluorescence imaging system for real-time detection of mRNA hybridization and for the visualization of oligonucleotide/mRNA interactions inside single living cells.     

Probing intrinsic and extrinsic components in single osteosarcoma cells by near-infrared surface-enhanced Raman scattering

We report on the capabilities of near-infrared surface-enhanced Raman scattering (SERS) using gold nanoparticles to obtain detailed chemical information with high spatial resolution from within single cancer cells, living or fixed. Colloidal gold particles, 60 nm in size, were introduced into live human osteosarcoma cells by endocytosis by adding them to the growth medium. Rapid SERS mapping of cells indicated that not only could rich vibrational spectra be obtained from intrinsic cellular constituents both in the cytoplasm and nucleus and but also the distribution of extrinsic molecules introduced into the cells, in this case, rhodamine 6G could be characterized, suggesting that the intracellular distribution of chemotherapeutic agents could potentially be measured by this technique. We show that the SERS signal intensity from the cellular components increases and more spectral detail is acquired from dried cells when compared with hydrated cells in buffer. The data also show spectral fluctuations, mainly in intensity but also in peak position, which are dependent upon the intensity of the excitation light and are probably due to diffusion of molecules on the surface of the gold nanoparticles. A detailed understanding of the origins of these effects is still not complete, but the ability to acquire very sensitive SERS inside living cancer cells indicates the potential of this technique as a useful tool in biomedicine.     

Probing the effects of conjugation path on the electronic transmission through single molecules using scanning tunneling microscopy

A systematic study of the relationship between the molecular structure of a series of thiol end-capped oligo-phenylenevinylenes (OPVs) and the coherent electronic transmission at the single molecule level was measured by scanning tunneling microscopy (STM). This reveals a significant change in the electronic transparency of various OPV derivatives due to the insertion of a methylene spacer group or due to nitro group substitution. Apparently, changes in the conjugation path through the central benzene ring from para to meta substitution does not have a profound effect on the electronic transparency of the molecules.     

Visualization of nonengineered single mRNAs in living cells using genetically encoded fluorescent probes

Single mRNA imaging in live cells is a useful technique to elucidate its precise localization and dynamics. We developed a method for visualizing endogenous mRNAs in living cells with single molecule sensitivity using genetically encoded probes. An RNA-binding protein of human PUMILIO1 (PUM-HD) was used for recognizing base sequences of a target mRNA, β-actin mRNA. Two PUM-HDs were modified by amino acid mutations to bind specifically to tandem 8-base sequences of the target mRNA. Because each PUM-HD was connected with amino- and carboxyl-terminal fragments of enhanced green fluorescent protein (EGFP), the probes emit fluorescence by reconstitution of EGFP fragments upon binding to β-actin mRNAs. The EGFP reconstituted on the mRNAs was monitored with a total internal reflection fluorescence microscope. Results show that each fluorescent spot in live cells represented a single β-actin mRNA and that distinct spatial and temporal movement of the individual β-actin mRNAs was visualized. We also estimated the average velocity of the movement of the single mRNAs along microtubules in live cells. This method is widely applicable to tracking various mRNAs of interest in the native state of living cells with single-mRNA sensitivity.     

Probing hydrogen molecules with a laboratory Raman lidar

Technical Physics Letters - The intensity of Raman backscattering from molecular hydrogen in a cell was studied by Raman lidar as a function of the sounding distance. From these data, the...     

Probing single quantum dots by micro-photoluminescence

Using micro-photoluminescence, emissions from single CdSe quantum dots were observed from the cleaved (110) facets of ZnSe/CdSe/ZnSe heterostructures grown on GaAs (001) substrates. The emission intensity of a single quantum dot was linearly proportional to the excitation intensity, demonstrating excitonic features. Emissions from these single quantum dots were found to polarize within the (001) plane, providing information on the shapes of the quantum dots.     

Probing molecules in integrated silicon-molecule-metal junctions by inelastic tunneling spectroscopy

Molecular electronics has drawn significant attention for nanoelectronic and sensing applications. A hybrid technology where molecular devices are integrated with traditional semiconductor microelectronics is a particularly promising approach for these applications. Key challenges in this area include developing devices in which the molecular integrity is preserved, developing in situ characterization techniques to probe the molecules within the completed devices, and determining the physical processes that influence carrier transport. In this study, we present the first experimental report of inelastic electron tunneling spectroscopy of integrated metal-molecule-silicon devices with molecules assembled directly to silicon contacts. The results provide direct experimental confirmation that the chemical integrity of the monolayer is preserved and that the molecules play a direct role in electronic conduction through the devices. Spectra obtained under varying measurement conditions show differences related to the silicon electrode, which can provide valuable information about the physics influencing carrier transport in these molecule/Si hybrid devices.     

On photo-oxidation of single molecules

Fluorescence and fluorescence excitation spectra of terrylene in 9,10-dibromoanthracene matrix were studied at 5 K. Characteristic singlet oxygen phosphorescence, O₂(¹Δ_g) → O₂(³Σ_g) with the line maximum at 1272.5 nm, was observed after excitation of terrylene molecules embedded into one of its two sites. It indicates that singlet oxygen, precursor in photo-oxidation of aromatic molecules, can be created only for those oxygen molecules which can form weak van der Waals complex with terrylene. According to quantum-chemical calculations terrylene and oxygen can form complex with the bonding energy 141 cm⁻¹, in which oxygen molecule is located along the long axis of terrylene, ∼0.3 nm apart, with the molecular axis inclined by 110°.     

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.