Probing single-molecule by surface-enhanced resonance Raman scattering with linearly and circularly polarized laser

Rhodamine 6G (R6G) was incubated in silver sols with different low concentrations and its surface-enhanced resonance Raman scattering (SERRS) spectra, excited by linearly and circularly polarized light, respectively, were studied. At the single-molecule level the SERRS spectra were recorded in 10(-13) M dye colloidal solution. Spectral inhomogeneous behaviors from single-molecule were observed such as spectral polarization, spectral diffusion and intensity fluctuations of vibrational lines. Difference between SERRS spectra of R6G excited by linearly and circularly polarized light and the effect of the polarizing angle of Raman signal relative to the slit of spectrograph on the Raman spectral polarization were analyzed and measured experimentally. Circularly polarized laser and the correction of the polarizing angle of Raman signal are necessary to avoid fake results in the measuring of Raman spectral of single-molecule, which was not noticed in initial papers. (c) 2005 Elsevier B.V. All rights reserved.

Constitutive plasma membrane targeting and microdomain localization of Dok5 studied by single-molecule microscopy

In the present study, single-molecule fluorescence microscopy was used to examine the characteristics of plasma membrane targeting and microdomain localization of enhanced yellow fluorescent protein (eYFP)-tagged wild-type Dok5 and its variants in living Chinese hamster ovary (CHO) cells. We found that Dok5 can target constitutively to the plasma membrane, and the PH domain is essential for this process. Furthermore, single-molecule trajectories analysis revealed that Dok5 can constitutively partition into microdomain on the plasma membrane. Finally, the potential mechanism of microdomain localization of Dok5 was discussed. This study provided insights into the characteristics of plasma membrane targeting and microdomain localization of Dok5 in living CHO cells. (C) 2008 Elsevier B.V. All rights reserved.

Heterodimerization of integrin Mac-1 subunits studied by single-molecule imaging

Heterodimerization of integrin Mac-1 (alpha(M) beta(2)) Subunits plays important role on regulating leukocytes adhesion to extracellular matrix or endothelial cells. Here, using total internal reflection microscopy, we investigated the heterodimerization of integrin Mac-1 subunits at the single-molecule level in live cells. Individual alpha(M) subunit fused to the enhanced yellow fluorescent protein (eYFP) was imaged at the basal plasma membrane of live Chinese hamster ovary (CHO) cells. Through analysis of mean square displacement (MSD), diffusion coefficient, the size of restricted domain and fraction of molecules undergoing restricted diffusion, we found that as compared with the diffusion in the absence of beta(2) subunit, the diffusion of single-molecule of alpha(M)-YFP was suppressed significantly in the presence of beta(2) subunit. Thus, based on the oligomerization-induced trapping model, we suggested that in the presence of beta(2) subunit, the am subunit may form heterodimer with it. (C) 2008 Elsevier Inc. All rights reserved.

Mechanistic studies of reactions at the single-molecule level using microfluidics with applications in molecular diagnostics

Motivated by needs in molecular diagnostics and advances in microfabrication, researchers started to seek help from microfluidic technology, as it provides approaches to achieve high throughput, high sensitivity, and high resolution. One strategy applied in microfluidics to fulfill such requirements is to convert continuous analog signal into digitalized signal. One most commonly used example for this conversion is digital PCR, where by counting the number of reacted compartments (triggered by the presence of the target entity) out of the total number of compartments, one could use Poisson statistics to calculate the amount of input target.

However, there are still problems to be solved and assumptions to be validated before the technology is widely employed. In this dissertation, the digital quantification strategy has been examined from two angles: efficiency and robustness. The former is a critical factor for ensuring the accuracy of absolute quantification methods, and the latter is the premise for such technology to be practically implemented in diagnosis beyond the laboratory. The two angles are further framed into a “fate” and “rate” determination scheme, where the influence of different parameters is attributed to fate determination step or rate determination step. In this discussion, microfluidic platforms have been used to understand reaction mechanism at single molecule level. Although the discussion raises more challenges for digital assay development, it brings the problem to the attention of the scientific community for the first time.

This dissertation also contributes towards developing POC test in limited resource settings. On one hand, it adds ease of access to the tests by incorporating massively producible, low cost plastic material and by integrating new features that allow instant result acquisition and result feedback. On the other hand, it explores new isothermal chemistry and new strategies to address important global health concerns such as cyctatin C quantification, HIV/HCV detection and treatment monitoring as well as HCV genotyping.

Cryogenic single-shot spectroscopy of a floating poly-silicon gate transistor

Trapped electrons, located close to the channel of a transistor, are promising as data storage elements in non-classical information processing. Cryogenic microwave spectroscopy has shown that these electrons give rise to high quality factor resonances in the drain current and a post excitation dynamic behaviour that is related to the system lifetime. Using a floating poly-silicon gate transistor, single shot spectroscopy is performed to characterise the dynamic behaviour during excitation. This behaviour is seen to be dominated by the decay of the transient component, which gives rise to oscillations around the high quality factor resonance. © 2012 American Institute of Physics.

Polychromatic single-shot spectroscopy on SOI-FET trapped electrons

The behavior of trapped electrons, in a dielectric close to the channel of a silicon SOI-FET, is studied by cryogenic microwave spectroscopy. On-resonance microwave excitation causes one of these trapped electrons to undergo spatial Rabi oscillations between widely separated trap sites. This charge displacement causes a change in the drain current of the transistor, resulting in high quality factor resonances in continuous wave spectroscopy. The potential of this effect for non-classical information processing is investigated through polychromatic single-shot spectroscopy, using on-resonance and difference frequencies. Interaction between different trapped electrons is seen in the post excitation behavior and the possibilities of quantum gate operations are discussed. © The Electrochemical Society.

Biofunctionalization of PET/SiO2 surfaces for single molecule experiments and medical applications

PET/SiO2 layers were chemically modified to maintain immobilization of functional single molecules. GFP molecules provide an ideal system due to their stability and intrinsic fluorescence. GFP in vivo biotinylated within its NH2-terminal region and attached on the substrate via the biotinstreptavidin bond was further investigated with confocal microscopy, atomic force microscopy (AFM) and spectroscopic ellipsometry (SE). AFM revealed monolayered donut-like structures representing assemblies of biotinstreptavidinbiotinGFP immobilized onto PET/SiO2 surfaces via mPEG. In particular, regions with an approximate height of 12 nm, which approaches the molecular dimensions of the above complex given by molecular modeling, could be detected. The dimensions of the donut-like structures suggest a close-to-each-other positioning of the GFP molecules - which, however, retain their functionality, as evidenced by confocal microscopy. © 2011 World Scientific Publishing Company.

Probing Charge Transport of Ruthenium-Complex-Based Molecular Wires at the Single-Molecule Level

A ruthenium(II) bis(sigma-arylacetylide)-complex-based molecular wire functionalized with thiolacetyl alligator clips at both ends (OPERu) was used to fabricate gold substrate-molecular wire-conductive tip junctions. To elucidate the ruthenium-complex-enhanced charge transport, we conducted a single-molecule level investigation using the technique-combination method, where electronic delay constant, single-molecular conductance, and barrier height were obtained by scanning tunneling microscopy (STM) apparent height measurements, STM break junction measurements, and conductive probe-atomic force microscopy (CP-AFM) measurements, respectively.

Four New Lanthanide-Nitronyl Nitroxide (Ln(III)=Pr-III, Sm-III, Eu-III, Tm-III) Complexes and a Tb-III Complex Exhibiting Single-Molecule Magnet Behavior

Five new complexes based on rare-earth-radical [Ln(hfac)(3)(NIT-5-Br-3py)](2) (Ln=Pr (1), Sm (2), Eu (3), Tb (4), Tm (5); hfac = hexafluoroacetylacetonate; NIT-5-Br-3py = 2-(4,4,5,5-tetramethyl-3-oxylimidazoline-1-oxide)-5-bromo-3-pyridine) have been synthesized and characterized by X-ray crystal diffraction. The single-crystal structures show that these complexes have similar structures, in which a NIT-5-Br-3py molecule acts as a bridging ligand linking two Ln(III) ions through the oxygen atom of the N-O group and nitrogen atom from the pyridine ring to form a four-spin system. Both static and dynamic magnetic properties were measured for complex 4, which exhibits single-molecule magnetism behavior.

A monometallic tri-spin single-molecule magnet based on rare earth radicals

A mononuclear tri-spin single-molecule magnet based on the rare earth radical [Tb(hfac)(3)(NITPhOEt)(2)] (NITPhOEt = 4'-ethoxy-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) has been synthesized, structurally characterized and the alternating current signals show a slow relaxation of magnetization and frequency-dependent signals.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.