Detection Of Single Protein Molecules Research Articles

Translocation of Specific DNA Nanocarrier through an Ultrasmall Nanopipette: Toward Single-Protein-Molecule Detection with Superior Signal-to-Noise Ratio.

The use of functional DNA nanostructures as carriers to ship proteins through solid-state nanopores has recently seen substantial growth in single-protein-molecule detection (SPMD), driven by the potential of this methodology and implementations that it may enable. Ultrasmall nanopores have exhibited obvious advantages in spatiotemporal biological detection due to the appropriate nanoconfined spaces and unique properties. Herein, a 6.8 nm DNA tetrahedron (TDN) with a target-specific DNA aptamer (TDN-apt) was engineered to carry the representative target of acetylcholinesterase (AChE) through an ultrasmall nanopipet with a 30 nm orifice, underpinning the advanced SPMD of AChE with good performance in terms of high selectivity, low detection limit (0.1 fM), and especially superior signal-to-noise ratio (SNR). The kinetic interaction between TDN-apt and AChE was studied and the practical applicability of the as-developed SPMD toward real samples was validated using serum samples from patients with Alzheimer's disease. This work not only presented a feasible SPMD solution toward low-abundance proteins in complex samples and but also was envisioned to inspire more interest in the design and implementation of synergized DNA nanostructure-ultrasmall nanopore systems for future SPMD development.

Sensitivity Analysis of Gold Nanorod Biosensors for Single Molecule Detection

Single protein molecule detection is important for investigating molecular behavior and diagnosing diseases at an early stage. Gold nanorod (GNR) biosensors have shown promise for label-free detection of single protein molecules. However, for widespread applications of GNR biosensors with high sensitivity, detail studies are needed to understand the effects of the sensing environment and the molecular binding dynamics on the sensitivity. In this work, a comprehensive theoretical analysis with variable substrate, buffer, ligand, and binding position of the target molecules shows that GNR biosensors are highly sensitive for single molecule detection of biological samples including critical pathogens such as cancer marker thyroglobulin and human immunodeficiency virus (HIV) marker glycoprotein. We also propose and show that a GNR biosensor with a dielectric cladding layer on the body increases the sensitivity by orders of magnitude compared to other state-of-the-art biosensors.

Observation of giant conductance fluctuations in a protein

Proteins are insulating molecular solids, yet even those containing easily reduced or oxidized centers can have single-molecule electronic conductances that are too large to account for with conventional transport theories. Here, we report the observation of remarkably high electronic conductance states in an electrochemically inactive protein, the ∼200 kD αVβ3 extracellular domain of human integrin. Large current pulses (up to nA) were observed for long durations (many ms, corresponding to many pC of charge transfer) at large gap (>5 nm) distances in an STM when the protein was bound specifically by a small peptide ligand attached to the electrodes. The effect is greatly reduced when a homologous, weakly binding protein (α4β1) is used as a control. In order to overcome the limitations of the STM, the time- and voltage-dependence of the conductance were further explored using a fixed-gap (5 nm) tunneling junction device that was small enough to trap a single protein molecule at any one time. Transitions to a high conductance (∼nS) state were observed, the protein being ‘on’ for times from ms to tenths of a second. The high-conductance states only occur above ∼100 mV applied bias, and thus are not an equilibrium property of the protein. Nanoamp two-level signals indicate the specific capture of a single molecule in an electrode gap functionalized with the ligand. This offers a new approach to label-free electronic detection of single protein molecules. Electronic structure calculations yield a distribution of energy level spacings that is consistent with a recently proposed quantum-critical state for proteins, in which small fluctuations can drive transitions between localized and band-like electronic states.

Single Protein Molecule Detection by Glass Nanopores

Nanopores can be used to detect and analyze single molecules in solution. We have used glass nanopores made by laser-assisted capillary-pulling, as a high-throughput and low cost method, to detect a range of label-free proteins: lysozyme, avidin, IgG, β-lactoglobulin, ovalbumin, bovine serum albumin (BSA), and β-galactosidase in solution. Furthermore, we show for the first time solid state nanopore measurements of mammalian prion protein, which in its abnormal form is associated with transmissible spongiform encephalopathies. Our approach provides a basis for protein characterization and the study of protein conformational diseases by nanopore detection.

Single Protein Molecule Detection with a Transfer-APTamer (Piston) Sliding in a Protein Pore

Aptamers are specific oligonucleotide molecules that bind to various biologically important target molecules. Nanopores are powerful tools for the identification and detection of single molecules, such as DNA, RNA and proteins. α-hemolysin nanopore is utilized to sense the single protein molecule with a transfer-aptamer (piston). The transfer-aptamer (piston) containing polyethylene glycol (PEG) has functions as identified which zone of the beta barrel of pore. Here we report the formation of reversible signature signals using protein engineering, and characterized change the pore conductance depend on special design of transfer-aptamer (piston). The transfer-aptamer was bound with thrombin, which can be trapped to the pore opening and distinguished signature current block compared the thrombin being released from the transfer-aptamer (piston). But, the signal of aptamer only contains DNA which is indistinguishable with or without thrombin. By containing specific tail of aptamer, presence of single protein molecule, we capture the reversible thrombin signature signal using protein pore. The transfer-aptamer (piston) can be used as detector of different ions for nanomachine, nanomaterials, and folding process.

Engineered nanopores for single-molecule detection of proteins

T underlying principle of nanopore probe techniques is quite simple: The application of a voltage bias across an electrically insulated membrane enables the measurement of a tiny picoamp-scale transmembrane current through a single hole of nanometer size, called a nanopore. Each molecule, translocating through the nanopore, produces a distinctive current blockade, the nature of which depends on its biophysical properties as well as the molecule-nanopore interaction. I will describe our recent strategies for engineering new functional nanopores for single-molecule protein detection, both in organic and siliconbased materials, and with properties that are not encountered in nature. From a practical point of view, this methodology shows promise for the integration of engineered nanopores into nanofluidic devices, which would provide a new generation of research tools in nanomedicine and in high-throughput applications for molecular biomedical diagnosis.

Single-pair fluorescence resonance energy transfer (spFRET) for the high sensitivity analysis of low-abundance proteins using aptamers as molecular recognition elements.

We have developed a strategy for the detection of single protein molecules, which uses single-pair fluorescence resonance energy transfer (spFRET) as the readout modality and provides exquisite analytical sensitivity and reduced assay turn-around-time by eliminating various sample pre-processing steps. The single-protein detection assay uses two independent aptamer recognition events to form an assembly conducive to intramolecular hybridization of oligonucleotide complements that are tethered to the aptamers. This hybridization brings a donor-acceptor pair within the Förster distance to create a fluorescence signature indicative of the presence of the protein-aptamer(s) association complex. As an example of spFRET, we demonstrate the technique for the analysis of serum thrombin. The assay requires co-association of two distinct epitope-binding aptamers, each of which is labeled with a donor or acceptor fluorescent dye (Cy3 or Cy5, respectively) to produce a FRET response. The FRET response between Cy3 and Cy5 was monitored by single-molecule photon-burst detection, which provides high analytical sensitivity when the number of single-molecule events is plotted versus the target concentration. We are able to identify thrombin with high efficiency based on photon burst events transduced in the Cy5 detection channel. We also demonstrate that the technique can discriminate thrombin molecules from its analogue prothrombin. The analytical sensitivity was >200-fold better than an ensemble measurement.

Ultrasensitive Fluorescence Detection of Single Protein Molecules Manipulated Electrically on Au Nanowire

Proteins assembled on an Au nanowire are manipulated by an electrical potential applied on the nanowire, which leads to the modulation of molecular fluorescence. The molecular modality can be unequivocally correlated with the modulated fluorescence, which enables the specific fluorescence from a single target protein to be unambiguously distinguished from background noise and nonspecific fluorescence. As demonstrated through a thrombin assay, this simple method can significantly improve the sensitivity and specificity of the protein detection down to the single molecule level.

Label-Free Detection of Single Protein Molecules and Protein−Protein Interactions Using Synthetic Nanopores

Nanofabricated pores in 20 nm-thick silicon nitride membranes were used to probe various protein analytes as well as to perform an antigen-antibody binding assay. A two-compartment electrochemical cell was separated by a single nanopore, 28 nm in diameter. Adding proteins to one compartment caused current perturbations in the ion current flowing through the pore. These perturbations correlated with both the charge and the size of the protein or of a protein-protein complex. The potential of this nanotechnology for studying protein-protein interactions is highlighted with the sensitive detection of beta-human chorionic gonadotropin, a hormone and clinical biomarker of pregnancy, by monitoring in real time and at a molecular level the formation of a complex between hormones and antibodies in solution. In this form, the assay compared advantageously to immunoassays, with the important difference that labels, immobilization, or amplification steps were no longer needed. In conclusion, we present proof-of-principle that properties of proteins and their interactions can be investigated in solution using synthetic nanopores and that these interactions can be exploited to measure protein concentrations accurately.

Polymer Nanochannels Fabricated by Thermomechanical Deformation for Single-Molecule Analysis

A simple method for fabricating nanoscale channels based on thermomechanical deformation of rigid polymer substrates is demonstrated. Polycarbonate preforms containing microchannels with cross-sectional dimensions on the order of tens of micrometers are controllably deformed to produce submicrometer dimensions. The reduced channel dimensions are achieved by heating the preform while applying a uniaxial tensile force to reduce channel cross sections through the Poisson effect. Nanochannels with circular or elliptical cross sections are defined by varying the channel position and preform geometry prior to deformation. Arrays of parallel nanochannels with critical dimensions down to 400 nm are described. Using the fabrication method, a nanochannel network is fabricated for the detection of single protein molecules via confocal fluorescence microscopy. The chip includes a detection channel with cross-sectional dimensions approaching the confocal volume dimensions of the detection optics and a larger adjacent reference channel used to optimize focusing. Detection of fluorescently labeled bovine serum albumin at 15 and 150 nM concentrations is presented, demonstrating the ability to perform single-molecule fluorescence measurements in polycarbonate chips using visible wavelengths for excitation and detection.

Novel solution-phase immunoassays for molecular analysis of tumor markers.

at 3 x 10(9) M(-1) and a step-wise binding process with PSA-free MAB. Thus, this solution-phase quantitative ECL immunoassay allowed measurement of the affinity of serum PSAs with their MABs and screening of PSAs based upon their affinity to MABs. Unlike other immunoassays, this immunoassay demonstrated one-step rapid analysis while simultaneously eliminating immobilization, separation and washing steps and detected PSA at a level of 1.7 pg mL(-1), which is 1000-fold more sensitive than current PSA immunoassays. Furthermore, single-molecule (SM) phosphorescence microscopy was developed to detect single serum PSA-free and PSA-complex molecules in solution with no use of antibody showing that PSA-free molecules diffused faster than PSA-complex molecules in solution. This finding is consistent with ECL measurements and implies the possibility of screening individual analytes in a complex mixture using their distinct SM diffusion distance. This is the first report describing the detection of single protein molecules labeled with a metal-complex using phosphorescence microscopy and also the screening of serum tumor markers using ECL and SM phosphorescence solution-phase assays.