Direct visualization of ligand-protein interactions using atomic force microscopy.
ABSTRACT 1. Streptavidin is a 60-kDa tetramer which binds four molecules of biotin with extremely high affinity (K(A) approximately 10(14) M(-1)). We have used atomic force microscopy (AFM) to visualize this ligand-protein interaction directly. 2. Biotin was tagged with a short (152-basepair; 50-nm) DNA rod and incubated with streptavidin. The resulting complexes were then imaged by AFM. The molecular volume of streptavidin calculated from the dimensions of the protein particles (105+/-3 nm(3)) was in close agreement with the value calculated from its molecular mass (114 nm(3)). Biotinylation increased the apparent size of streptavidin (to 133+/-2 nm(3)), concomitant with an increase in the thermal stability of the tetramer. 3. Images of streptavidin with one to four molecules of DNA-biotin bound were obtained. When two ligands were bound, the angle between the DNA rods was either acute or obtuse, as expected from the relative orientations of the biotin binding sites. The ratio of acute : obtuse angles (1 : 3) was lower than the expected value (1 : 2), indicating a degree of steric hindrance in the binding of the DNA-biotin. The slight under-representation of higher occupancy states supported this idea. 4. Streptavidin with a single molecule of DNA-biotin bound was used to tag biotinylated beta-galactosidase, a model multimeric enzyme. 5. The ability to image directly the binding of a ligand to its protein target by AFM provides useful information about the nature of the interaction, and about the effect of complex formation on the structure of the protein. Furthermore, the use of DNA-biotin/streptavidin tags could potentially shed light on the architecture of multi-subunit proteins.
Article: High sensitivity photonic crystal biosensor incorporating nanorod structures for enhanced surface area[show abstract] [hide abstract]
ABSTRACT: The surface area of a photonic crystal biosensor is greatly enhanced through the incorporation of a porous TiO2 film possessing the structure of nanorods into the device. The film is deposited by the glancing angle deposition technique in an e-beam evaporation system. The sensitivity of high surface area sensors is compared with sensors without the high surface area coating. Results for detection of polymer films, large proteins and small molecules indicate up to a four-fold enhancement of detected adsorbed mass density.Sensors and Actuators B: Chemical.
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ABSTRACT: We present the development of an analytical model that can be used for the rational design of a biosensor based on shifts in the local surface plasmon resonance (LSPR) of individual gold nanoparticles. The model relates the peak wavelength of light scattered by an individual plasmonic nanoparticle to the number of bound analyte molecules and provides an analytical formulation that predicts relevant figures-of-merit of the sensor such as the molecular detection limit (MDL) and dynamic range as a function of nanoparticle geometry and detection system parameters. The model calculates LSPR shifts for individual molecules bound by a nanorod, so that the MDL is defined as the smallest number of bound molecules that is measurable by the system, and the dynamic range is defined as the maximum number of molecules that can be detected by a single nanorod. This model is useful because it will allow a priori design of an LSPR sensor with figures-of-merit that can be optimized for the target analyte. This model was used to design an LSPR sensor based on biotin-functionalized gold nanorods that offers the lowest MDL for this class of sensors. The model predicts a MDL of 18 streptavidin molecules for this sensor, which is in good agreement with experiments and estimates. Further, we discuss how the model can be utilized to guide the development of future generations of LSPR biosensors.ACS Nano 04/2009; 3(4):795-806. · 10.77 Impact Factor
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ABSTRACT: Synthetic nanopores have been used to study individual biomolecules in high throughput, but their performance as sensors does not match that of biological ion channels. Challenges include control of nanopore diameters and surface chemistry, modification of the translocation times of single-molecule analytes through nanopores, and prevention of non-specific interactions with pore walls. Here, inspired by the olfactory sensilla of insect antennae, we show that coating nanopores with a fluid lipid bilayer tailors their surface chemistry and allows fine-tuning and dynamic variation of pore diameters in subnanometre increments. Incorporation of mobile ligands in the lipid bilayer conferred specificity and slowed the translocation of targeted proteins sufficiently to time-resolve translocation events of individual proteins. Lipid coatings also prevented pores from clogging, eliminated non-specific binding and enabled the translocation of amyloid-beta (Aβ) oligomers and fibrils. Through combined analysis of their translocation time, volume, charge, shape and ligand affinity, different proteins were identified.Nature Nanotechnology 02/2011; 6(4):253-60. · 27.27 Impact Factor