Real time measurements of elongation by a reverse transcriptase using surface plasmon resonance.

A rapid direct assay for polymerase-induced elongation along a given template is an obligate requirement for understanding the processivity of polymerization and the mode of action of drugs and inhibitors on this process. Surface plasmon resonance can be used to follow the association and the dissociation rates of a given reverse transcriptase on DNA.RNA and DNA.DNA hybrids immobilized on a biotin-streptavidin surface. The addition of nucleotides complementary to the template strand produces an increase in the local mass, as deduced from an increase in the measured signal, due to elongation of the primer strand that allows an estimation of both the extent and rate of the polymerization process. The terminator drug 3'-deoxy-3'-azidothymidine triphosphate completely abolishes the increase in signal as would be expected from an inhibition of elongation. This technique provides a sensitive assay for the affinities of different polymerases for specific templates and for the effects of terminators of the elongation process.

Low concentrations of diacylglycerol promote the binding of apolipophorin III to a phospholipid bilayer: a surface plasmon resonance spectroscopy study.

The binding of the exchangeable apolipoprotein apolipophorin III (apoLp-III) to an egg phosphatidylcholine bilayer as a function of the concentration of diacylglycerol (DG) in the bilayer was studied by surface plasmon resonance spectroscopy. At a DG concentration of 2 mol % in the bilayer, the binding of apoLp-III reached saturation. Under saturating conditions, apoLp-III forms a closely packed monolayer approximately 55 A thick, in which each molecule of protein occupies approximately 500 A2 at the membrane surface. These dimensions are consistent with the molecular size of the apoLp-III molecule determined by x-ray crystallography, if apoLp-III binds to the bilayer with the long axis of the apoLp-III normal to the membrane surface. In the absence of protein, the overall structure of the lipid bilayer was not significantly changed up to 2.5 mol% DG. However, at 4 and 6 mol % DG, the presence of nonbilayer structures was observed. The addition of apoLp-III to a membrane containing 6 mol % DG promoted the formation of large lipid-protein complexes. These data support a two-step sequential binding mechanism for binding of apoLp-III to a lipid surface. The first step is a recognition process, consisting of the adsorption of apoLp-III to a nascent hydrophobic defect in the phospholipid bilayer caused by the presence of DG. This recognition process might depend on the presence of a hydrophobic sensor located at one of the ends of the long axis of the apoLp-III molecule but would be consolidated through H-bond and electrostatic interactions. Once primary binding is achieved, subsequent enlargement of the hydrophobic defect in the lipid surface would trigger the unfolding of the apolipoprotein and binding via the amphipathic alpha-helices. This two-step sequential binding mechanism could be a general mechanism for all exchangeable apolipoproteins. A possible physiological role of the ability of apoLp-III to bind to lipid structures in two orientations is also proposed.

Studies on the membrane interactions of the cyclotides kalata B1 and kalata B6 on model membrane systems by surface plasmon resonance

In this study we have demonstrated the interactions of kalata B1 and its naturally occurring analogue kalata B6 with five model lipid membranes and have analyzed the binding kinetics using surface plasmon resonance. Two kalata peptides showed a higher affinity for the phosphatidylethanolamine-containing membranes, indicating that the peptides would bind selectively to bacterial membranes. Also we have optimized the procedure for the immobilization of five liposome mixtures and have shown that the procedure provides reproducible levels of immobilized liposomes and could be used to screen the selective binding of putative antimicrobial peptides to model mammalian or microbial phospholipid membranes. (C) 2004 Elsevier Inc. All rights reserved.

Low refractive index gas sensing using a Surface Plasmon Resonance fibre device

A series of surface plasmonic fibre devices were fabricated using multiple coatings deposited on a lapped section of a single mode fibre. Coupling from the guided mode to surface plasmons was promoted following UV laser irradiation of the coated region through a phase mask, which generated a surface relief grating structure. The devices showed high spectral sensitivities and strong coupling for low refractive indices as compared to other grating-type fibre devices. The plasmonic devices were used to detect the variation in the refractive indices of alkane gases with measured wavelength and coupling sensitivity to index of 3400 nm RIU-1 and 8300 dB RIU-1, respectively. As a demonstration of the performance of these gas sensors, a minimum concentration of 2% by volume of butane in ethane was achieved.

Exploitation of multilayer coatings for infrared surface plasmon resonance fiber sensors

We demonstrate surface plasmon resonance (SPR) fiber devices based upon ultraviolet inscription of a grating-type structure into both single-layered and multilayered thin films deposited on the flat side of a lapped D-shaped fiber. The single-layered devices were fabricated from germanium, while the multilayered ones comprised layers of germanium, silica, and silver. Some of the devices operated in air with high coupling efficiency in excess of 40 dB and an estimated index sensitivity of Delta lambda/Delta n = 90 mn from 1 to 1.15 index range, while others provided an index sensitivity of Delta lambda/Delta n = 6790 mn for refractive indices from 1.33 to 1.37. (C) 2009 Optical Society of America

Multilayered coated infra-red surface plasmon resonance fibre sensors for aqueous chemical sensing

A series of surface plasmonic fibre devices were fabricated by depositing multiple thin coatings on a lapped section of a standard single mode telecoms fibre forming a D-shaped section and then inscribing a grating-type structure using UV light. The coatings consisted of base coatings of semi-conductor (germanium) and dielectric (silicon dioxide) materials, followed by different metals. These fibre devices showed high spectral refractive index sensitivity with high coupling efficiency in excess of 40 dB for indices in the aqueous regime and below, with estimated index sensitivities of Lambda lambda/Lambda n = 90-800 nm from 1 to 1.15 index range and Lambda lambda/Lambda n = 1200-4000 nm for refractive indices from 1.33 to 1.39. (C) 2009 Elsevier Inc. All rights reserved.

Characterization of infrared surface plasmon resonances generated from a fiber-optical sensor utilizing tilted Bragg gratings

We demonstrate the use of tilted fiber gratings to assist with the generation of infrared surface plasmons on a metal film coating the flat of a D-shaped fiber. The wavelength of the strong (>25 dB) resonance is tunable over similar to 1000 nm by adjusting the polarization state of the light and is highly sensitive to the refractive index of any aqueous medium surrounding the fiber (sensitivity= 3365 nm).

Generation of infrared surface plasmon resonances with high refractive index sensitivity utilizing tilted fiber Bragg gratings

We demonstrate the use of tilted fiber gratings to assist the generation of localized infrared surface plasmons with short propagation lengths and a sensitivity of d lambda/dn = 3365 nm in the aqueous index regime. It was also found that the resonances could be spectrally tuned over 1000 nm at the same spatial region with high coupling efficiency (in excess of 25 dB) by altering the polarization of the light illuminating the device.

Formation and characterization of ultra-sensitive surface plasmon resonance sensor based upon a nano-scale corrugated multi-layered coated D-shaped optical fiber

We present experimental results on the performance of a series of coated, D-shaped optical fiber sensors that display high spectral sensitivities to external refractive index. Sensitivity to the chosen index regime and coupling of the fiber core mode to the surface plasmon resonance (SPR) is enhanced by using specific materials as part of a multi-layered coating. We present strong evidence that this effect is enhanced by post ultraviolet radiation of the lamellar coating that results in the formation of a nano-scale surface relief corrugation structure, which generates an index perturbation within the fiber core that in turn enhances the coupling. We have found reasonable agreement when we modeling the fiber device. It was found that the SPR devices operate in air with high coupling efficiency in excess of 40 dB with spectral sensitivities that outperform a typical long period grating, with one device yielding a wavelength spectral sensitivity of 12000 nm/RIU in the important aqueous index regime. The devices generate SPRs over a very large wavelength range, (visible to 2 mu m) by alternating the polarization state of the illuminating light.

Aptamer-based surface plasmon sensor for thrombin detection

A series of surface plasmonic fibre devices were fabricated using multiple coatings deposited on a lapped section of a single mode fibre and post-fabrication UV laser irradiation processing with a phase mask, producing a surface relief grating structure. These devices showed high spectral sensitivity in the aqueous index regime ranging up to 4000 nm/RIU for wavelength and 800 dB/RIU for intensity. The devices were then coated with human thrombin binding aptamer. Several concentrations of thrombin in buffer solution were made, ranging from 1nM to 1µM. All the concentrations were detectable by the devices demonstrating that sub-nM concentrations may be monitored.

Generation of infrared surface plasmon resonances with high refractive index sensitivity utilizing tilted fiber Bragg gratings

We demonstrate the use of tilted fiber gratings to assist the generation of localized infrared surface Plasmons with short propagation lengths and a sensitivity of dλ/dn = 3365 nm in the aqueous index regime. It was also found that the resonances could be spectrally tuned over 1000 nm at the same spatial region with high coupling efficiency (in excess of 25 dB) by altering the polarization of the light illuminating the device. © 2007 Optical Society of America.

An ultra-sensitive localised surface plasmon resonance fibre device for environmental sensing based upon a structured bi-metal coating

We demonstrate a bi-metal coating (platinum and gold or silver) localised surface plasmon resonance fibre device that produces an index spectral sensitivity of over 11,000 nm/RIU, yielding an index resolution of 5×10-6in the aqueous index regime, consisting of a structured multi-layered thin film on D-shaped fibre. © 2014 SPIE.

Surface plasmon resonance generation utilising gratings for biochemical sensing

We demonstrate the use of gratings to assist in the generation of surface plasmon resonances resulting in a device having a high index resolution of 3×10-5 in the aqueous index regime.

Highly sensitive, localized surface plasmon resonance fiber device for environmental sensing, based upon a structured bi-metal array of nano-wires

We demonstrate a bi-metal coated (platinum and gold or silver), localized surface plasmon resonance fiber sensor with an index sensitivity exceeding 11,900 nm/RIU, yielding an index resolution of 2 × 10-5 in the aqueous index regime. This is one of the highest index sensitivities achieved with an optical fiber sensor. The coatings consist of arrays of bi-metal nano-wires (typically 36 nm in radius and 20 μm in length), supported by a silicon dioxide thin film on a thin substrate of germanium, the nano-wires being perpendicular to the longitudinal axis of the D-shaped fiber.

Photonic gas sensors exploiting directly the optical properties of hybrid carbon nanotube localized surface plasmon structures

We investigate the modification of the optical properties of carbon nanotubes (CNTs) resulting from a chemical reaction triggered by the presence of a specific compound (gaseous carbon dioxide (CO2)) and show this mechanism has important consequences for chemical sensing. CNTs have attracted significant research interest because they can be functionalized for a particular chemical, yielding a specific physical response which suggests many potential applications in the fields of nanotechnology and sensing. So far, however, utilizing their optical properties for this purpose has proven to be challenging. We demonstrate the use of localized surface plasmons generated on a nanostructured thin film, resembling a large array of nano-wires, to detect changes in the optical properties of the CNTs. Chemical selectivity is demonstrated using CO2 in gaseous form at room temperature. The demonstrated methodology results additionally in a new, electrically passive, optical sensing configuration that opens up the possibilities of using CNTs as sensors in hazardous/explosive environments.