Spectral properties and dynamics of gold nanorods revealed by EMCCD‐based spectral phasor method

Gold nanorods (NRs) with tunable plasmon‐resonant absorption in the near‐infrared region have considerable advantages over organic fluorophores as imaging agents due to their brightness and lack of photobleaching. However, the luminescence spectral properties of NRs have not been fully characterized at the single particle level due to lack of proper analytic tools. Here, we present a spectral phasor analysis method that allows investigations of NRs' spectra at single particle level showing the spectral variance and providing spatial information during imaging. The broad phasor distribution obtained by the spectral phasor analysis indicates that spectra of NRs are different from particle to particle. NRs with different spectra can be identified in images with high spectral resolution. The spectral behaviors of NRs under different imaging conditions, for example, different excitation powers and wavelengths, were revealed by our laser‐scanning multiphoton microscope using a high‐resolution spectrograph with imaging capability. Our results prove that the spectral phasor method is an easy and efficient tool in hyper‐spectral imaging analysis to unravel subtle changes of the emission spectrum. We applied this method to study the spectral dynamics of NRs during direct optical trapping and by optothermal trapping. Interestingly, different spectral shifts were observed in both trapping phenomena. Microsc. Res. Tech. 78:283–293, 2015. © 2015 Wiley Periodicals, Inc.     

Field enhancement and apertureless near-field optical spectroscopy of single molecules

We report on fluorescence enhancement in near field optical spectroscopy by apertureless microscopy. Our apertureless microscope is designed around a confocal fluorescence microscope associated with an AFM head. First, we show that the confocal microscope alone allows single molecule imaging and single molecule fluorescence analysis. When associated with the AFM head, we demonstrate, for the first time to our knowledge, that single molecule fluorescence is enhanced under the silicon tip. We tentatively attribute this effect to field enhancement under the tip.     

Field enhancement and apertureless near-field optical spectroscopy of single molecules

We report on fluorescence enhancement in near field optical spectroscopy by apertureless microscopy. Our apertureless microscope is designed around a confocal fluorescence microscope associated with an AFM head. First, we show that the confocal microscope alone allows single molecule imaging and single molecule fluorescence analysis. When associated with the AFM head, we demonstrate, for the first time to our knowledge, that single molecule fluorescence is enhanced under the silicon tip. We tentatively attribute this effect to field enhancement under the tip.     

Laser scanning gradient index optics microscope: submicrometre scale spectroscopy and imaging at cryogenic temperatures

A laser scanning far-field optical microscope for low-temperature imaging and spectroscopy based on gradient index optics is presented. A rod-shaped gradient index microlens is used as a zero-working-distance solid immersion objective lens. The obtained lateral resolution is 310 nm of the FWHM at a wavelength of 545 nm. A laser scanning mechanism located outside an optical cryostat enables one to achieve large scanning ranges independent of temperature. The use of the microscope for submicrometre-scale spectroscopy and low-temperature photochemistry performed on molecular J aggregates in thin polymer films is presented.     

Laser scanning gradient index optics microscope: submicrometre scale spectroscopy and imaging at cryogenic temperatures

A laser scanning far-field optical microscope for low-temperature imaging and spectroscopy based on gradient index optics is presented. A rod-shaped gradient index microlens is used as a zero-working-distance solid immersion objective lens. The obtained lateral resolution is 310 nm of the FWHM at a wavelength of 545 nm. A laser scanning mechanism located outside an optical cryostat enables one to achieve large scanning ranges independent of temperature. The use of the microscope for submicrometre-scale spectroscopy and low-temperature photochemistry performed on molecular J aggregates in thin polymer films is presented.     

Fluorescence imaging with a laser trapping scanning near-field optical microscope

We investigated fluorescence imaging using a near-field scanning optical microscope which uses a laser-stabilized gold nanoparticle as a near-field probe. This microscope is suitable for observations of biological specimens in aqueous solutions because the probe particle is held by a noncontact force exerted by a laser beam. Theoretical calculations based on Mie scattering theory are presented to evaluate the near-field enhancement by a gold particle of 40 nm diameter. We also present fluorescence images of a single fluorescent bead and discuss the near-field contribution to the fluorescence image in this type of microscope.     

Fluorescence imaging with a laser trapping scanning near-field optical microscope

We investigated fluorescence imaging using a near-field scanning optical microscope which uses a laser-stabilized gold nanoparticle as a near-field probe. This microscope is suitable for observations of biological specimens in aqueous solutions because the probe particle is held by a noncontact force exerted by a laser beam. Theoretical calculations based on Mie scattering theory are presented to evaluate the near-field enhancement by a gold particle of 40 nm diameter. We also present fluorescence images of a single fluorescent bead and discuss the near-field contribution to the fluorescence image in this type of microscope.     

Combined AFM and confocal fluorescence microscope for applications in bio-nanotechnology

We present a custom-designed atomic force fluorescence microscope (AFFM), which can perform simultaneous optical and topographic measurements with single molecule sensitivity throughout the whole visible to near-infrared spectral region. Integration of atomic force microscopy (AFM) and confocal fluorescence microscopy combines the high-resolution topographical imaging of AFM with the reliable (bio)-chemical identification capability of optical methods. The AFFM is equipped with a spectrograph enabling combined topographic and fluorescence spectral imaging, which significantly enhances discrimination of spectroscopically distinct objects. The modular design allows easy switching between different modes of operation such as tip-scanning, sample-scanning or mechanical manipulation, all of which are combined with synchronous optical detection. We demonstrate that coupling the AFM with the fluorescence microscope does not compromise its ability to image with a high spatial resolution. Examples of several modes of operation of the AFFM are shown using two-dimensional crystals and membranes containing light-harvesting complexes from the photosynthetic bacterium Rhodobacter sphaeroides.     

Optics clustered to output unique solutions: a multi-laser facility for combined single molecule and ensemble microscopy

Optics clustered to output unique solutions (OCTOPUS) is a microscopy platform that combines single molecule and ensemble imaging methodologies. A novel aspect of OCTOPUS is its laser excitation system, which consists of a central core of interlocked continuous wave and pulsed laser sources, launched into optical fibres and linked via laser combiners. Fibres are plugged into wall-mounted patch panels that reach microscopy end-stations in adjacent rooms. This allows multiple tailor-made combinations of laser colours and time characteristics to be shared by different end-stations minimising the need for laser duplications. This setup brings significant benefits in terms of cost effectiveness, ease of operation, and user safety. The modular nature of OCTOPUS also facilitates the addition of new techniques as required, allowing the use of existing lasers in new microscopes while retaining the ability to run the established parts of the facility. To date, techniques interlinked are multi-photon/multicolour confocal fluorescence lifetime imaging for several modalities of fluorescence resonance energy transfer (FRET) and time-resolved anisotropy, total internal reflection fluorescence, single molecule imaging of single pair FRET, single molecule fluorescence polarisation, particle tracking, and optical tweezers. Here, we use a well-studied system, the epidermal growth factor receptor network, to illustrate how OCTOPUS can aid in the investigation of complex biological phenomena.     

Near-field and confocal surface-enhanced resonance Raman spectroscopy at cryogenic temperatures

For laser spectroscopy at variable temperatures with high spatial resolution a combined scanning near‐field optical and confocal microscope was developed. Rhodamine 6G (R6G) dye molecules dispersed on silver nano‐particles or nano‐clusters were investigated. For optical excitation of the molecules, either an aperture probe or a focused laser spot in confocal arrangement were employed. Raman spectra in the wavenumber range between 300 cm^?1 and 3000 cm^?1 at room temperatures down to 8.5 K were recorded. Many of the observed Raman lines can be associated with the structure of the adsorbed molecule. Intensity fluctuations in spectral sequences were observed down to 77 K and are indicative of single molecule sensitivity.     

Large-area topography analysis and near-field Raman spectroscopy using bent fibre probes

We present a method for combined far‐field Raman imaging, topography analysis and near‐field spectroscopy. Surface‐enhanced Raman spectra of Rhodamine 6G (R6G) deposited on silver nanoparticles were recorded using a bent fibre aperture‐type near‐field scanning optical microscope (NSOM) operated in illumination mode. Special measures were taken to enable optical normal‐force detection for control of the tip–sample distance. Comparisons between far‐field Raman images of R6G‐covered Ag particle aggregates with topographic images recorded using atomic force microscopy (AFM) indicate saturation effects due to resonance excitation.     

基于SiO2微球颗粒的成像研究

远场显微成像是近年来的研究热点,而微球颗粒在远场成像中具有一定的放大作用。针对这种现象,通过对微球颗粒的分离,对单个微球颗粒的成像特性进行了理论研究。实验表明,利用一定尺寸的二氧化硅微球颗粒,可以使远场显微镜的分辨率提高一倍。在尼康显微镜下,利用普通卤素灯光源、二氧化硅和相应的增强介质,对1 200线的光栅实现了近一倍的放大成像效果,证实了微球颗粒的远场显微成像能力。     

Combining optical tweezers and scanning probe microscopy to study DNA-protein interactions

We present the first results obtained with a new instrument designed and built to study DNA-protein interactions at the single molecule level. This microscope combines optical tweezers with scanning probe microscopy and allows us to locate DNA-binding proteins on a single suspended DNA molecule. A single DNA molecule is stretched taut using the optical tweezers, while a probe is scanned along the molecule. Interaction forces between the probe and the sample are measured with the optical tweezers. The instrument thus enables us to correlate mechanical and functional properties of bound proteins with the tension within the DNA molecule. The typical friction force between a micropipette used as probe and a naked DNA molecule was found to be <1 pN. A 16 micro m DNA molecule with approximately 10-15 digoxygenin (DIG) molecules located over a 90 nm range in the middle of the DNA was used as a model system. By scanning with an antidigoxygenin (alpha-DIG) antibody-coated pipette we were able to localize these sites by exploiting the high binding affinity between this antibody-antigen pair. The estimated experimental resolution assuming an infinitesimally thin and rigid probe and a single alpha-DIG/DIG bond was 15 nm.     

A universal fluid cell for the imaging of biological specimens in the atomic force microscope

Recently, atomic force microscope (AFM) manufacturers have begun producing instruments specifically designed to image biological specimens. In most instances, they are integrated with an inverted optical microscope, which permits concurrent optical and AFM imaging. An important component of the set‐up is the imaging chamber, whose design determines the nature of the experiments that can be conducted. Many different imaging chamber designs are available, usually designed to optimize a single parameter, such as the dimensions of the substrate or the volume of fluid that can be used throughout the experiment. In this report, we present a universal fluid cell, which simultaneously optimizes all of the parameters that are important for the imaging of biological specimens in the AFM. This novel imaging chamber has been successfully tested using mammalian, plant, and microbial cells. Microsc. Res. Tech. 76:357–363, 2013. © 2013 Wiley Periodicals, Inc.     

Single beam optical tweezers setup with backscattered light detection for three-dimensional measurements on DNA and nanopores

We introduce a versatile and high precision three-dimensional optical tweezers setup with minimal optical interference to measure small forces and manipulate single molecules in the vicinity of a weak reflective surface. Our tweezers system integrates an inverted optical microscope with a single IR-laser beam that is spatially filtered in an appropriate way to allow force measurements in three dimensions with remarkably high precision when operated in backscattered light detection mode. The setup was tested by overstretching a lambda-DNA in x and z directions (perpendicular and along the optical axis), and by manipulating individual lambda-DNA molecules in the vicinity of a nanopore that allowed quantitative single molecule threading experiments with minimal optical interference.     

Minimizing light exposure with the programmable array microscope

The exposure of fluorophores to intense illumination in a microscope often results in photobleaching and phototoxicity, thus constituting a major limiting factor in time lapse live cell or single molecule imaging. Laser scanning confocal microscopes are particularly prone to this problem, inasmuch as they require high irradiances to compensate for the inherently low duty cycle of point scanning systems. In the attempt to maintain adequate speed and signal-to-noise ratios, the fluorophores are often driven into saturation, thereby generating a nonlinear response. One approach for reducing photodegradation in the laser scanning confocal microscope is represented by controlled light exposure microscopy, introduced by Manders and colleagues. The strategy is to reduce the illumination intensity in both background areas (devoid of information) as well as in bright foreground regions, for which an adequate signal-to-noise ratio can be achieved with lower excitation levels than those required for the less intense foreground pixels/voxels. Such a variable illumination scheme can also be exploited in widefield microscopes that employ lower irradiance but higher illumination duty cycles. We report here on the adaptation of the controlled light exposure microscopy principle to the programmable array microscope, which achieves optical sectioning by use of a spatial light modulator (SLM) in an image plane as a programmable mask for illumination and conjugate (and nonconjugate) detection. By incorporating the basic controlled light exposure microscopy concept for minimizing exposure, we have obtained a reduction in the rate of photobleaching of up to ~5-fold, while maintaining an image quality comparable to regular imaging with the programmable array microscope.     

Time-gated fluorescence lifetime imaging and microvolume spectroscopy using two-photon excitation

A scanning microscope utilizing two-photon excitation in combination with fluorescence lifetime contrast is presented. The microscope makes use of a tunable femtosecond titanium:sapphire laser enabling the two-photon excitation of a broad range of fluorescent molecules, including UV probes. Importantly, the penetration depth of the two-photon exciting (infra)red light is substantially greater than for the corresponding single-photon wavelength while photobleaching is significantly reduced. The time structure of the Ti:Sa laser can be employed in a straightforward way for the realization of fluorescence lifetime imaging. The fluorescence lifetime is sensitive to the local environment of the fluorescent molecule. This behaviour can be used for example to quantify concentrations of ions, such as pH and Ca²⁺, or pO₂ and pCO₂. In the set-up presented here the fluorescence lifetime imaging is accomplished by time-gated single photon counting. The performance and optical properties of the microscope are investigated by a number of test measurements on fluorescent test beads. Point-spread functions calculated from measurements on 230-nm beads using an iterative restoration procedure compare well with theoretical expectations. Lifetime imaging experiments on a test target containing two different types of test bead in a fluorescent buffer all with different lifetimes (2.15 ns, 2.56 ns and 3.34 ns) show excellent quantitative agreement with reference values obtained from time correlated single photon counting measurements. Moreover, the standard deviation in the results can be wholly ascribed to the photon statistics. Measurements of acridine orange stained biofilms are presented as an example of the potential of two-photon excitation combined with fluorescence lifetime contrast. Fluorescence lifetime and intensity images were recorded over the whole sample depth of 100 μm. Fluorescence intensity imaging is seriously hampered by the rapid decrease of the fluorescence signal as a function of the depth into the sample. Fluorescence lifetime imaging on the other hand is not affected by the decrease of the fluorescence intensity.     

High-resolution microscope for tip-enhanced optical processes in ultrahigh vacuum

An optical microscope based on tip-enhanced optical processes that can be used for studies on adsorbates as well as thin layers and nanostructures is presented. The microscope provides chemical and topographic informations with a resolution of a few nanometers and can be employed in ultrahigh vacuum as well as gas phase. The construction involves a number of improvements compared to conventional instruments. The central idea is to mount, within an UHV system, an optical platform with all necessary optical elements to a rigid frame that also carries the scanning tunneling microscope unit and to integrate a high numerical aperture parabolic mirror between the scanning probe microscope head and the sample. The parabolic mirror serves to focus the incident light and to collect a large fraction of the scattered light. The first experimental results of Raman measurements on silicon samples as well as brilliant cresyl blue layers on single crystalline gold and platinum surfaces in ultrahigh vacuum are presented. For dye adsorbates a Raman enhancement of approximately 10(6) and a net signal gain of up to 4000 was observed. The focus diameter ( approximately lambda2) was measured by Raman imaging the focal region on a Si surface. The requirements of the parabolic mirror in terms of alignment accuracy were experimentally determined as well.     

Dual-trap optical tweezers with real-time force clamp control

Single molecule force clamp experiments are widely used to investigate how enzymes, molecular motors, and other molecular mechanisms work. We developed a dual-trap optical tweezers instrument with real-time (200 kHz update rate) force clamp control that can exert 0-100 pN forces on trapped beads. A model for force clamp experiments in the dumbbell-geometry is presented. We observe good agreement between predicted and observed power spectra of bead position and force fluctuations. The model can be used to predict and optimize the dynamics of real-time force clamp optical tweezers instruments. The results from a proof-of-principle experiment in which lambda exonuclease converts a double-stranded DNA tether, held at constant tension, into its single-stranded form, show that the developed instrument is suitable for experiments in single molecule biology.