Fluorescence lifetime imaging of quantum dot labeled DNA microarrays

Allergen Microarrays and New Physical Approaches to More Sensitive and Specific Detection of Allergen-Specific Antibodies

The prevalence of allergic diseases has increased tremendously in recent decades, which can be attributed to growing exposure to environmental triggers, changes in dietary habits, comorbidity, and the increased use of medications. In this context, the multiplexed diagnosis of sensitization to various allergens and the monitoring of the effectiveness of treatments for allergic diseases become particularly urgent issues. The detection of allergen-specific antibodies, in particular, sIgE and sIgG, is a modern alternative to skin tests due to the safety and efficiency of this method. The use of allergen microarrays to detect tens to hundreds of allergen-specific antibodies in less than 0.1 mL of blood serum enables the transition to a deeply personalized approach in the diagnosis of these diseases while reducing the invasiveness and increasing the informativeness of analysis. This review discusses the technological approaches underlying the development of allergen microarrays and other protein microarrays, including the methods of selection of the microarray substrates and matrices for protein molecule immobilization, the obtainment of allergens, and the use of different types of optical labels for increasing the sensitivity and specificity of the detection of allergen-specific antibodies.

Effect of CaS Nanostructures in the Proliferation of Human Breast Cancer and Benign Cells In Vitro

We report on the effect of naked CaS nanostructures on the proliferation of carcinoma cancer cells and normal fibroblasts in vitro. The CaS nanostructures were prepared via the microwave-mediated decomposition of dimethyl sulfoxide (DMSO) in the presence of calcium acetate Ca ( CH 3 CO 2 ) 2 . Light scattering measurements revealed that dispersions contain CaS nanostructures in the size range of a few Å to about 1 nanometer, and are formed when DMSO is decomposed in the presence of Ca ( CH 3 CO 2 ) 2 . Theoretical calculations at the DFT/B3LYP/DGDZVP level of theory on ( C a S ) n clusters ( n = 1 , 2 , 3 , and 4) are consistent with clusters in this size range. The absorption spectra of the CaS nanostructures are dominated by strong bands in the UV, as well as weaker absorption bands in the visible. We found that a single dose of CaS nanoclusters smaller than 0.8 nm in diameter does not affect the survival and growth rate of normal fibroblasts and inhibits the proliferation rate of carcinoma cells in vitro. Larger CaS nanostructures, approximately (1.1 ± 0.2) nm in diameter, have a similar effect on carcinoma cell proliferation and survival rate. The CaS nanoclusters have little effect on the normal fibroblast cell cycle. Human carcinoma cells treated with CaS nanocluster dispersion exhibited a decreased ability to properly enter the cell cycle, marked by a decrease in cell concentration in the G0/G1 phase in the first 24 h and an increase in cells held in the SubG1 and G0/G1 phases up to 72 h post-treatment. Apoptosis and necrotic channels were found to play significant roles in the death of human carcinoma exposed to the CaS nanoclusters. In contrast, any effect on normal fibroblasts appeared to be short-lived and non-detrimental. The interaction of CaS with several functional groups was further investigated using theoretical calculations. CaS is predicted to interact with thiol ( R-SH ), hydroxide ( R - OH ), amino ( R - NH 2 ), carboxylic acid ( R - COOH ), ammonium ( R-NH 3 + ), and carboxylate ( R-COO - ) functional groups. None of these interactions are predicted to result in the dissociation of CaS. Thermodynamic considerations, on the other hand, are consistent with the dissociation of CaS into Ca 2 + ions and H 2 S in acidic media, both of which are known to cause apoptosis or cell death. Passive uptake and extracellular pH values of carcinoma cells are proposed to result in the observed selectivity of CaS to inhibit cancer cell proliferation with no significant effect on normal fibroblast cells. The results encourage further research with other cell lines in vitro as well as in vivo to translate this nanotechnology into clinical use.

Resonant Electro-Optic Imaging for Microscopy at Nanosecond Resolution

We demonstrate an electro-optic wide-field method to enable fluorescence lifetime microscopy (FLIM) with high throughput and single-molecule sensitivity. Resonantly driven Pockels cells are used to efficiently gate images at 39 MHz, allowing fluorescence lifetime to be captured on standard camera sensors. Lifetime imaging of single molecules is enabled in wide field with exposure times of less than 100 ms. This capability allows combination of wide-field FLIM with single-molecule super-resolution localization microscopy. Fast single-molecule dynamics such as FRET and molecular binding events are captured from wide-field images without prior spatial knowledge. A lifetime sensitivity of 1.9 times the photon shot-noise limit is achieved, and high throughput is shown by acquiring wide-field FLIM images with millisecond exposure and >10⁸ photons per frame. Resonant electro-optic FLIM allows lifetime contrast in any wide-field microscopy method.

Luminescent Nanomaterials (II)

In this review, we focus on sensing techniques and biological applications of various luminescent nanoparticles including quantum dot (QD), up-conversion nanoparticles (UCNPs) following the previous chapter. Fluorescent phenomena can be regulated or shifted by interaction between biological targets and luminescence probes depending on their distance, which is so-called Fӧrster resonance energy transfer (FRET). QD-based FRET technique, which has been widely applied as a bioanalytical tool, is described. We discuss time-resolved fluorescence (TRF) imaging and flow cytometry technique, using photoluminescent nanoparticles with unique properties for effectively improving selectivity and sensitivity. Based on these techniques, bioanalytical and biomedical application, bioimaging with QD, UCNPs, and Euripium-activated luminescent nanoprobes are covered. Combination of optical property of these luminescent nanoparticles with special functions such as drug delivery, photothermal therapy (PTT), and photodynamic therapy (PDT) is also described.

Nanomedicines for Near-Infrared Fluorescent Lifetime-Based Bioimaging

Nanomedicines refer to the application of nanotechnology in disease diagnosis, treatment, and monitoring. Bioimaging provides crucial biological information for disease diagnosis and treatment monitoring. Fluorescent bioimaging shows the advantages of good contrast and a vast variety of signal readouts and yet suffers from imaging depth due to the background noise from the autofluorescence of tissue and light scattering. Near-infrared fluorescent lifetime bioimaging (NIR- FLTB) suppresses such background noises and significantly improves signal-to-background ratio. This article gives an overview of recent advances in NIR- FLTB using organic compounds and nanomaterials as contrast agent (CA). The advantages and disadvantages of each CA are discussed in detail. We survey relevant reports about NIR-FLTB in recent years and summarize important findings or progresses. In addition, emerging hybrid bioimaging techniques are introduced, such as ultrasound-modulated FLTB. The challenges and an outlook for NIR- FLTB development are discussed at the end, aiming to provide references and inspire new ideas for future nanomedicine development.

Wide-field time-correlated single photon counting-based fluorescence lifetime imaging microscopy

Wide-field time-correlated single photon counting detection techniques, where the position and the arrival time of the photons are recorded simultaneously using a camera, have made some advances recently. The technology and instrumentation used for this approach is employed in areas such as nuclear science, mass spectroscopy and positron emission tomography, but here, we discuss some of the wide-field TCSPC methods, for applications in fluorescence microscopy. We describe work by us and others as presented in the Ulitima fast imaging and tracking conference at the Argonne National Laboratory in September 2018, from phosphorescence lifetime imaging (PLIM) microscopy on the microsecond time scale to fluorescence lifetime imaging (FLIM) on the nanosecond time scale, and highlight some applications of these techniques.

Fluorescence lifetime based bioassays

Fluorescence lifetime (FLT) is a robust intrinsic property and material constant of fluorescent matter. Measuring this important physical indicator has evolved from a laboratory curiosity to a powerful and established technique for a variety of applications in drug discovery, medical diagnostics and basic biological research. This distinct trend was mainly driven by improved and meanwhile affordable laser and detection instrumentation on the one hand, and the development of suitable FLT probes and biological assays on the other. In this process two essential working approaches emerged. The first one is primarily focused on high throughput applications employing biochemical in vitro assays with no requirement for high spatial resolution. The second even more dynamic trend is the significant expansion of assay methods combining highly time and spatially resolved fluorescence data by fluorescence lifetime imaging. The latter approach is currently pursued to enable not only the investigation of immortal tumor cell lines, but also specific tissues or even organs in living animals. This review tries to give an actual overview about the current status of FLT based bioassays and the wide range of application opportunities in biomedical and life science areas. In addition, future trends of FLT technologies will be discussed.

A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms

In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs.

Melamine-DNA encoded periodicity of quantum dot arrays

Formation of QD-array in solution phase guided by the self-assembly with DNA-melamine hybrid molecules is reported here. Melamine was conjugated with ssDNA using phosphoramidate chemistry. Aqueous soluble ZnSe/ZnS QDs conjugated to complementary ssDNA was self-assembled with the DNA-melamine hybrid molecules by DNA-hybridization. The self-assembly leads to the precise positioning of the QDs in QDs array where the inter QD distance is being maintained by the DNA sequence length. The QD array was characterized by gel electrophoresis, UV-visible and fluorescence spectrophotometry and circular dichroism. Direct visualization of the DNA-melamine hybrid molecule mediated QD array was made possible by atomic force microscopy (AFM) and transmission electron microscopy (TEM) analysis. Substantial increase in the fluorescence intensity and lifetime of the QDs was observed on array formation by DNA self-assembly.

Intravital multiphoton imaging of the selective uptake of water-dispersible quantum dots into sinusoidal liver cells

Although many studies reporting the organ-level biodistribution of nanoparticles (NPs) in animals, very few have addressed the fate of NPs in organs at the cellular level. The liver appears to be the main organ for accumulation of NPs after intravenous injection. In this study, for the first time, the in vivo spatiotemporal disposition of recently developed mercaptosuccinic acid (MSA)-capped cadmium telluride/cadmium sulfide (CdTe/CdS) quantum dots (QDs) is explored in rat liver using multiphoton microscopy (MPM) coupled with fluorescence lifetime imaging (FLIM), with subcellular resolution (∼1 μm). With high fluorescence efficiency and largely improved stability in the biological environment, these QDs show a distinct distribution pattern in the liver compared to organic dyes, rhodamine 123 and fluorescein. After intravenous injection, fluorescent molecules are taken up by hepatocytes and excreted into the bile, while negatively charged QDs are retained in the sinusoids and selectively taken up by sinusoidal cells (Kupffer cells and liver sinusoidal endothelial cells), but not by hepatocytes within 3 h. The results could help design NPs targeting the specific types of liver cells and choose the fluorescent markers for appropriate cellular imaging.

Combined two-photon excitation and d→f energy transfer in a water-soluble Ir(III)/Eu(III) dyad: two luminescence components from one molecule for cellular imaging

The first example of cell imaging using two independent emission components from a dinuclear d/f complex is reported. A water-stable, cell-permeable Ir(III) /Eu(III) dyad undergoes partial Ir→Eu energy transfer following two-photon excitation of the Ir unit at 780 nm. Excitation in the near-IR region generated simultaneously green Ir-based emission and red Eu-based emission from the same probe. The orders-of-magnitude difference in their timescales (Ir ca. μs; Eu ca. 0.5 ms) allowed them to be identified by time-gated detection. Phosphorescence lifetime imaging microscopy (PLIM) allowed the lifetime of the Ir-based emission to be measured in different parts of the cell. At the same time, the cells are simultaneously imaged by using the Eu-based emission component at longer timescales. This new approach to cellular imaging by using dual d/f emitters should therefore enable autofluorescence-free sensing of two different analytes, independently, simultaneously and in the same regions of a cell.

Near-infrared-emitting nanoparticles for lifetime-based multiplexed analysis and imaging of living cells

The increase in information content from bioassays and bioimaging requires robust and efficient strategies for the detection of multiple analytes or targets in a single measurement, thereby addressing current health and security concerns. For fluorescence techniques, an attractive alternative to commonly performed spectral or color multiplexing presents lifetime multiplexing and the discrimination between different fluorophores based on their fluorescence decay kinetics. This strategy relies on fluorescent labels with sufficiently different lifetimes that are excitable at the same wavelength and detectable within the same spectral window. Here, we report on lifetime multiplexing and discrimination with a set of nanometer-sized particles loaded with near-infrared emissive organic fluorophores chosen to display very similar absorption and emission spectra, yet different fluorescence decay kinetics in suspension. Furthermore, as a first proof-of-concept, we describe bioimaging studies with 3T3 fibroblasts and J774 macrophages, incubated with mixtures of these reporters employing fluorescence lifetime imaging microscopy. These proof-of-concept measurements underline the potential of fluorescent nanoparticle reporters in fluorescence lifetime multiplexing, barcoding, and imaging for cellular studies, cell-based assays, and molecular imaging.

Fluorescence lifetime imaging microscopy for the detection of intracellular pH with quantum dot nanosensors

While the use of quantum dot (QD) nanoparticles for bioimaging and sensing has been improved and exploited during the last several years, most studies have used emission intensity-based techniques. Fluorescence lifetime imaging microscopy (FLIM) can also be employed for sensing purposes, overcoming many of the limitations of the aforementioned systems. Herein, we show that the photoluminescence (PL) lifetime of mercaptopropionic acid-capped QDs (MPA-QDs) collected from FLIM images can be used to determine intracellular pH. The PL average lifetime of MPA-QDs varied from 8.7 ns (pH < 5) to 15.4 ns (pH > 8) in media mimicking the intracellular environment. These long decay times of QD nanoparticles make them easily distinguishable from intrinsic cell autofluorescence, improving selectivity in sensing applications. We demonstrate, for the first time, the successful detection of changes in the intracellular pH of different cell types by examining the PL decay time of QDs. In particular, the combination of FLIM methodologies with QD nanoparticles exhibits greatly improved sensitivity compared with other fluorescent dyes for pH imaging. A detailed description of the advantages of the FLIM technique is presented.

Efficient Dual-Modal NIR-to-NIR Emission of Rare Earth Ions Co-doped Nanocrystals for Biological Fluorescence Imaging

A novel approach has been developed for the realization of efficient near-infrared to near-infrared (NIR-to-NIR) upconversion and down-shifting emission in nanophosphors. The efficient dual-modal NIR-to-NIR emission is realized in a β-NaGdF4/Nd(3+)@NaGdF4/Tm(3+)-Yb(3+) core-shell nanocrystal by careful control of the identity and concentration of the doped rare earth (RE) ion species and by manipulation of the spatial distributions of these RE ions. The photoluminescence results reveal that the emission efficiency increases at least 2-fold when comparing the materials synthesized in this study with those synthesized through traditional approaches. Hence, these core-shell structured nanocrystals with novel excitation and emission behaviors enable us to obtain tissue fluorescence imaging by detecting the upconverted and down-shifted photoluminescence from Tm(3+) and Nd(3+) ions, respectively. The reported approach thus provides a new route for the realization of high-yield emission from RE ion doped nanocrystals, which could prove to be useful for the design of optical materials containing other optically active centers.

A platform for combined DNA and protein microarrays based on total internal reflection fluorescence

We have developed a novel microarray technology based on total internal reflection fluorescence (TIRF) in combination with DNA and protein bioassays immobilized at the TIRF surface. Unlike conventional microarrays that exhibit reduced signal-to-background ratio, require several stages of incubation, rinsing and stringency control, and measure only end-point results, our TIRF microarray technology provides several orders of magnitude better signal-to-background ratio, performs analysis rapidly in one step, and measures the entire course of association and dissociation kinetics between target DNA and protein molecules and the bioassays. In many practical cases detection of only DNA or protein markers alone does not provide the necessary accuracy for diagnosing a disease or detecting a pathogen. Here we describe TIRF microarrays that detect DNA and protein markers simultaneously, which reduces the probabilities of false responses. Supersensitive and multiplexed TIRF DNA and protein microarray technology may provide a platform for accurate diagnosis or enhanced research studies. Our TIRF microarray system can be mounted on upright or inverted microscopes or interfaced directly with CCD cameras equipped with a single objective, facilitating the development of portable devices. As proof-of-concept we applied TIRF microarrays for detecting molecular markers from Bacillus anthracis, the pathogen responsible for anthrax.

The application of semiconductor quantum dots for enhancing peptide desorption, improving peak resolution and sensitivity of detection in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry

The interest in quantum dots (QD) and a number of reported life sciences applications increased dramatically over the last decade. The popularity of QDs stems from better photostability, higher extinction -co-efficients, and unique optical properties such as superior light absorption. Here we report methods for improving matrix-assisted laser desorption/ionization desorption of crude tryptic protein digests by using CdSe/ZnS QDs. The addition of QDs to the matrix improves the signal-to-noise ratio, peak quality and increases the number of detected peptides and the overall sequence coverage.

Video-rate fluorescence lifetime imaging camera with CMOS single-photon avalanche diode arrays and high-speed imaging algorithm

A high-speed and hardware-only algorithm using a center of mass method has been proposed for single-detector fluorescence lifetime sensing applications. This algorithm is now implemented on a field programmable gate array to provide fast lifetime estimates from a 32 × 32 low dark count 0.13 μm complementary metal-oxide-semiconductor single-photon avalanche diode (SPAD) plus time-to-digital converter array. A simple look-up table is included to enhance the lifetime resolvability range and photon economics, making it comparable to the commonly used least-square method and maximum-likelihood estimation based software. To demonstrate its performance, a widefield microscope was adapted to accommodate the SPAD array and image different test samples. Fluorescence lifetime imaging microscopy on fluorescent beads in Rhodamine 6G at a frame rate of 50 fps is also shown.

Peptide-tags for enhanced DNA microarray performance

DNA microarrays are powerful tools for gene expression analysis and genotyping studies in research and diagnostic applications. A high sensitivity and short time-to-result are prerequisites for their practical application in the clinic. The hybridization efficiency of DNA microarrays depends on the probe density and the probe orientation and thus their accessibility for target molecules. In order to find an optimal probe immobilization procedure a set of different oligonucleotide modifications was tested on epoxy silane functionalized glass slides. It was found that histidine-tagged oligonucleotides resulted in the highest amount of bound probe and by far the best hybridization efficiencies. The detection limit obtained with histidine-tagged probes was up to two orders of magnitude lower compared to commonly used probe modifications. In order to further investigate the binding mechanism of histidine-tags towards functionalized glass substrates a set of different peptide-tags with and without free terminal amino-groups and with different amino acid compositions was tested. The results indicate an impact of the terminal amino group on the covalent surface binding and of aromatic amino acid residues on the enhanced hybridisation efficiency.

Highly efficient detection in fluorescence tomography of quantum dots using time-gated acquisition and ultrafast pulsed laser

Quantum dots (QDs) are widely used in fluorescence tomography due to its unique advantages. Despite the very high quantum efficiency of the QDs, low fluorescent signal and autofluorescence are the most fundamental limitations in optical data acquisition. These limitations are particularly detrimental to image reconstruction for animal imaging, e.g., free-space in vivo fluorescence tomography. In animals studies, fluorescent emission from exogenous fluorescent probes (e.g. QDs) cannot be effectively differentiated from endogenous broad-spectral substances (mostly proteins) using optical filters. In addition, a barrow-band fluorescent filter blocks the majority of the fluorescent light and thus makes signal acquisition very inefficient. We made use of the long fluorescent lifetime of the QDs to reject the optical signal due to the excitation light pulse, and therefore eliminated the need for a fluorescent filter during acquisition. Fluorescent emission from the QDs was excited with an ultrafast pulsed laser, and was detected using a time-gated image intensifier. A tissue-simulating imaging phantom was used to validate the proposed method. Compared to the standard acquisition method that uses a narrow-band fluorescent filter, the proposed method is significantly more efficient in data acquisition (by a factor of >10 in terms of fluorescent signal intensity) and demonstrated reduction in autofluorescence. No additional imaging artifact was observed in the tomographic reconstruction.

Fluorescence lifetime biosensing with DNA microarrays and a CMOS-SPAD imager

Fluorescence lifetime of dye molecules is a sensitive reporter on local microenvironment which is generally independent of fluorophores concentration and can be used as a means of discrimination between molecules with spectrally overlapping emission. It is therefore a potentially powerful multiplexed detection modality in biosensing but requires extremely low light level operation typical of biological analyte concentrations, long data acquisition periods and on-chip processing capability to realize these advantages. We report here fluorescence lifetime data obtained using a CMOS-SPAD imager in conjunction with DNA microarrays and TIRF excitation geometry. This enables acquisition of single photon arrival time histograms for a 320 pixel FLIM map within less than 26 seconds exposure time. From this, we resolve distinct lifetime signatures corresponding to dye-labelled HCV and quantum-dot-labelled HCMV nucleic acid targets at concentrations as low as 10 nM.

Amplified energy transfer in conjugated polymer nanoparticle tags and sensors

Nanoparticles primarily consisting of π-conjugated polymers have emerged as extraordinarily bright fluorescent tags with potential applications in biological imaging and sensing. As fluorescent tags, conjugated polymer nanoparticles possess a number of advantageous properties, such as small particle size, extraordinary fluorescence brightness, excellent photostability, and high emission rate. Exciton diffusion occurring in the nanoparticles results in amplified energy transfer, doubling the energy transfer efficiency in some cases. Amplified energy transfer has been exploited to obtain highly red-shifted emission, oxygen-sensing nanoparticles, and fluorescence photoswitching. Additional observed phenomena are attributable to amplified energy transfer in conjugated polymers, including superquenching by metal nanoparticles, and fluorescence modulation by hole polarons. This feature article presents an overview of recent investigations of optical properties and energy transfer phenomena of this relatively novel type of fluorescent nanoparticle with a viewpoint towards demanding fluorescence-based imaging and sensing applications.

Quantum dots-from synthesis to applications in biomedicine and life sciences

Imagine devices or particles so small that they are invisible to the naked eye. Imagine that such entities could be used to patrol our bodies and autonomously augment endogenous defense and repair mechanisms. Imagine the defeat of illness at a fraction of the current costs. Bionanotechnology is the field of science that deals with just that: the development of imaging, tracking, targeting, sensing, diagnostic, and eventually therapeutic capabilities based on particles in the nanometer range, i.e., “nanoparticles”. Within the extensive group of nanoparticles, semiconducting quantum dots play a central and prominent role. Quantum dots excel at a myriad of physical properties, most notably their fluorescent properties, such as high quantum yield, photo-stability, broad absorption spectra, and their remarkable size-dependent emission-tunability.

Whole-body, real-time preclinical imaging of quantum dot fluorescence with time-gated detection

We describe a wide-field preclinical imaging system optimized for time-gated detection of quantum dot fluorescence emission. As compared to continuous wave measurements, image contrast was substantially improved by suppression of short-lifetime background autofluorescence. Real-time (8 frames/s) biological imaging of subcutaneous quantum dot injections is demonstrated simultaneously in multiple living mice.