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1. Ultrabright Fluorescent Silica Nanoparticles for Dual pH and Temperature Measurements

   https://doi.org/10.3390/nano11061524  

   Peerzade, Saquib ; Makarova, Nadezhda ; Sokolov, Igor ( June 2021 , Nanomaterials)

   null (Ed.)

   The mesoporous nature of silica nanoparticles provides a novel platform for the development of ultrabright fluorescent particles, which have organic molecular fluorescent dyes physically encapsulated inside the silica pores. The close proximity of the dye molecules, which is possible without fluorescence quenching, gives an advantage of building sensors using FRET coupling between the encapsulated dye molecules. Here we present the use of this approach to demonstrate the assembly of ultrabright fluorescent ratiometric sensors capable of simultaneous acidity (pH) and temperature measurements. FRET pairs of the temperature-responsive, pH-sensitive and reference dyes are physically encapsulated inside the silica matrix of ~50 nm particles. We demonstrate that the particles can be used to measure both the temperature in the biologically relevant range (20 to 50 °C) and pH within 4 to 7 range with the error (mean absolute deviation) of 0.54 °C and 0.09, respectively. Stability of the sensor is demonstrated. The sensitivity of the sensor ranges within 0.2–3% °C−1 for the measurements of temperature and 2–6% pH−1 for acidity. 

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2. Ultrabright Fluorescent Silica Nanoparticles for Multiplexed Detection

   https://doi.org/10.3390/nano10050905  

   Peerzade, Saquib Ahmed ; Makarova, Nadezda ; Sokolov, Igor ( May 2020 , Nanomaterials)

   null (Ed.)

   Fluorescent tagging is a popular method in biomedical research. Using multiple taggants of different but resolvable fluorescent spectra simultaneously (multiplexing), it is possible to obtain more comprehensive and faster information about various biochemical reactions and diseases, for example, in the method of flow cytometry. Here we report on a first demonstration of the synthesis of ultrabright fluorescent silica nanoporous nanoparticles (Star-dots), which have a large number of complex fluorescence spectra suitable for multiplexed applications. The spectra are obtained via simple physical mixing of different commercially available fluorescent dyes in a synthesizing bath. The resulting particles contain dye molecules encapsulated inside of cylindrical nanochannels of the silica matrix. The distance between the dye molecules is sufficiently small to attain Forster resonance energy transfer (FRET) coupling within a portion of the encapsulated dye molecules. As a result, one can have particles of multiple spectra that can be excited with just one wavelength. We show this for the mixing of five, three, and two dyes. Furthermore, the dyes can be mixed inside of particles in different proportions. This brings another dimension in the complexity of the obtained spectra and makes the number of different resolvable spectra practically unlimited. We demonstrate that the spectra obtained by different mixing of just two dyes inside of each particle can be easily distinguished by using a linear decomposition method. As a practical example, the errors of demultiplexing are measured when sets of a hundred particles are used for tagging. 

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3. Ultrabright fluorescent nanothermometers

   https://doi.org/10.1039/D1NA00449B  

   Kalaparthi, V. ; Peng, B. ; Peerzade, S. A. ; Palantavida, S. ; Maloy, B. ; Dokukin, M. E. ; Sokolov, I. ( August 2021 , Nanoscale Advances)

   Here we report on the first ultrabright fluorescent nanothermometers, ∼50 nm-size particles, capable of measuring temperature in 3D and down to the nanoscale. The temperature is measured through the recording of the ratio of fluorescence intensities of fluorescent dyes encapsulated inside the nanochannels of the silica matrix of each nanothermometer. The brightness of each particle excited at 488 nm is equivalent to the fluorescence coming from 150 molecules of rhodamine 6G and 1700 molecules of rhodamine B dyes. The fluorescence of both dyes is excited with a single wavelength due to the Förster resonance energy transfer (FRET). We demonstrate repeatable measurements of temperature with the uncertainty down to 0.4 K and a constant sensitivity of ∼1%/K in the range of 20–50 °C, which is of particular interest for biomedical applications. Due to the high fluorescence brightness, we demonstrate the possibility of measurement of accurate 3D temperature distributions in a hydrogel. The accuracy of the measurements is confirmed by numerical simulations. We further demonstrate the use of single nanothermometers to measure temperature. As an example, 5–8 nanothermometers are sufficient to measure temperature with an error of 2 K (with the measurement time of >0.7 s). 

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4. Direct measurement of the pH of aerosol particles using carbon quantum dots

   https://doi.org/10.1039/D2AY01005D  

   Tackman, Emma C. ; Grady, Rachel S. ; Freedman, Miriam Arak ( August 2022 , Analytical Methods)

   The pH of aerosol particles remains challenging to measure because of their small size, complex composition, and high acidity. Acidity in aqueous aerosol particles, which are found abundantly in the atmosphere, impacts many chemical processes from reaction rates to cloud formation. Only one technique – pH paper – currently exists for directly determining the pH of aerosol particles, and this is restricted to measuring average acidity for entire particle populations. Other methods for evaluating aerosol pH include filter samples, particle-into-liquid sampling, Raman spectroscopy, organic dyes, and thermodynamic models, but these either operate in a higher pH range or are unable to assess certain chemical species or complexity. Here, we present a new method for determining acidity of individual particles and particle phases using carbon quantum dots as a novel in situ fluorophore. Carbon quantum dots are easily synthesized, shelf stable, and sensitive to pH in the highly acidic regime from pH 0 to pH 3 relevant to ambient aerosol particles. To establish the method, a calibration curve was formed from the ratiometric fluorescence intensity of aerosolized standard solutions with a correlation coefficient ( R 2 ) of 0.99. Additionally, the pH of aerosol particles containing a complex organic mixture (COM) representative of environmental aerosols was also determined, proving the efficacy of using carbon quantum dots as pH-sensitive fluorophores for complex systems. The ability to directly measure aerosol particle and phase acidity in the correct pH range can help parametrize atmospheric models and improve projections for other aerosol properties and their influence on health and climate. 

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5. Delineating Ultrafast Structural Dynamics of a Green-Red Fluorescent Protein for Calcium Sensing

   https://doi.org/10.3390/bios13020218  

   Krueger, Taylor D. ; Tang, Longteng ; Fang, Chong ( February 2023 , Biosensors)

   Fluorescent proteins (FPs) are indispensable tools for noninvasive bioimaging and sensing. Measuring the free cellular calcium (Ca2+) concentrations in vivo with genetically encodable FPs can be a relatively direct measure of neuronal activity due to the complex signaling role of these ions. REX-GECO1 is a recently developed red-green emission and excitation ratiometric FP-based biosensor that achieves a high dynamic range due to differences in the chromophore response to light excitation with and without calcium ions. Using steady-state electronic measurements (UV/Visible absorption and emission), along with time-resolved spectroscopic techniques including femtosecond transient absorption (fs-TA) and femtosecond stimulated Raman spectroscopy (FSRS), the potential energy surfaces of these unique biosensors are unveiled with vivid details. The ground-state structural characterization of the Ca2+-free biosensor via FSRS reveals a more spacious protein pocket that allows the chromophore to efficiently twist and reach a dark state. In contrast, the more compressed cavity within the Ca2+-bound biosensor results in a more heterogeneous distribution of chromophore populations that results in multi-step excited state proton transfer (ESPT) pathways on the sub-140 fs, 600 fs, and 3 ps timescales. These results enable rational design strategies to enlarge the spectral separation between the protonated/deprotonated forms and the Stokes shift leading to a larger dynamic range and potentially higher fluorescence quantum yield, which should be broadly applicable to the calcium imaging and biosensor communities. 

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