More Like this

1. Effect of vortex‐induced physical stress on fluorescent properties of dye‐containing poly(ethylene glycol)‐ block‐poly (lactic acid) micelles

   https://doi.org/10.1002/app.49743  

   Odom, Tyler L.; Blankenship, Jacob R.; Campos, Giselle; Mart, Devin C.; Liu, Wenyan; Wang, Risheng; Yoshimatsu, Keiichi (January 2021, Journal of Applied Polymer Science)

   Abstract The effect of vortex‐induced mechanical stresses on the fluorescent properties of dye‐containing poly(ethylene glycol)‐block‐poly(lactic acid) (PEG‐b‐PLA) block copolymer micelles has been investigated. PEG‐b‐PLA block copolymer micelles containing fluorescent dyes, 3,3′‐dioctadecyloxacarbocyanine perchlorate (DiO) and/or 1,1′‐dioctadecyl‐3,3,3′,3′‐tetramethylindocarbocyanine perchlorate (DiI), are prepared by a simple one‐step procedure that involves the self‐assembly of block copolymers and spontaneous incorporation of hydrophobic dyes into the core of the micelles. Upon vortexing, the micelle dispersion samples showed a decrease in fluorescence intensity in a rotational speed‐ and time‐dependent manner. The results demonstrated that the vortexing can alter the fluorescent properties of the dye‐containing PEG‐b‐PLA block copolymer micelle dispersion samples, suggesting the potential utility of block copolymer micelles as a mechanical stress‐responsive nanomaterial. 

   more » « less
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. 

   more » « less
3. Structural basis for ring-opening fluorescence by the RhoBAST RNA aptamer

   https://doi.org/10.1093/nar/gkaf555  

   Siwik, Shea H; Wierzba, Aleksandra J; Lennon, Shelby R; Olenginski, Lukasz T; Palmer, Amy E; Batey, Robert T (June 2025, Nucleic Acids Research)

   Abstract Tagging RNAs with fluorogenic aptamers has enabled imaging of transcripts in living cells, revealing novel aspects of RNA metabolism and dynamics. While a diverse set of fluorogenic aptamers has been developed, a new generation of aptamers uses the ring-opening of spirocyclic rhodamine dyes to achieve robust performance in live mammalian cells. These fluorophores have two chemical states: a cell-permeable spirocyclic state and a fluorescent zwitterionic state. The SpyRho555 dye is mostly non-fluorescent in solution and becomes fluorescent in complex with the RhoBAST aptamer. To understand the basis for RhoBAST-SpyRho555 fluorogenicity, we have determined crystal structures of RhoBAST in complex with 5-carboxytetramethylrhodamine and a SpyRho555 analogue, MaP555. RhoBAST is organized by a perfect four-way junction that positions two loops to form the dye-binding pocket. The core of the ligand resides between a tri-adenine floor and a single guanine base, largely driven by π-stacking interactions. Importantly, the unpaired guanine interacts with the 3-position group of MaP555 to stabilize the open conformation, supported by mutagenesis data, and may play an active role in promoting the open conformation of the dye. This work has implications for the development of new fluorogenic aptamers with improved properties using structure-guided design approaches. 

   more » « less
4. Quantum Chemical Determination of Molecular Dye Candidates for Non-Invasive Bioimaging

   https://doi.org/10.3390/molecules29245860  

   Cron, Remy R; South, Jordan; Fortenberry, Ryan C (December 2024, Molecules)

   Molecular dyes containing carbazole-based π bridges and/or julolidine-based donors should be promising molecules for intense SWIR emission with potential application to molecular bioimaging. This study stochastically analyzes the combinations of more than 250 organic dyes constructed within the D-π-D (or equivalently D-B-D) motif. These dyes are built from 22 donors (D) and 14 π bridges (B) and are computationally examined using density functional theory (DFT). The DFT computations provide optimized geometries from which the excited state transition wavelengths and associated oscillator strengths and orbital overlaps are computed. While absorption is used as a stand-in for emission, the longer the absorption wavelength, the longer the emission should be as well for molecules of this type. Nearly 100 novel dyes reported in this work have electronic absorptions at or beyond 1200 nm, opening the possibility for future synthesis and experimental characterization of new molecular dyes with promising properties for bioimaging. 

   more » « less
5. A Generalizable Fluorescence Sensor Platform for Sample Preparation‐Free Protein Detection

   https://doi.org/10.1002/adma.202419662  

   Wu, Helen D; Trinh, Tuan; Li, Tongtong; Thapa, Subhadra; Lee, Robert B; Nguyen, Thuy‐Tien Thi; Petrakian, Camille F; Eisenstein, Michael; Schneebeli, Severin T; Li, Jianing; et al (November 2025, Advanced Materials)

   Abstract Modern molecular detection assays such as enzyme‐linked immunosorbent assays (ELISAs) offer excellent sensitivity and specificity, but typically require multiple reagents and extensive sample preparation, limiting their usefulness as rapid diagnostics. A generalizable biosensor platform is introduced that enables single‐step, sample preparation‐free detection of protein analytes with high sensitivity in complex samples. The NanoFluor system employs Janelia Fluor dyes coupled to a nanobody via HaloTag conjugation with a flexible glycine‐serine linker, where the dye undergoes a switch from a non‐fluorescent to a fluorescent state when the coupled nanobody binds to its target. It is demonstrated that the NanoFluor design achieves detection limits as low as picomolar concentrations across diverse protein targets. Molecular dynamics simulations, coupled with quantum mechanics/molecular mechanics computational models, reveal the mechanistic basis for the fluorescence change, and demonstrate the feasibility of multiplexed detection in complex samples including undiluted serum. This versatile, simple biosensor design can prove valuable for point‐of‐care diagnostics and other molecular detection applications. 

   more » « less