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1. Protein-, polymer-, and silica-based luminescent nanomaterial probes for super resolution microscopy: a review

   https://doi.org/10.1039/d0na00971g  

   Thompson, S.; Pappas, Dimitri (April 2021, Nanoscale Advances)

   null (Ed.)

   Super resolution microscopy was developed to overcome the Abbe diffraction limit, which effects conventional optical microscopy, in order to study the smaller components of biological systems. In recent years nanomaterials have been explored as luminescent probes for super resolution microscopy, as many have advantages over traditional fluorescent dye molecules. This review will summarize several different types of nanomaterial probes, covering quantum dots, carbon dots, and dye doped nanoparticles. For the purposes of this review the term “nanoparticle” will be limited to polymer-based, protein-based, and silica-based nanoparticles, including core–shell structured nanoparticles. Luminescent nanomaterials have shown promise as super-resolution probes, and continued research in this area will yield new advances in both materials science and biochemical microscopy at the nanometer scale. 

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2. Luminescent lanthanide probes for cations and anions: Promises, compromises, and caveats

   https://doi.org/10.1016/j.cbpa.2023.102374  

   Martinon, Thibaut L.M.; Pierre, Valérie C. (October 2023, Current Opinion in Chemical Biology)

   The long luminescence lifetimes and sharp emission bands of luminescent lanthanide complexes have long been recognized as invaluable strengths for sensing and imaging in complex aqueous biological or environmental media. Herein we discuss the recent developments of these probes for sensing metal ions and, increasingly, anions. Underappreciated in the field, buffers and metal hydrolysis influence the response of many responsive lanthanide probes. The inherent complexities arising from these interactions are further discussed. 

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3. Blinking-Based Multiplexing (BBM): Harnessing Molecular Photophysics for Single-Emitter Classification

   Wustholz, K.; Hoy, G.; DeSalvo, G; Kogan, I.; Haile, S.; Smith, E. (April 2023, Bulletin of the American Physical Society)

   Single-molecule fluorescence approaches have revolutionized biological and materials microscopy. However, many questions can only be addressed by multicolor imaging of multiple targets, a capability that is limited by the small subset of available, well-performing, and spectrally-distinct fluorescent probes. We recently introduced an alternative single-molecule multiplexing approach termed blinking-based multiplexing (BBM), wherein individual molecules are classified on the basis of their intrinsic blinking dynamics. We demonstrate accurate (>93.5%) binary classification of spectrally-overlapped rhodamine and quantum dot emitters using BBM, even when substantial blinking heterogeneity is observed. Classification can be accomplished using change point detection (CPD) analysis of blinking dynamics or a deep learning (DL) algorithm, the latter of which provides up to 96.6% accuracy. Here, we use CPD and DL algorithms to probe the excitation power, environmental, and molecular dependence of BBM. In addition to providing new opportunities in single-molecule spectroscopy and imaging, BBM represents a new take on single-molecule research, where blinking dynamics can be harnessed for more than just traditional localization or nanoreporting. 

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4. Accessing lanthanide-based, in situ illuminated optical turn-on probes by modulation of the antenna triplet state energy

   https://doi.org/10.1039/d1sc02148f  

   Cosby, Alexia G.; Woods, Joshua J.; Nawrocki, Patrick; Sørensen, Thomas J.; Wilson, Justin J.; Boros, Eszter (July 2021, Chemical Science)

   Luminescent lanthanides possess ideal properties for biological imaging, including long luminescent lifetimes and emission within the optical window. Here, we report a novel approach to responsive luminescent Tb( iii ) probes that involves direct modulation of the antenna excited triplet state energy. If the triplet energy lies too close to the 5 D 4 Tb( iii ) excited state (20 500 cm −1 ), energy transfer to 5 D 4 competes with back energy transfer processes and limits lanthanide-based emission. To validate this approach, a series of pyridyl-functionalized, macrocyclic lanthanide complexes were designed, and the corresponding lowest energy triplet states were calculated using density functional theory (DFT). Subsequently, three novel constructs L3 (nitro-pyridyl), L4 (amino-pyridyl) and L5 (fluoro-pyridyl) were synthesized. Photophysical characterization of the corresponding Gd( iii ) complexes revealed antenna triplet energies between 25 800 and 30 400 cm −1 and a 500-fold increase in quantum yield upon conversion of Tb( L3 ) to Tb( L4 ) using the biologically relevant analyte H 2 S. The corresponding turn-on reaction can be monitored using conventional, small-animal optical imaging equipment in presence of a Cherenkov radiation emitting isotope as an in situ excitation source, demonstrating that antenna triplet state energy modulation represents a viable approach to biocompatible, Tb-based optical turn-on probes. 

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5. Oxidative degradation of sequence-defined peptoid oligomers

   https://doi.org/10.1039/D2ME00179A  

   Schunk, Hattie C.; Austin, Mariah J.; Taha, Bradley Z.; McClellan, Matthew S.; Suggs, Laura J.; Rosales, Adrianne M. (January 2023, Molecular Systems Design & Engineering)

   Due to their N -substitution, peptoids are generally regarded as resistant to biological degradation, such as enzymatic and hydrolytic mechanisms. This stability is an especially attractive feature for therapeutic development and is a selling point of many previous biological studies. However, another key mode of degradation remains to be fully explored, namely oxidative degradation mediated by reactive oxygen and nitrogen species (ROS/RNS). ROS and RNS are biologically relevant in numerous contexts where biomaterials may be present. Thus, improving understanding of peptoid oxidative susceptibility is crucial to exploit their full potential in the biomaterials field, where an oxidatively-labile but enzymatically stable molecule can offer attractive properties. Toward this end, we demonstrate a fundamental characterization of sequence-defined peptoid chains in the presence of chemically generated ROS, as compared to ROS-susceptible peptides such as proline and lysine oligomers. Lysine oligomers showed the fastest degradation rates to ROS and the enzyme trypsin. Peptoids degraded in metal catalyzed oxidation conditions at rates on par with poly(prolines), while maintaining resistance to enzymatic degradation. Furthermore, lysine-containing peptide–peptoid hybrid molecules showed tunability in both ROS-mediated and enzyme-mediated degradation, with rates intermediate to lysine and peptoid oligomers. When lysine-mimetic side-chains were incorporated into a peptoid backbone, the rate of degradation matched that of the lysine peptide oligomers, but remained resistant to enzymatic degradation. These results expand understanding of peptoid degradation to oxidative and enzymatic mechanisms, and demonstrate the potential for peptoid incorporation into materials where selectivity towards oxidative degradation is necessary, or directed enzymatic susceptibility is desired. 

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