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1. Tandem Affinity Purification (TAP) of Low-Abundance Protein Complexes in Filamentous Fungi Demonstrated Using Magnaporthe oryzae

   https://doi.org/10.1007/978-1-0716-1613-0_8  

   Li, G; Wilson, RA. (January 2021, Methods in molecular biology)

   Jacob, S. (Ed.)

   Protein–protein interactions underlie cellular structure and function. In recent years, a number of methods have been developed for the identification of protein complexes and component proteins involved in the control of various biological pathways. Tandem affinity purification (TAP) coupled with mass spectrometry (MS) is a powerful method enabling the isolation of high-purity native protein complexes under mild conditions by performing two sequential purification steps using two different epitope tags. In this protocol, we describe a TAP-MS methodology for identifying protein-protein interactions present at very low levels in the fungal cell. Using the 6xHis-3xFLAG double tag, we start the affinity purification process for our protein of interest using high-capacity Ni²⁺ columns. This allows for greatly increased sample input compared to antibody-based first-step purification in conventional TAP protocols and provides a large amount of highly concentrated and preliminarily purified protein complexes to be used in a second purification step involving FLAG immunoprecipitation. The second step greatly facilitates the capture of low-level interacting partners under in vivo conditions. Our TAP-MS method has been proven to secure the characterization of low-abundance protein complexes under physiological conditions with high efficiency, specificity, and economy in the filamentous fungus Magnaporthe oryzae and might benefit gene function and proteomics studies in plants and other research fields. 

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2. Effective, Rapid, and Small-Scale Bioconjugation and Purification of “Clicked” Small-Molecule DNA Oligonucleotide for Nucleic Acid Nanoparticle Functionalization

   https://doi.org/10.3390/ijms24054797  

   Doe, Erwin; Hayth, Hannah L.; Brumett, Ross; Khisamutdinov, Emil F. (March 2023, International Journal of Molecular Sciences)

   Nucleic acid-based therapeutics involves the conjugation of small molecule drugs to nucleic acid oligomers to surmount the challenge of solubility, and the inefficient delivery of these drug molecules into cells. “Click” chemistry has become popular conjugation approach due to its simplicity and high conjugation efficiency. However, the major drawback of the conjugation of oligonucleotides is the purification of the products, as traditionally used chromatography techniques are usually time-consuming and laborious, requiring copious quantities of materials. Herein, we introduce a simple and rapid purification methodology to separate the excess of unconjugated small molecules and toxic catalysts using a molecular weight cut-off (MWCO) centrifugation approach. As proof of concept, we deployed “click” chemistry to conjugate a Cy3-alkyne moiety to an azide-functionalized oligodeo-xynucleotide (ODN), as well as a coumarin azide to an alkyne-functionalized ODN. The calculated yields of the conjugated products were found to be 90.3 ± 0.4% and 86.0 ± 1.3% for the ODN-Cy3 and ODN-coumarin, respectively. Analysis of purified products by fluorescence spectroscopy and gel shift assays demonstrated a drastic amplitude of fluorescent intensity by multiple folds of the reporter molecules within DNA nanoparticles. This work is intended to demonstrate a small-scale, cost-effective, and robust approach to purifying ODN conjugates for nucleic acid nanotechnology applications. 

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3. An isocyanide ligand for the rapid quenching and efficient removal of copper residues after Cu/TEMPO-catalyzed aerobic alcohol oxidation and atom transfer radical polymerization

   https://doi.org/10.1039/D0SC00623H  

   Szczepaniak, Grzegorz; Piątkowski, Jakub; Nogaś, Wojciech; Lorandi, Francesca; Yerneni, Saigopalakrishna S.; Fantin, Marco; Ruszczyńska, Anna; Enciso, Alan E.; Bulska, Ewa; Grela, Karol; et al (April 2020, Chemical Science)

   Transition metal catalysts play a prominent role in modern organic and polymer chemistry, enabling many transformations of academic and industrial significance. However, the use of organometallic catalysts often requires the removal of their residues from reaction products, which is particularly important in the pharmaceutical industry. Therefore, the development of efficient and economical methods for the removal of metal contamination is of critical importance. Herein, we demonstrate that commercially available 1,4-bis(3-isocyanopropyl)piperazine can be used as a highly efficient quenching agent ( QA ) and copper scavenger in Cu/TEMPO alcohol aerobic oxidation (Stahl oxidation) and atom transfer radical polymerization (ATRP). The addition of QA immediately terminates Cu-mediated reactions under various conditions, forming a copper complex that can be easily separated from both small molecules and macromolecules. The purification protocol for aldehydes is based on the addition of a small amount of silica gel followed by QA and filtration. The use of QA@SiO2 synthesized in situ results in products with Cu content usually below 5 ppm. Purification of polymers involves only the addition of QA in THF followed by filtration, leading to polymers with very low Cu content, even after ATRP with high catalyst loading. Furthermore, the addition of QA completely prevents oxidative alkyne–alkyne (Glaser) coupling. Although isocyanide QA shows moderate toxicity, it can be easily converted into a non-toxic compound by acid hydrolysis. 

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4. Insulator Based Dielectrophoresis: Micro, Nano, and Molecular Scale Biological Applications

   https://doi.org/10.3390/s20185095  

   Benhal, Prateek; Quashie, David; Kim, Yoontae; Ali, Jamel (September 2020, Sensors)

   null (Ed.)

   Insulator based dielectrophoresis (iDEP) is becoming increasingly important in emerging biomolecular applications, including particle purification, fractionation, and separation. Compared to conventional electrode-based dielectrophoresis (eDEP) techniques, iDEP has been demonstrated to have a higher degree of selectivity of biological samples while also being less biologically intrusive. Over the past two decades, substantial technological advances have been made, enabling iDEP to be applied from micro, to nano and molecular scales. Soft particles, including cell organelles, viruses, proteins, and nucleic acids, have been manipulated using iDEP, enabling the exploration of subnanometer biological interactions. Recent investigations using this technique have demonstrated a wide range of applications, including biomarker screening, protein folding analysis, and molecular sensing. Here, we review current state-of-art research on iDEP systems and highlight potential future work. 

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5. Towards nanovesicle-based disease diagnostics: a rapid single-step exosome assay within one hour through in situ immunomagnetic extraction and nanophotonic label-free detection

   https://doi.org/10.1039/D1LC00446H  

   Zhang, Qinming; Loghry, Hannah J.; Qian, Jingjing; Kimber, Michael J.; Dong, Liang; Lu, Meng (September 2021, Lab on a Chip)

   Exosomes have been considered as high-quality biomarkers for disease diagnosis, as they are secreted by cells into extracellular environments as nanovesicles with rich and unique molecular information, and can be isolated and enriched from clinical samples. However, most existing exosome assays, to date, require time-consuming isolation and purification procedures; the detection specificity and sensitivity are also in need of improvement for the realization of exosome-based disease diagnostics. This paper reports a unique exosome assay technology that enables completing both magnetic nanoparticle (MNP)-based exosome extraction and high-sensitivity photonic crystal (PC)-based label-free exosome detection in a single miniature vessel within one hour, while providing an improved sensitivity and selectivity. High specificity of the assay to membrane antigens is realized by functionalizing both the MNPs and the PC with specific antibodies. A low limit of detection on the order of 10 7 exosome particles per milliliter (volume) is achieved because the conjugated MNP–exosome nanocomplexes offer a larger index change on the PC surface, compared to the exosomes alone without using MNPs. Briefly, the single-step exosome assay involves (i) forming specific MNP–exosome nanocomplexes to enrich exosomes from complex samples directly on the PC surface at the bottom of the vessel, with a >500 enrichment factor, and (ii) subsequently, performing in situ quantification of the nanocomplexes using the PC biosensor. The present exosome assay method is validated in analyzing multiple membrane proteins of exosomes derived from murine macrophage cells with high selectivity and sensitivity, while requiring only about one hour. This assay technology will provide great potential for exosome-based disease diagnostics. 

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