Second-harmonic generation-based methods to detect and characterize ligand-induced RNA conformational changes

Enhanced third harmonic generation in ultrathin free-standing β-Ga2O3 nanomembranes: study on surface and bulk contribution

Third harmonic generation (THG) has proven its value in surface and interface characterization, high-contrast bio-imaging, and sub-wavelength light manipulation. Although THG is observed widely in general solid and liquid substances, when laser pulses are focused at nanometer-level ultra-thin films, the bulk THG has been reported to play the dominant role. However, there are still third harmonics (TH) generated at the surface of the thin-films, not inside the bulk solid - so-called surface TH, whose relative contribution has not been quantitatively revealed to date. In this study, we quantitatively characterized the surface and bulk contributions of THG at ultra-thin β-Ga₂O₃ nanomembranes with control of both the laser and thin-nanomembranes parameters, including the laser peak power, polarization state, number of layers, and nanomembranes thicknesses. Their contributions were studied in detail by analyzing the TH from freestanding β-Ga₂O₃ nanomembranes compared with TH from β-Ga₂O₃ nanomembranes on glass substrates. The contribution of the TH field from the β-Ga₂O₃-air interface was found to be 5.12 times more efficient than that from the β-Ga₂O₃-glass interface, and also 1.09 times stronger than the TH excited at bulk 1-μm-thick β-Ga₂O₃. Besides, TH from the β-Ga₂O₃-air interface was found to be 20% more sensitive to the crystalline structure than that from the β-Ga₂O₃-glass interface. This research work deepens our understanding of surface and bulk THG from crystalline materials and provides new possibilities towards designing highly efficient nonlinear optical materials for bio-imaging, energy-harvesting, and ultrafast laser development.

Fragment-Based Drug Discovery for RNA Targets

Rapid development within the fields of both fragment-based drug discovery (FBDD) and medicinal targeting of RNA provides possibilities for combining technologies and methods in novel ways. This review provides an overview of fragment-based screening (FBS) against RNA targets, including a discussion of the most recently used screening and hit validation methods such as NMR spectroscopy, X-ray crystallography, and virtual screening methods. A discussion of fragment library design based on research from small-molecule RNA binders provides an overview on both the currently limited guidelines within RNA-targeting fragment library design, and future possibilities. Finally, future perspectives are provided on screening and hit validation methods not yet used in combination with both fragment screening and RNA targets.

Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor

Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.