DNA Nanotechnology for Application in Targeted Protein Degradation

DNA is a kind of flexible and versatile biomaterial for constructing nanostructures and nanodevices. Due to high biocompatibility and programmability and easy modification and fabrication, DNA nanotechnology has emerged as a powerful tool for application in intracellular targeted protein degradation. In this review, we summarize the recent advances in the design and mechanism of targeted protein degradation technologies such as protein hydrolysis targeted chimeras, lysosomal targeted chimeras, and autophagy based protein degradation. Subsequently, we introduce the DNA nanotechnologies of DNA cascade circuits, DNA nanostructures, and dynamic machines. Moreover, we present the latest developments in DNA nanotechnologies in targeted protein degradation. Finally, the vision and challenges are discussed.

Native top-down mass spectrometry for monitoring the rapid chymotrypsin catalyzed hydrolysis reaction

Enzymes play crucial roles in life sciences, pharmaceuticals and industries as biological catalysts that speed up biochemical reactions in living organisms. New catalytic reactions are continuously developed by enzymatic engineering to meet industrial needs, which thereby drives the development of analytical approaches for real-time reaction monitoring to reveal catalytic processes. Here, taking the hydrolase- chymotrypsin as a model system, we proposed a convenient method for monitoring catalytic processes through native top-down mass spectrometry (native TDMS). The chymotrypsin sample heterogeneity was first explored. By altering sample introduction modes and pHs, covalent and noncovalent enzymatic complexes, substrates and products can be monitored during the catalysis and further confirmed by tandem MS. Our results demonstrated that native TDMS based catalysis monitoring has distinctive strength on real-time inspection and continuous observation, making it a promising tool for characterizing more biocatalysts.

Mass Spectrometry of Nucleic Acid Noncovalent Complexes

Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.

Gas-Phase UV Spectroscopy of Chemical Intermediates Produced in Solution: Oxidation Reactions of Phenylhydrazines by DDQ

In this study, we demonstrated cold gas-phase spectroscopy of chemical intermediates produced in solution. Herein, we combined an electrospray ion source with a T-shaped solution mixer for introducing chemical intermediates in solution into the gas phase. Specifically, the oxidation reaction of 2-(4-nitrophenyl)hydrazinecarboxaldehyde (NHCA) by 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) was initiated by mixing the methanol solutions of NHCA and DDQ in the T-shaped mixer, and the chemical species were injected into the vacuum apparatus for ultraviolet photodissociation (UVPD) spectroscopy. A cationic intermediate was strongly observed at m/z 150 in the mass spectrum, and the UVPD spectrum was observed under cold (∼10 K) gas-phase conditions. The UVPD spectrum showed a strong, broad absorption at ∼38,000 cm^-1, accompanied by a relatively weak component at ∼34,000 cm^-1. These spectral patterns can be ascribed to a diazonium cation intermediate, whose existence has been predicted in a previous study. This report indicates that cold gas-phase UV spectroscopy can be a useful method for identifying the structure of chemical intermediates produced in solution.

Structural Investigation of Photochemical Intermediates in Solution by Cold UV Spectroscopy in the Gas Phase: Photosubstitution of Dicyanobenzenes by Allylsilanes

Electrospray ion sources with an in-line quartz cell were constructed to produce photochemical intermediates in solution. These ion sources can detect photochemical intermediates having lifetimes longer than a few seconds. Intermediates formed by photosubstitution of 1,4-dicyanobenzene (DCB) by allyltrimethylsilane (AMS) in acetonitrile using a Xe lamp were injected into the mass spectrometer. The cationic intermediate (C₁₁H₁₀N₂·H⁺) was observed at m/z = 171, but no anionic intermediate was found, although C₁₁H₉N₂^- was expected based on prior studies. Theoretical studies suggested that C₁₁H₉N₂^- was simultaneously converted to neutral C₁₁H₁₀N₂ and cationic C₁₁H₁₀N₂·H⁺ species, which can be stable intermediates in the photosubstitution reaction. The UV photodissociation (UVPD) spectrum of C₁₁H₁₀N₂·H⁺ under cold (∼10 K) gas-phase conditions determined the conformation of the C₁₁H₁₀N₂ unit of the C₁₁H₁₀N₂·H⁺ cation. This report demonstrates that cold gas-phase UV spectroscopy is a prospectively powerful tool for investigation of the electronic and geometric structures of photochemical intermediates produced in solution.

Reactive Laser Ablation Electrospray Ionization Time-Resolved Mass Spectrometry of Click Reactions

Reactions in confined compartments like charged microdroplets are of increasing interest, notably because of their substantially increased reaction rates. When combined with ambient ionization mass spectrometry (MS), reactions in charged microdroplets can be used to improve the detection of analytes or to study the molecular details of the reactions in real time. Here, we introduce a reactive laser ablation electrospray ionization (reactive LAESI) time-resolved mass spectrometry (TRMS) method to perform and study reactions in charged microdroplets. We demonstrate this approach with a class of reactions new to reactive ambient ionization MS: so-called click chemistry reactions. Click reactions are high-yielding reactions with a high atom efficiency, and are currently drawing significant attention from fields ranging from bioconjugation to polymer modification. Although click reactions are typically at least moderately fast (time scale of minutes to a few hours), in a reactive LAESI approach a substantial increase of reaction time is required for these reactions to occur. This increase was achieved using microdroplet chemistry and followed by MS using the insertion of a reaction tube-up to 1 m in length-between the LAESI source and the MS inlet, leading to near complete conversions due to significantly extended microdroplet lifetime. This novel approach allowed for the collection of kinetic data for a model (strain-promoted) click reaction between a substituted tetrazine and a strained alkyne and showed in addition excellent instrument stability, improved sensitivity, and applicability to other click reactions. Finally, the methodology was also demonstrated in a mass spectrometry imaging setting to show its feasibility in future imaging experiments.