Site-specific protein labeling strategies for super-resolution microscopy

Super-resolution microscopy (SRM) has transformed our understanding of proteins' subcellular organization and revealed cellular details down to nanometers, far beyond conventional microscopy. While localization precision is independent of the number of fluorophores attached to a biomolecule, labeling density is a decisive factor for resolving complex biological structures. The average distance between adjacent fluorophores should be less than half the desired spatial resolution for optimal clarity. While this was not a major limitation in recent decades, the success of modern microscopy approaching molecular resolution down to the single-digit nanometer range will depend heavily on advancements in fluorescence labeling. This review highlights recent advances and challenges in labeling strategies for SRM, focusing on site-specific labeling technologies. These advancements are crucial for improving SRM precision and expanding our understanding of molecular interactions.

PCNA as Protein-Based Nanoruler for Sub-10 nm Fluorescence Imaging

Super-resolution microscopy has revolutionized biological imaging enabling direct insight into cellular structures and protein arrangements with so far unmatched spatial resolution. Today, refined single-molecule localization microscopy methods achieve spatial resolutions in the one-digit nanometer range. As the race for molecular resolution fluorescence imaging with visible light continues, reliable biologically compatible reference structures will become essential to validate the resolution power. Here, PicoRulers (protein-based imaging calibration optical rulers), multilabeled oligomeric proteins designed as advanced molecular nanorulers for super-resolution fluorescence imaging are introduced. Genetic code expansion (GCE) is used to site-specifically incorporate three noncanonical amino acids (ncAAs) into the homotrimeric proliferating cell nuclear antigen (PCNA) at 6 nm distances. Bioorthogonal click labeling with tetrazine-dyes and tetrazine-functionalized oligonucleotides allows efficient labeling of the PicoRuler with minimal linkage error. Time-resolved photoswitching fingerprint analysis is used to demonstrate the successful synthesis and DNA-based points accumulation for imaging in nanoscale topography (DNA-PAINT) is used to resolve 6 nm PCNA PicoRulers. Since PicoRulers maintain their structural integrity under cellular conditions they represent ideal molecular nanorulers for benchmarking the performance of super-resolution imaging techniques, particularly in complex biological environments.

Overcoming Non-Specific Interactions for Efficient Encapsulation of Doxorubicin in Ferritin Nanocages for Targeted Drug Delivery

Due to its beneficial pharmacological properties, ferritin (Ftn) is considered as an interesting drug delivery vehicle to alleviate the cardiotoxicity of doxorubicin (DOX) in chemotherapy. However, the encapsulation of DOX in Ftn suffers from heavy precipitation and low protein recovery yield which limits its full potential. Here, a new DOX encapsulation strategy by cysteine-maleimide conjugation is proposed. In order to demonstrate that this strategy is more efficient compared to the other approaches, DOX is encapsulated in Ftn variants carrying different surface charges. Furthermore, in contrast to the common belief, this data show that DOX molecules are also found to bind non-specifically to the surface of Ftn. This can be circumvented by the use of Tris(2-carboxyethyl)phosphine (TCEP) during encapsulation or by washing with acidic buffer. The biocompatibility studies of the resulting DOX Ftn variants in MCF-7 and MHS cancer cells shows a complex relationship between the cytotoxicity, the DOX loading and the different surface charges of Ftn. Further investigation on the cell uptake mechanism provides reasonable explanations for the cytotoxicity results and reveals that surface charging of Ftn hinders its transferrin receptor 1 (TfR-1) mediated cellular uptake in MCF-7 cells.

Protecting redesigned supercharged ferritin containers against protease by integration into acid-cleavable polyelectrolyte microgels

HYPOTHESIS

The application of ferritin containers as a promising drug delivery vehicle is limited by their low bioavailability in blood circulation due to unfavorable environments, such as degradation by protease. The integration of ferritin containers into the polymeric network of microgels through electrostatic interactions is expected to be able to protect ferritin against degradation by protease. Furthermore, a stimuli-responsive microgel system can be designed by employing an acid-degradable crosslinker during the microgel synthesis. This should enable ferritin release in an acidic environment, which will be useful for future drug delivery applications.

EXPERIMENTS

Nanoparticle/fluorophores-loaded ferritin was integrated into microgels during precipitation polymerization. The integration was monitored by transmission electron microscopy (TEM)² and fluorescence microscopy, respectively. After studying ferritin release in acidic solutions, we investigated the stability of ferritin inside microgels against degradation by chymotrypsin.

FINDINGS

About 80% of the applied ferritin containers were integrated into microgels and around 85% and 50% of them could be released in buffer pH 2.5 and 4.0, respectively. Total degradation of the microgels was not achieved due to the self-crosslinking of N-isopropylacrylamide (NIPAM). Finally, we prove that microgels could protect ferritin against degradation by chymotrypsin at 37 °C.

Higher-Order Structures Based on Molecular Interactions for the Formation of Natural and Artificial Biomaterials

The assembly of molecular building blocks into highly ordered structures is crucial, both in nature and for the development of novel functional materials. In nature, noncovalent interactions, such as hydrogen bonds or hydrophobic interactions, enable the reversible assembly of biopolymers, such as DNA or proteins. Inspired by these design principles, scientists have created biohybrid materials that employ natural building blocks and their assembly properties. Thus, structures and materials are attainable that cannot be made through other synthetic procedures. Herein, we review current concepts and highlight recent advances.