To maintain experimental lab course work during the COVID-19 lockdowns, we chose a hybrid approach for our electronic instrumentation course and developed thereto the Advanced Learning Platform for Analog Circuits and Automation (ALPACA). To further meet our goals and standards, the ALPACA platform has been updated, using a Raspberry Pi Pico with Python instead of an Arduino. Our educational materials and approach are illustrated here through the typical example of a relaxation oscillator assignment. As student's feedback was overall positive and grades remained comparable, we continue the use of the ALPACA in the non-COVID era.

This manuscript presents the first practical guide to build a Raspberry Pi Pico based potentiostat for electrical and electrochemical instrumentation education. The circuit enables us to perform different types of voltammetry such as cyclic and square wave voltammetry. Voltammograms of paracetamol tablets in a neutral buffer solution were successfully recorded and compared to lab equipment. Thereafter, the effect of different scan rates and different concentrations was studied as a proof of concept. Furthermore, the experiments were expanded with measurements of other pharmaceutical tablets such as vitamin C. Over 80 nanobiology bachelor students successfully built their own potentiostat in an electronic instrumentation course. They validated their systems successfully with electrochemical experiments using paracetamol as a conventional pharmaceutical that can be performed in a classroom. The students acquired a valuable understanding of the electronic building blocks and system architecture within electrochemical instrumentation, equipping them with the requisite knowledge to effectively optimize instrumentation parameters in their future research work.

Super-resolution imaging allows for the visualization of cellular structures on a nanoscale level. DNA-PAINT (DNA point accumulation in nanoscale topology) is a super-resolution method that depends on the binding and unbinding of DNA imager strands. The current DNA-PAINT technique suffers from slow acquisition due to the low binding rate of the imager strands. Here we report on a method where imager strands are loaded into a protein, Argonaute (Ago), which allows for faster binding. Ago preorders the DNA imager strand into a helical conformation, allowing for 10 times faster target binding. Using a 2D DNA origami structure, we demonstrate that Ago-assisted DNA-PAINT (Ago-PAINT) can speed up the current DNA-PAINT technique by an order of magnitude, while maintaining the high spatial resolution. We envision this tool to be useful for super-resolution imaging and other techniques that rely on nucleic acid interactions.

Finding the target site and associating in a specific orientation are essential tasks for DNA-binding proteins. In order to make the target search process as efficient as possible, proteins should not only rapidly diffuse to the target site but also dynamically explore multiple local configurations before diffusing away. Protein flipping is an example of this second process that has been observed previously, but the underlying mechanism of flipping remains unclear. Here, we probed the mechanism of protein flipping at the single molecule level, using HIV-1 reverse transcriptase (RT) as a model system. In order to test the effects of long-range attractive forces on flipping efficiency, we varied the salt concentration and macromolecular crowding conditions. As expected, increased salt concentrations weaken the binding of RT to DNA while increased crowding strengthens the binding. Moreover, when we analyzed the flipping kinetics, i.e. the rate and probability of flipping, at each condition we found that flipping was more efficient when RT bound more strongly. Our data are consistent with a view that DNA bound proteins undergo multiple rapid re-binding events, or short hops, that allow the protein to explore other configurations without completely dissociating from the DNA.

In all organisms, DNA molecules are tightly compacted into a dynamic 3D nucleoprotein complex. In bacteria, this compaction is governed by the family of nucleoid-associated proteins (NAPs). Under conditions of stress and starvation, an NAP called Dps (DNA binding protein from starved cells) becomes highly up-regulated and can massively reorganize the bacterial chromosome. Although static structures of Dps-DNA complexes have been documented, little is known about the dynamics of their assembly. Here, we use fluorescence microscopy and magnetic-tweezers measurements to resolve the process of DNA compaction by Dps. Real-time in vitro studies demonstrated a highly cooperative process of Dps binding characterized by an abrupt collapse of the DNA extension, even under applied tension. Surprisingly, we also discovered a reproducible hysteresis in the process of compaction and decompaction of the Dps-DNA complex. This hysteresis is extremely stable over hour-long timescales despite the rapid binding and dissociation rates of Dps. A modified Ising model is successfully applied to fit these kinetic features. We find that long-lived hysteresis arises naturally as a consequence of protein cooperativity in large complexes and provides a useful mechanism for cells to adopt unique epigenetic states.