My paper with the title ‘An Ultrastable and Dense Single‐Molecule Click Platform for Sensing Protein–Deoxyribonucleic Acid Interactions’ is published in Small Methods! Find it here: doi.org/10.1002/smtd.202001180.
In the paper we describe stable click TPM (scTPM) a silanization and click chemistry based assay to create a flexible, modular interface to couple molecules to the surface. The entire system remains stable for up to half a year in our observations, reaches very dense particle tethering densities and is stable at elevated temperatures and buffers.
We used the scTPM system to study the interaction between the H-NS, a protein found in certain bacteria, and DNA. H-NS will interact with DNA and affect the expression of the DNA it binds to. What we observed was an interesting sequence dependent effect. Exchanging just 6 nucleotides was enough to change the interaction between the DNA and H-NS showing that there is a strong sequence dependency in the interaction. We also observed the temperature dependence of the H-NS interaction and found that the effect of H-NS diminishes with increasing temperature. H-NS is known to have a build-in temperature switch of which we likely see the effect.
If you want to know more details, go read the paper! It’s Open Access so anyone can read it (as it should be).
Also many thanks to Jovana who as an undergraduate student worked on the measurements, prof. Josh Milstein with whom we planned and discussed the project, prof. Paul Piunno for his help with optimizing the silanization, prof. William Navarre for the H-NS proteins and Marie Elliot and Xiafei Zhang for providing the natural DNA templates from Streptomyces venezuelae. I received funding from this project from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 796345