Protein-DNA/RNA Binding Test

One-tenth of human genes produce proteins called transcription factors (TFs) that bind to our genome and read the local DNA sequence. They work together to regulate the degree to which each gene is expressed. The affinity with which DNA is bound by a particular TF can vary more than a thousand-fold with different DNA sequences.

These interactions affect fundamental processes such as replication, transcription, and repair in the case of DNA, as well as transport, translation, splicing, and silencing in the case of RNA. Analytical or preparative experimental approaches, both in vivo and in vitro, have been developed to isolate and identify DNA/RNA binding proteins by exploiting the advantage of the affinity shown by these proteins toward a specific oligonucleotide sequence. 

The SPR protocol for measuring biomolecular interactions starts by arresting one of the binding partners to the surface of a chip, followed by injecting the other binding partner. A real-time interaction curve is then recorded, measuring the increase in mass due to the binding as a function of time. Flowing buffer over the chip leads to the dissociation of both partners and the signal decreases. This way, the kinetics of the interaction can be studied and the association and dissociation rate constants can be accessed.