IDENTIFICATION OF PROTEIN-DNA INTERACTIONS
Identifying and investigating protein–DNA interactions, which play significant roles in many biological processes, is essential for basic and clinical research. Current techniques for identification of protein–DNA interactions are laborious, time-consuming, and suffer from nonspecific binding and limited sensitivity. To overcome these challenges and assess protein–DNA interactions, we use a magnetic modulation biosensing (MMB) system. In MMB, one of the interacting elements (protein or DNA) is immobilized to magnetic beads, and the other is coupled to a fluorescent molecule. Thus, the link between the magnetic bead and the fluorescent molecule is established only when binding occurs, enabling detection of the protein–DNA interaction. Using magnetic forces, the beads are concentrated and manipulated in a periodic motion in and out of a laser beam, producing a detectable oscillating signal. Using MMB, we detected protein–DNA interactions between short GC-rich DNA sequences and both a purified specificity protein 1 (Sp1) and an overexpressed Buttonhead (BTD) protein in a cell lysate. The specificity of the interactions was assessed using mutated DNA sequences and competition experiments. The assays were experimentally compared with commonly used electrophoretic mobility shift assay, which takes approximately 4–72 h. In comparison, the MMB-based assay’s turnaround time is ∼2 h, and it provides unambiguous results and quantitative measures of performance. The MMB system uses simple and cheap components, making it an attractive alternative method over current costly and time-consuming techniques for analyzing protein–DNA interactions. The work is done in collaboration with Prof. Tamar Juven-Gershon and Dr. Diana Ideses from the Faculty of Life Sciences in Bar Ilan University.
Our paper on the new method for rapid and sensitive identification of protein-DNA fragments interactions using the magnetic modulation biosensing (MMB) system was published at "ACS Sensors". The paper, entitled: "Rapid Biosensing Method for Detecting Protein–DNA Interactions", can be found in the Publications section, and at DOI:10.1021/acssensors.1c01579.