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. Therefore,
we anticipate that the MMB-based technique will significantly advance
the detection of protein–DNA interactions in biomedical research.