Transcription factors (TFs) are proteins that can boost or suppress the expression of genes by binding to DNA. How they do this remains a mystery: what happens to the DNA when TFs bind to it? It has recently been discovered that TFs can cluster on the DNA, producing droplets that behave as a fluid. The biological purpose of these droplets remains a mystery, and much is still unknown about how these droplets form.
Human transcription factor droplets on DNA visualized by optical tweezers. Taken from.
To find answers, we develop a single-molecule fluorescence technique to visualize how TFs bind to individual strands of DNA. This method has the benefit of being cheaper, simpler and faster (multiple strands are measured in parallel) than other commonly used methods such as optical tweezers.
Microfluidic force spectroscopy allows many DNA strands to be observed simultaneously.
The steps needed to develop our method can be subdivided into three main branches:
•Surface functionalization: controlling the attachment of DNA to a surface.
•Single-molecule imaging: visualizing DNA and interacting proteins for extended duration.
•DNA/protein engineering: sequence manipulation or the addition of functional groups (e.g. fluorescent markers, binding sites).
Each branch can serve as a BSc/MSc thesis topic and projects are tailored to the student’s interest. Possible projects to work on include:
•Improving the attachment of DNA to the surface using a method called DNA curtains. This is a technique where DNA is stretched across a surface like a guitar string[1, 3].
•Attach quantum dots to the ends of DNA to allow for prolonged measurements.
•Produce fluorescent transcription factors from cell cultures (partially at BIC).
•Introduce target sequences into the DNA.
1.Larson et al. (2017) Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236–240.
2.Morin et al. (2022) Sequence-dependent surface condensation of a pioneer transcription factor on DNA. Nature Physics 18, 271–276.
3.Collins, B., Ye, L., Duzdevich, D., Greene, C. (2014) DNA curtains: Novel tools for imaging protein–nucleic acid interactions at the single-molecule level. Methods in Cell Biology 123, 217-234.