Question

“ Sequence-specific DNA-binding proteins play a key role in many fundamental biological processes, such as transcription, DNA replication and recombination. Very often, these DNA-binding proteins introduce structural changes to the target DNAbinding sites including DNA bending, twisting or untwisting and wrapping, which in many cases induce a linking number change (∆Lk ) to the DNAbinding site. Due to the lack of a feasible approach, ∆Lk induced by sequence-specific DNA-binding proteins has not been fully explored. In this paper we successfully constructed a series of DNA plasmids that carry many tandem copies of a DNA binding site for one sequence-specific DNA-binding protein, such as λO, LacI, GalR, CRP and AraC. In this case, the protein-induced ∆Lk was greatly amplified and can be measured experimentally. Indeed, not only were we able to simultaneously determine the protein-induced ∆Lk and the DNA-binding constant for λO and GalR, but also we demonstrated that the protein-induced ∆Lk is an intrinsic property for these sequence-specific DNA-binding proteins. Our results also showed that protein-mediated DNA looping by AraC and LacI can induce a ∆Lk to the plasmid DNA templates. Furthermore, we demonstrated that the protein-induced ∆Lk does not correlate with the protein-induced DNA bending by the DNA-binding proteins.” NAR 38:3643.

1. What is the definition of ∆Lk?

2. If DNA is negatively supercoiled, what is the value of ∆Lk?

3. In general, how do DNA-binding proteins, such as λO, LacI, GalR, CRP and AraC, effect ∆Lk and DNA supercoiling?

4. How might DNA supercoiling, and the DNA binding proteins (λO, LacI, GalR, CRP and AraC), effect transcription?