Kaplan Lab Summer Project
The Kaplan lab uses advanced biophysical tools, such as high-resolution optical tweezers and single-molecule fluorescence, to study protein-DNA interactions. In particular, we are interested in the structure and dynamics of chromatin1–3 and the machine-like function of polymerases4,5 and helicases6,7.
During the summer we invite you to participate in the following project:
How do nucleosomes affect a transcription factor’s binding kinetics?
We will characterize the rates of binding and dissociation for a model transcription factor in the vicinity of a nucleosome, using a recently developed single-molecule method8.
We plan to explore how post-translational modifications of the histone proteins, known to regulate gene expression, modulate these kinetic rates.
1. Rudnizky, S. et al. Extended and dynamic linker histone-DNA Interactions control chromatosome compaction. Mol. Cell 81, 2020.10.10.334474 (2021).
2. Rudnizky, S. et al. H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes. Nat. Commun. 7, 12958 (2016).
3. Rudnizky, S., Khamis, H., Malik, O., Melamed, P. & Kaplan, A. The base pair-scale diffusion of nucleosomes modulates binding of transcription factors. Proc. Natl. Acad. Sci. 116, 12161–12166 (2019).
4. Malik, O., Khamis, H., Rudnizky, S. & Kaplan, A. The mechano-chemistry of a monomeric reverse transcriptase. Nucleic Acids Res. 45, 12954–12962 (2017).
5. Malik, O., Khamis, H., Rudnizky, S., Marx, A. & Kaplan, A. Pausing kinetics dominates strand-displacement polymerization by reverse transcriptase. Nucleic Acids Res. 45, 10190–10205 (2017).
6. Zananiri, R. et al. Synergy between RecBCD subunits is essential for efficient DNA unwinding. Elife 8, e40836 (2019).
7. Zananiri, R. et al. Auxiliary ATP binding sites support DNA unwinding by RecBCD. Nat. Commun. 2022 131 13, 1–14 (2022).
8. Khamis, H., Rudnizky, S., Melamed, P. & Kaplan, A. Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation. Nucleic Acids Res. 49, 10975–10987 (2021).