We are a molecular biophysics lab with a general emphasis in studying the role of mechanical forces in biology, and in particular in the function of the nucleic-acids processing machinery, using methods rooted in the physical sciences. We develop experimental setups capable of applying mechanical forces on biological molecules and complexes, and directly measure molecular movements as small as Angstroms. We use these instruments to study the structure of chromatin, and the machine-like function of polymerases, helicases and translocases.
(1) The structure and dynamics of chromatin, and its effect on transcription
S. Rudnizky, O. Malik, A. Bavly, L. Pnueli, P. Melamed and A. Kaplan, “Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies“, Protein Science DOI: 10.1002/pro.3159 (2017). PDF
S. Rudnizky, A. Bavly, O. Malik, L. Pnueli, P. Melamed and A. Kaplan, “H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes”, Nature Communications 7, 12958 (2016). PDF
(2) The retroviral reverse transcriptase, and its its interplay with the template’s secondary structure
O. Malik*, H. Khamis*, S. Rudnizky, A. Marx and A. Kaplan, “Pausing kinetics dominates strand-displacement polymerization by Reverse Transcriptase”, Nucleic Acids Research, doi: 10.1093/nar/gkx720, (2017). PDF
(*) Equal contribution.
(3) DNA unwinding by the bacterial RecBCD helicase
R. Zananiri, V. Gaydar, D. Yahalom, O. Malik, S. Rudnizky, A. Kaplan*, and A. Henn*, “Auxiliary ATP binding sites power rapid unwinding by RecBCD”, under review (2017)
* Corresponding authors