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*, H. Khamis*, O. Malik, P. Melamed, and A. Kaplan, “The base pair-scale diffusion of nucleosomes modulates binding of transcription factors”, PNAS doi: 10.1073/pnas.1815424116 (2019). PDF

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) Interactions between transcription factors and DNA

S. Rudnizky*, H. Khamis*, O. Malik, A. Squires, A. Meller, P. Melamed and A. Kaplan, “Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context”, Nucleic Acids Research, gkx1252 (2017). PDF


(3) 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 45, 10190 (2017). PDF

O. Malik*, H. Khamis*, S. Rudnizky and A. Kaplan, “The mechano-chemistry of a monomeric reverse transcriptase”, Nucleic Acids Research 45, 12954 (2017). PDF


(4) DNA unwinding by the bacterial RecBCD helicase

R. Zananiri, O. Malik, S. Rudnizky, V. Gaydar, R. Kreiserman, A. Henn and A. Kaplan, “Synergy between RecBCD subunits is essential for efficient DNA unwinding”, eLife 8, e40836 (2019). PDF

R. Zananiri*, V. Gaydar*, D. Yahalom, O. Malik, S. Rudnizky, A. Kaplan#, and A. Henn#, “Auxiliary ATP binding sites power rapid unwinding by RecBCD”, bioRxiv 210823 (2017). PDF