Publications

Relevant publications of the CIGR participants.

Dame Lab

Henneman, B., Brouwer, T.B., Erkelens, A.M., Kuijntjes, G.J., van Emmerik, C., van der Valk, R.A., Timmer, M., Kirolos, N.C.S., van Ingen, H., van Noort, J. and Dame, R.T. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Res. 2021 doi: 10.1093/nar/gkaa1196.
Qin, L., Bdira, F.B., Sterckx, Y.G.J., Volkov, A.N., Vreede, J., Giachin, G., van Schaik, P., Ubbink, M. and Dame, R.T. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Res. 2020 48(4):2156-2172. doi: 10.1093/nar/gkz1226.
Henneman, B., van Emmerik, C.L., van Ingen, H. and Dame, R.T. Structure and function of archaeal histones. PLOS Gen. 2018 14(9):e1007582. doi: 10.1371/journal.pgen.1007582.
van der Valk, R.A, Vreede, J., Moolenaar, G.F., Hofmann, A., Goosen, N. and Dame, R.T. Environmentally driven conformational changes modulate the function of H-NS. eLife. 2017 6: 27369.

Heidari M., Schiessel H. and Mashaghi A. Circuit topology analysis of polymer folding reactions. ACS Central Science 2020, 2(7) P609-622. doi: 10.1021/acscentsci.0c00308.
Scalvini B, Sheikhhassani V., .Woodard J, Aupič J., Dame R.T., Jerala R. and Mashaghi A. Topology of folded molecular chains: from single biomolecules to engineered origami. Trends in Chemistry 2020, 2(7) P609-622. doi: 10.1016/j.trechm.2020.04.009.
Heidari M., Satarifard V. and Mashaghi A. Mapping a single-molecule folding process onto a topological space. Physical Chemistry Chemical Physics 2019, 21(36), 20338-20345. doi: 10.1039/C9CP03175H.
Satarifard V., Heidari M., Mashaghi S., Tans S.J., Ejtehadi M.R. and Mashaghi A. Topology of polymer chains under nanoscale confinement. Nanoscale 2017, 9, 12170 – 12177. doi: 10.1039/C7NR04220E.
Mashaghi A., Bezrukavnikov S., Minde D., Kityk R., Zachmann-Brand B., Mayer M., Kramer G., Bukau B. and Tans S.J. Functional plasticity in Hsp70 enabled by diverse modes of client binding. Nature 2016, 539(7629):448-451. doi: 10.1038/nature20137.

Keizer V.I.P., Coppola S., Houtsmuller A.B., Geverts B., van Royen M.E., Schmidt T. and Schaaf M.J.M. Repetitive switching between DNA-binding modes enables target finding by the glucocorticoid receptor. J Cell Sci. 2019 Feb 25;132(5):jcs217455. doi: 10.1242/jcs.217455.
Carattino A., Keizer V.I.P., Schaaf M.J.M. and Orrit M. Background Suppression in Imaging Gold Nanorods through Detection of Anti-Stokes Emission. Biophys J. 2016 Dec 6;111(11):2492-2499. doi: 10.1016/j.bpj.2016.10.035.
Harkes R., Keizer V.I., Schaaf M.J. and Schmidt T. Depth-of-Focus Correction in Single-Molecule Data Allows Analysis of 3D Diffusion of the Glucocorticoid Receptor in the Nucleus. PLoS One. 2015 Nov 10;10(11):e0141080. doi: 10.1371/journal.pone.0141080. eCollection 2015.
Groeneweg F.L., van Royen M.E., Fenz S., Keizer V.I., Geverts B., Prins J., de Kloet E.R., Houtsmuller A.B., Schmidt T.S. and Schaaf M.J. Quantitation of glucocorticoid receptor DNA-binding dynamics by single-molecule microscopy and FRAP. PLoS One. 2014 Mar 14;9(3):e90532. doi: 10.1371/journal.pone.0090532. eCollection 2014.
Van Royen M.E., van Cappellen W.A., Geverts B., Schmidt T., Houtsmuller A.B. and Schaaf M.J. Androgen receptor complexes probe DNA for recognition sequences by short random interactions. J Cell Sci. 2014 Apr 1;127(Pt 7):1406-16. doi: 10.1242/jcs.135228. Epub 2014 Jan 30.

Henneman, B., Brouwer, T.B., Erkelens, A.M., Kuijntjes, G.-J., van Emmerik, C., van der Valk, R.A., … Dame, R. T. (2020). Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Research. doi: 10.1093/nar/gkaa1196.
Kaczmarczyk, A., Meng, H., Ordu, O., Noort, J. van and Dekker, N.H. (2020). Chromatin fibers stabilize nucleosomes under torsional stress. Nature Communications, 11(1), 126. doi: 10.1038/s41467-019-13891-y.
De Jong, B.E., Van Noort, J. (2019). Overcoming chromatin barriers. ELife, 8. doi: 10.7554/eLife.50761.
Kaczmarczyk, A., Allahverdi, A., Brouwer, T.B., Nordenskiöld, L., Dekker, N.H. and Van Noort, J. (2017). Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding. Journal of Biological Chemistry, 292(42), 17506–17513. doi: 10.1074/jbc.M117.791830.
Hermans, N., Huisman, J.J., Brouwer, T.B., Schächner, C., van Heusden, G.P.H., Griesenbeck, J. and van Noort, J. (2017). Toehold-enhanced LNA probes for selective pull down and single-molecule analysis of native chromatin. Scientific Reports, 7(1), 16721. doi: 10.1038/s41598-017-16864-7.