John van Noort
Professor Biofysica
- Name
- Prof.dr.ir. S.J.T. van Noort
- Telephone
- +31 71 527 5980
- noort@physics.leidenuniv.nl
- ORCID iD
- 0000-0002-9094-5598
More information about John van Noort
PhD Candidates
News
-
New SPARXS technique reveals DNA behaviour at unprecedented speed -
Can we live longer? Leiden physicist makes discovery in protective layer in genes -
LION in lockdown -
Two-photon microscope captures plant cells -
Bending DNA costs less energy than assumed -
Our genome captured in numbers -
NWO ECHO grant for research on fickle RNA production -
Biophysicists unravel exact folding of a single gene -
John van Noort appointed Professor in Biophysics -
New funding for advanced microscopy using gold nanorods
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Folded DNA unravelled -
DNA folded in compliant helix
In the media
Former PhD candidates
Professor Biofysica
- Science
- Leiden Instituut Onderzoek Natuurkunde
- LION - Biological & Soft Matter
- Agam G., Gebhardt C., Popara M., Mächtel R., Folz J., Ambrose B., Chamachi N., Yoon Chung S., Craggs T.D., Boer M. de, Grohmann D., Ha T., Harmann A., Hendrix J., Hirschfeld V., Hübner C.G., Hugel T., Kammerer D., Kang H.-S., Kapanidis A.N., Krainer G., Kramm K., Lemke E.A., Lerner E., Margeat E., Martens K., Michaelis J., Mitra J., Moya Munoz G.G., Quast R.B., Robb N.C., Sattler M., Schlierf M., Schneider J., Schröder T., Sefer A., Siong Tan P., Thurn J., Tinnefeld P., Noort S.J.T. van, Weiss S., Wendler N., Zijlstra N., Barth A., Seidel C.A.M., Lamb D.C. & Cordes T. (2023), Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins, Nature Methods 20: 523-535.
- Wong S.Y., Soman A., Korolev N., Surya W., Chen Q., Shum W., Noort S.J.T. van & Nordenskiold L. (2023), The shelterin component TRF2 mediates columnar stacking of human telomeric chromatin, The EMBO Journal 43(1): 87-111.
- Radoslaw J., Jong B. de, Hage P. van, Rhiemus M., Steenis F. van, Noort S.J.T. van, Schmidt T. & Schaaf M.J.M (2022), Analysis of the H-Ras mobility pattern in vivo shows cellular heterogeneity inside epidermal tissue, Disease Models & Mechanisms 15(2): dmm049099.
- Vlieg R.C. & Noort S.J.T. van (2022), Multiplexed two-photon excitation spectroscopy of single gold nanorods, The Journal of Chemical Physics 156: 094201.
- Egorova E.A., Arias Alpizar G., Vlieg R.C., Gooris G.S., Bouwstra J.A., Noort S.J.T. van, Kros A. & Boyle A.L. (2022), Coating gold nanorods with self-assembling peptide amphiphiles promotes stability and facilitates in vivo two-photon imaging, Journal of Materials Chemistry B 10: 1612-1622.
- Soman A., Wong S.Y., Korolev N., Surya W., lattmann S., Vogirala V.K., Chen Q., Berezhnoy N.V., Noort S.J.T. van, Rhodes D. & Nordenskiöld L. (2022), Columnar structure of human telomeric chromatin, Nature 609(7929): 1048-1055.
- Severins I.W.H., Joo C. & Noort S.J.T. van (2022), Exploring molecular biology in sequence space: the road to next-generation single-molecule biophysics, Molecular Cell 82(10): 1788-1805.
- Korolev N., Zinchenko A., Soman A., Chen Q., Wong S.Y., Berezhnov N.V., Basak R., Maarel J.R.C. van der, Noort S.J.T. van & Nordenskiöld L. (2022), Reconstituted TAD-size chromatin fibers feature heterogeneous nucleosome clusters, Scientific Reports 12(1): 15558.
- Henneman B., Brouwer T.B., Erkelens A.M., Kuijntjes G.A.J.T., Emmerik C. van, Valk R.A. van der, Timmer M., Kirolos N., Ingen H. van, Noort S.J.T. van & Dame R.T. (2021), Mechanical and structural properties of archaeal hypernucleosomes, Nucleic Acids Research 49(8): 4338-4394.
- Brinkmann B.W., Beijk W.F., Vlieg R.C., Noort S.J.T. van, Mejia J., Colaux J.L., Lucas S., Lamers G.E.M., Peijnenburg W.J.G.M. & Vijver M.G. (2021), Adsorption of titanium dioxide nanoparticles onto zebrafish eggs affects colonizing microbiota, Aquatic Toxicology 232: 105744.
- Brouwer T.B., Pham L., Kaczmarczyk A.P., Voogd W. de, Botto M., Vizjak P., Mueller-Planitz F. & Noort S.J.T. van (2021), A critical role for linker DNA in higher-order folding of chromatin fibers, Nucleic Acids Research 49(5): 2537-2551.
- Erkelens A.M., Henneman B., Brouwer T.B., Kuijntjes G.A.J.T., Emmerik C.L. van, Valk R.A. van der, Timmer M., Kirolos N.C.S., Ingen H. van & Noort S.J.T. van (2021), (A)Specific DNA binding of archaeal histones, the formation and positioning of hypernucleosomes, Biophysical Journal 120(3): 317a.
- Arias-Alpizar G., Kong L., Vlieg R.C., Rabe A., Papadopoulou P., Meijer M.S., Bonnet S., Vogel S., Noort J. van, Kros A. & Campbell F. (2020), Light-triggered switching of liposome surface charge directs delivery of membrane impermeable payloads in vivo, Nature Communications 11: 3638.
- Brouwer T.B., Hermans N. & Noort S.J.T. van (2020), Multiplexed nanometric 3D tracking of microbeads using an FFT-phasor algorithm, Biophysical Journal 118(9): 2245-2257.
- Kaczmarczyk A., Meng H., Ordu O., Noort S.J.T. van & Dekker N.H. (2020), Chromatin fibers stabilize nucleosomes under torsional stress, Nature Communications 11(1): 126.
- Pomeren M. van, Peijnenburg W.J.G.M., Vlieg R.C., Noort S.J.T. van & Vijver M.G. (2019), The biodistribution and immuno-responses of differently shaped non-modified gold particles in zebrafish embryos, Nanotoxicology 13(4): 558-571.
- Jong B.E. de & Noort S.J.T. van (2019), Overcoming chromatin barriers, eLife 8: e50761.
- Brouwer T.B., Hermans N. & Noort S.J.T. van (2019), Multiplexed nanometric 3D tracking of microbeads using a FFT-phasor algorithm, Biophysical Journal 118(9): 2245-2257.
- Nordenskiold L., Soman A., Korolev N., Wahyu S., Wong S.Y., Liew C.W., Lattmann S., Teo H.L., Noort S.J.T. van & Rhodes D. (2019), Structure and Dynamics of the Telomeric Nucleosome and Chromatin, Biophysical Journal 116(3): 71A-71A.
- Jong B.E. de, Brouwer T.B., Kaczmarczyk A., Visscher B. & Noort S.J.T. van (2018), Rigid Basepair Monte Carlo Simulations of One-Start and Two-Start Chromatin Fiber Unfolding by Force, Biophysical Journal 115(10): 1848-1859.
- Kaczmarczyk A., Brouwer T.B., Pham C. & Noort S.J.T. van (2018), Probing Chromatin Structure with Magnetic Tweezers. In: Yubchenko Y.L. (Ed.), Nanoscale Imaging. Methods in Molecular Biology no. 1814. New York, NY, U.S.A.: Humana Press. 297-323.
- Brouwer T.B., Kaczmarczyk A.P., Pham L. & Noort S.J.T. van (2018), Unraveling DNA Organization with Single-Molecule Force Spectroscopy Using Magnetic Tweezers. In: Dame R.T. (Ed.), Bacterial Chromatin. Methods in Molecular Biology no. 1837. New York: Humana Press. 317-349.
- Carozza S., Culkin J. & Noort S.J.T. van (2017), Accuracy of the detection of binding events using 3d single particle tracking, BMC Biophysics 10: 3.
- Cortijo S., Charoensawan V., Brestovitsky A., Buning R., Ravarani C., Rhodes D., Noort S.J.T. van, Jaeger K.E. & Wigge P.A. (2017), Transcriptional regulation of the ambient temperature response by h2a.z nucleosomes and hsf1 transcription factors in arabidopsis, Molecular Plant 10(10): 1258-1273.
- Hermans N., Huisman J.J., Brouwer T.B., Schachner C., Heusden G.P.H., Griesenbeck J. & Noort S.J.T. van (2017), Toehold-enchanced lna probes for selective pull down and single-molecule analysis of native chromatin, Scientific Reports 7: 16721.
- Kaczmarczyk A.P., Allahverdi A., Brouwer T.B., Nordenskiold L., Dekker N.H. & Noort S.J.T. van (2017), Single-molecule force spectroscopy on histone h4 tail cross-linked chromatin reveals fiber folding, Journal of Biological Chemistry 292: 17506-17513.
- Eslami Mossallam B., Schiessel H. & Noort S.J.T. van (2016), Nucleosome dynamics: Sequence matters, Advances in Colloid and Interface Science 232: 101-113.
- Eslami-Mossallam B., Schram R.D., Tompitak M., Noort S.J.T. van & Schiessel H. (2016), Multiplexing genetic and nucleosome positioning codes: A computational approach, 11(6): 0156905.
- Noort J. van (Ed.) (2015), Editor Nature Scientific Reports. Scientific Reports.
- Noort J. van (Ed.) (2015), Editor BMC Biophysics. BMC Biophysics.
- Buning R., Kropff W., Martens K. & Noort J. van (2015), spFRET reveals changes in nucleosome breathing by neighboring nucleosomes, Journal of Physics: Condensed Matter 27 (6)(064103): .
- Meng H., Andresen K. & Noort J. van (2015), Quantitative analysis of single-molecule force spectroscopy on folded chromatin fibers, Nucleic Acids Research 43: 3578-3590.
- North J.A., Simon M., Ferdinand M.B., Shoffner M.A., Picking J.W., Howard C.J., Mooney A.M., Noort S.J.T. van, Poirier M.G. & Ottesen J.J. (2014), Histone H3 phosphorylation near the nucleosome dyad alters chromatin structure, Nucleic Acids Research 42(8): 4922-4933.
- Noort S.J.T. van (Ed.) (2014), BMC Biophysics. BMC Biophysics.
- Noort S.J.T. van (Ed.) (2014), Nature Scientific Reports. Scientific Reports.
- Meng H., Bosman J., Heijden T. van der & Noort S.J.T. van (2014), Coexistence of Twisted, Plectonemic, and Melted DNA in Small Topological Domains, Biophysical Journal 106(5): 1174-1181.
- Buning R., Kropff W., Martens C.L.G. & Noort S.J.T. van (2014), spFRET reveals changes in nucleosome breathing by neighboring nucleosomes, Journal of Physics: Condensed Matter : .
- Noort S.J.T. van (Ed.) (2013), . BMC Biophysics.
- Noort S.J.T. van (Ed.) (2013), . Scientific Reports.
- Noort S.J.T. van (Ed.) (2013), . TheScientificWorldJournal.
- Broek B. van den, Ashcroft B.A., Oosterkamp T.H. & Noort S.J.T. van (2013), Parallel nanometric 3D tracking of intracellular gold nanorods using multifocal two-photon microscopy, Nano Letters 13(3): 980-986.
- Driessen R.P.C., Meng H., Suresh G., Shahapure R., Lanzani G., Priyakumar U.D., White M.F., Schiessel H., Noort S.J.T. van & Dame R.T. (2013), Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends, Nucleic Acids Research 41(1): 196-205.
- Heijden T. van der, Vugt J.F.A. van, Logie C. & Noort S.J.T. van (2012), Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy, Proceedings of the National Academy of Sciences 109(38): E2514-E2522.
- Peng K., Tomatsu I., Broek B. van den, Cui C., Korobko A.V., Noort J. van, Meijer A.H., Spaink H.P. & Kros A. (2011), Dextran based photodegradable hydrogels formed via a Michael addition, Soft Matter 7: 4881-4887.
- Buning R. & Noort S.J.T. van (2010), Single-pair FRET experiments on nucleosome conformational dynamics, Biochimie 92(12): 1-13.
- Koopmans W.J.A., Buning R., Schmidt T. & Noort S.J.T. van (2009), spFRET using alternating excitation and FCS reveals progressive DNA unvwrapping in nucleosomes, Biophysical Journal 97: 195-204.
- Vugt J.F.A. van, Jager M. de, Murawska M., Brehm A., Noort S.J.T. van & Logie C. (2009), Multiple aspects of atp-dependent nucleosome translocation by rsc and mi-2 are directed by the underlying dna sequence, PLoS ONE 4(7): e6345.
- Kruithof M.C., Chien F.-T., Routh A., Logie C., Rhodes D. & Noort S.J.T. van (2009), Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber, Nature Structural & Molecular Biology 16: 534-540.
- Schaaf M.J.M., Koopmans W., Meckel T.M., Noort S.J.T. van, Snaar B.E., Schmidt T. & Spaink H.P. (2009), Single-molecule microscopy reveals membrane microdomain organization of cells in a living vertebrate, Biophysical Journal 97(4): 1206-1214.
- Neumann H., Hancock S.M., Buning R., Routh A., Chapman L., Somers J., Owen-Hughes T., Noort S.J.T. van, Rhodes D. & Chin J.W. (2009), A method for genetically installing site-specific acetylation in recombinant histones defines the effect of h3 k56 acetylation, Molecular Cell 36: 153-163.
- Chien F.-T. & Noort S.J.T. van (2009), 10 years of tension on chromatin: results fromsingle-molecule spectroscopy, Curr. Pharm. Biotechnology 10: 474-485.
- Engeholm M., Jager M. de, Flaus A., Brenk R., Noort S.J.T. van & Owen-Hughes T. (2009), Nucleosomes can invade DNA territories occupied by their neighbors, Natural Structural & Molecular Biology 16: 151-158.
- Noort S.J.T. van & Jager M. de (2009), Botsende eiwitkralen leggen DNA bloot, Universitaire Nieuwsbrief 2: .
- Kruithof M.C. & Noort S.J.T. van (2009), Hidden Markov analysis of nucleosome unwrapping under force, Biophysical Journal 96: 3708-3715.
- Kruithof M.C., Chien F.-T., Jager M. de & Noort S.J.T. van (2008), Sub-piconeutron dynamic force spectroscopy using magnetic tweezers, Biophysical Journal 94: 2343-2348.
- Koopmans W., Schmidt T. & Noort S.J.T. van (2008), Nucleosome immobilization strategies for single-pair FRET microscopy, ChemPhysChem 9: 2002-2009.
- Koopmans W., Brehm A., Logie C., Schmidt T. & Noort S.J.T. van (2007), Single-pair FRET microscopy reveals mononucleosome dynamics, Journal of Fluoresc. : .
- Jager M. de & Noort S.J.T. van (2007), Atomic force microscopy. In: , Encyclopedia of Life Sciences: John Wiley & Sons, Ltd.. 1-10.
- Noort J. van, Verbrugge S., Goosen N., Dekker C. & Dame R.T. (2004), Dual architectural roles of HU: Formation of flexible hinges and rigid filaments, Proceedings of the National Academy of Sciences 101(18): 6969-6974.
- shareholder/consultant