Remus Dame
Hoogleraar moleculaire en cellulaire biochemie
- Naam
- Prof.dr. R.T. Dame
- Telefoon
- +31 71 527 5605
- rtdame@chem.leidenuniv.nl
- ORCID iD
- 0000-0001-9863-1692
Meer informatie is beschikbaar op de Engelse profielpagina.
Nieuws
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Innovatief DNA-label opent deuren voor nieuw onderzoek -
‘Kijk buiten de eigen vakdisciplines’ -
Drie nieuwe hoogleraren Leids Instituut voor Chemisch Onderzoek -
Eiwitten en DNA-lussen: ENW-Groot-subsidie voor Remus Dame -
ENW-Groot-subsidies voor Leidse bètawetenschappers -
Hoe onze eencellige verwanten hun DNA opwinden -
Nieuw fundamenteel inzicht in de bestrijding van bacteriën -
Vici-beurzen voor 7 Leidse wetenschappers -
Miljoenen voor Leidse onderzoeksprogramma’s -
Genomen van bacteriën in kaart brengen om infectieziektes te bestrijden -
Hoe oerbacteriën hun DNA-structuur veranderen -
Leidse bèta-blogs over wetenschappelijke doorbraken
In de media
Onderwijs
Oud-promovendi
Hoogleraar moleculaire en cellulaire biochemie
- Wiskunde en Natuurwetenschappen
- Leiden Institute of Chemistry
- LIC/Chemical Biology
- Erkelens A.M., Qin L., Erp. B. van, Miguel-Arribas A., Avia D., Keek H.G.J., Markus D., Cajili M.K.M., Schwab S., Meijer W.J.J. & Dame R.T. (2022), The B. subtilis Rok protein is an atypical H-NS-like protein irresponsive to physico-chemical cues, Nucleic Acids Research 50(21): 12166-12185.
- Griend C. van de, Vijver J.J.. van de, Siegler M.A. & Dame R.T. Bonnet S. (2022), Ruthenium-Locked Helical Chirality: A Barrier of Inversion and Formation of an Asymmetric Macrocycle, Inorganic Chemistry 61(40): 16045–16054.
- Du C., Willemse J.J., Erkelens A.M., Carrion Bravo V.J., Dame R.T. & Wezel G.P. van (2022), System-wide analysis of the GATC-binding nucleoid-associated protein Gbn and its impact on Streptomyces development, mSystems 7(3): e00061-22.
- Forrest D., Warman E.A., Erkelens A.M., Dame R.T. & Grainger D.C. (2022), Xenogeneic silencing strategies in bacteria are dictated by RNA polymerase promiscuity, Nature Communications 13(1): 1149.
- Rashid F.M.Z., Detmar L. & Dame R.T. (2022), Chromosome conformation capture in bacteria and archaea. In: Peeters E. & Bervoets I. (red.) Prokaryotic gene regulation. Methods in Molecular Biology nr. 2516 New York: Humana Press. 1-28.
- Dame R.T. (2021), Special Issue: role of bacterial chromatin in environmental sensing, adaptation and evolution, Microorganisms 9(11): 2406.
- Rashid F.Z.M., Mahlandt E., Vaart M. van der, Boer D.E.C., Valera Alvarez M., Henneman B., Brocken D.J.W., Voskamp P., Blok A.J., Shimizu T.S., Meijer A.H., Luijsterburg M.S., Goedhart J., Cremazy F.G.E. & Dame R.T. (2022), HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein, Nucleic Acids Research 50(2): e10.
- Rashid F.Z.M., Mahlandt E., Vaart M van der, Boer D.E.C., Varela Alvarez M., Henneman B., Brocken D.J.W., Voskamp P., Blok A.J., Shimizu T.S., Meijer A.H., Luijsterburg M.S., Goedhart J., Crémazy F.G.E. & Dame R.T. (2021), HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein, Nucleic Acids Research 50(2): e10.
- Lin S.-N., Dame R.T. & Wuite G.J.L. (2021), Direct visualization of the effect of DNA structure and ionic conditions on HU–DNA interactions, Scientific Reports 11: 18492.
- Ben Bdira F., Erkelens A.M., Qin L., Volkov A.N., Lippa A.M., Bowring N., Boyle A.L., Ubbink M., Dove S.L. & Dame R.T. (2021), Novel anti-repression mechanism of H-NS proteins by a phage protein, Nucleic Acids Research 49(18): 10770-10784.
- Gilbert B.R., Thornburg Z.R., Lam V., Rashid F.-Z.M., Glass J.I., Villa E., Dame R.T. & Luthey-Schulten Z. (2021), Generating chromosome geometries in a minimal cell from cryo-electron tomograms and chromosome conformation capture maps, Frontiers in Molecular Biosciences 8: 644133.
- Dame R.T. (10 mei 2021), Molecular and cellular principles of genome folding and genome function (Oratie. Leiden Institute of Chemistry (LIC), Faculty of Science, Leiden University). Leiden: Universiteit Leiden.
- Jewett A.I., Stelter D., Lambert J., Saladi S.M., Roscioni O.M., Ricci M., Autin L., Maritan M., Bashusqeh S.M., Keyes T., Dame R.T., Shea J.-E., Jensen G.J. & Goodsell D.S. (2021), Moltemplate: a tool for coarse-grained modeling of complex biological matter and soft condensed matter physics, Journal of Molecular Biology 433(11): 166841.
- 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.
- Lin S., Wuite G.J.L. & Dame R.T. (2020), Effect of different crowding agents on the architectural properties of the bacterial nucleoid-associated protein HU, International Journal of Molecular Sciences 21(24): 9553.
- Qin L., Ben Bdira F., Sterckx Y.G.J., Volkov A.N., Vreede J., Giachin G., Schaik P., Ubbink M. & Dame R.T. (2020), Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins, Nucleic Acids Research 48(4): 2156-2172.
- Scalvini B., Sheikhhassani V., Woodard J., Aupič J., Dame R.T, Jerala R. & Mashaghi A. (2020), Topology of folded molecular chains: from single biomolecules to engineered origami, Trends in Chemistry 2(7): 609-622.
- Qin L., Erkelens A.M., Ben Bdira F. & Dame R.T. (2019), The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins, Open Biology 9(12): 190223.
- Dame R.T., Rashid F.Z.M. & Grainger D.C. (2019), Chromosome organization in bacteria: mechanistic insights into genome structure and function, Nature Reviews Genetics 21: 227-242.
- Ultee E., Ramijan K., Dame R.T., Briegel A. & Claessen D. (2019), Stress-induced adaptive morphogenesis in bacteria. In: Poole R.K (red.) Advances in Microbial Physiology. nr. 74: Academic Press. 97-141.
- Oliveira Paiva A.M., Friggen A.H., Qin L., Douwes R., Dame R.T. & Smits W.K. (2019), The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile, Journal of Molecular Biology 431(4): 653-672.
- Scolari V., Gherardi M., Dame R.T. & Consentino-Lagomarsino M. (2019), Chromosome structure and dynamics in bacteria: theory and experiments. In: Tiana G. & Giorgetti L. (red.) Modelling the 3D conformation of genomes. Series in Computational Physics: CRC Press. 207-230.
- Dilweg I.W. & Dame R.T. (2018), Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria?, Biochemical Society Transactions 46(5): 1381-1392.
- Crémazy F.G.E., Rashid F.Z.M., Haycocks J.R., Lamberte L.E., Grainger D.C. & Dame R.T. (2018), Determination of the 3D genome organization of bacteria using Hi-C. In: Dame R.T. (red.) Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology nr. 1837 New York, U.S.A.: Humana Press. 3-18.
- Corbeski I., Horn V., Valk R.A. van der, Paige U. le, Dame R.T. & Ingen H. van (2018), Microscale thermophoresis analysis of chromatin interactions. In: Dame R.T. (red.) Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology nr. 1837. 177-197.
- Henneman B., Heinsman J., Battjes J. & Dame R.T. (2018), Quantitation of DNA-binding affinity using Tethered Particle Motion. In: Dame R.T. (red.) Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology nr. 1837 New York, NY, U.S.A.: Humana Press. 257-275.
- Valk R.A. van der, Qin L., Moolenaar G.F. & Dame R.T. (2018), Quantitative determination of DNA bridging efficiency of chromatin proteins. In: Dame R.T. (red.) Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology nr. 1837 New York, NY, U.S.A.: Humana Press. 199-209.
- Lin S.N., Qin L., Wuite G.J.L. & Dame R.T. (2018), Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. In: Dame R.T. (red.) Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology nr. 1837 New York, NY, U.S.A.: Humana Press. 301-316.
- Brocken D.J.W., Tark-Dame M. & Dame R.T. (2018), The organization of bacterial genomes: towards understanding the interplay between structure and function, Current Opinion in Systems Biology 8: 137-143.
- Brocken D.J.W., Tark-Dame M. & Dame R.T. (2018), dCas9: A Versatile Tool For Epigenome Editing, Current Issues in Molecular Biology 26: 15-32.
- Boudreau B.A., Hron D.R., Qin L., Valk R.A. van der, Kotlajich M.V., Dame R.T. & Landick R. (2018), StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments, Nucleic Acids Research 46(11): 5525-5546.
- Henneman B., Emmerik C.L. van, Ingen H. van & Dame R.T. (2018), Structure and function of archaeal histones, PLoS Genetics 14(9): e1007582.
- Chaurasiya K.R. & Dame R.T. (2018), Single molecule FRET analysis of DNA binding proteins. In: Peterman E. (red.) Single Molecule Analysis. Methods in Molecular Biology nr. 1665 New York, NY, U.S.A.: Humana Press. 217-239.
- Hoekstra T.P., Depken M., Lin S., Cabanas-Danes J., Gross P., Dame R.T., Peterman E.J.G. & Wuite G.J.L. (2017), Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity, Biophysical Journal 112(4): 575-583.
- Dame R.T. (2016), Datamanagementplan. [overig].
- Valk R.A. van der, Vreede J., Qin L., Moolenaar G.F., Hofmann A., Goosen N. & Dame R.T. (2017), Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity, ELIFE 6: e27369.
- Liang Y., Valk R.A. van der, Dame R.T., Roos W.H. & Wuite G.J.L. (2017), Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling, Scientific Reports 7: 15275.
- Valk R.A. van der, Laurens N. & Dame R.T. (2017), Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins. In: Espélin O. (red.) The Bacterial Nucleoid. Methods in Molecular Biology nr. 1624 New York, NY, U.S.A.: Humana Press. 127-143.
- Lin S.N., Dame R.T. & Wuite G.J.L. (2017), The Interplay between a Bacterial Chromatin Protein and DNA Polymerase, Biophysical Journal 112(3): 513A-513A.
- Dame R.T. & Tark-Dame M. (2016), Bacterial chromatin: converging views at different scales, Current Opinion in Cell Biology 40: 60-65.
- Driessen R.P.C., Lin S.N., Waterreus W.J., Meulen A.L.H. van der, Valk R.A. van der, Laurens N., Moolenaar G.F., Pannu N.S., Wuite G.J.L., Goosen N. & Dame R.T. (2016), Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization, Scientific Reports 6: 29422.
- Chintakayala K., Sellars L.E., Singh S.S., Shahapure R., Westerlaken I., Meyer A.S., Dame R.T. & Grainger D.C. (2015), DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction, Nucleic Acids Research 43(4): 2282-92.
- Henneman B. & Dame R.T. (2015), Archaeal histones: dynamic and versatile genome architects, AIMS Microbiology 1(1): 72-81.
- Peeters E., Driessen R.P.C., Werner F. & Dame R.T. (2015), The interplay between nucleoid organization and transcription in archaeal genomes, Nature Reviews Microbiology 13(6): 333-341.
- Valk R.A. van der, Vreede J., Cremazy F. & Dame R.T. (2014), Genomic Looping: A Key Principle of Chromatin Organization, JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY 24(5-6): 344-359.
- Driessen R.P.C., Sitters G., Laurens N., Moolenaar G.F., Wuite G.J.L., Goosen N. & Dame R.T. (2014), Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins, Biochemistry 53(41): 6430-6438.
- Shahapure R., Driessen R.P.C., Haurat M.F., Albers S.V. & Dame R.T. (2014), The archaellum: a rotating type IV pilus, Molecular Microbiology 91(1): 716-723.
- Dame R.T., Hall M.A. & Wang M.D. (2013), Single-Molecule Unzipping Force Analysis of HU-DNA Complexes, ChemBioChem 14(15): 1954-1957.
- Driessen R.P.C. & Dame R.T. (2013), Structure and dynamics of the crenarchaeal nucleoid, Biochemical Society Transactions 41: 321-325.
- Chintakayala K., Singh S.S., Rossiter A.E., Shahapure R., Dame R.T. & Grainger D.C. (2013), E. coli Fis Protein Insulates the cbpA Gene from Uncontrolled Transcription, PLOS GENETICS 9(1): e1003152.
- Driessen R.P.C., Valk R.A. van der, Moolenaar G.F., Goosen N. & Dame R.T. (2013), The Architects of the Archaeal Chromatin, Biophysical Journal 104(2): 581A-581A.
- Laurens N., Driessen R.P.C., Heller I., Vorselen D., Noom M.C., Hol F.J.H., White M.F., Dame R.T. & Wuite G.J.L. (2012), Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA, NATURE COMMUNICATIONS 3: 1328.
- Dame R.T., Espeli O., Grainger D.C. & Wiggins P.A. (2012), Multidisciplinary perspectives on bacterial genome organization and dynamics, Molecular Microbiology 86(5): 1023-1030.
- 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.
- Westra E.R., Nilges B., Erp P.B.G. van, Oost J. van der, Dame R.T. & Brouns S.J.J. (2012), Cascade-mediated binding and bending of negatively supercoiled DNA, RNA BIOLOGY 9(9): 1134-1138.
- Vreede J. & Dame R.T. (2012), Predicting the Effect of Ions on the Conformation of the H-NS Dimerization Domain, Biophysical Journal 103(1): 89-98.
- Westra E.R., Erp P.B.G. van, Kunne T., Wong S.P., Staals R.H.J., Seegers C.L.C., Bollen S., Jore M.M., Semenova E., Severinov K., Vos W.M. de, Dame R.T., Vries R. de, Brouns S.J.J. & Oost J. van der (2012), CRISPR Immunity Relies on the Consecutive Binding and Degradation of Negatively Supercoiled Invader DNA by Cascade and Cas3, MOLECULAR CELL 46(5): 595-605.
- Liu Z., Galli F., Waterreus W.J., Meulenbroek E.M., Koning R.I., Lamers G.E.M., Olsthoorn R.R.C.L., Pannu N.S., Oosterkamp T.H., Koster A.J., Dame R.T. & Abrahams J.P. (2012), Single-Walled Carbon Nanotubes as Scaffolds to Concentrate DNA for the Study of DNA-Protein Interactions, CHEMPHYSCHEM 13(6): 1569-1575.
- Dame R.T., Tark-Dame M. & Schiessel H. (2011), A physical approach to segregation and folding of the Caulobacter crescentus genome, Molecular Microbiology 82(6): 1311-1315.
- Sznee K., Dekker J.P., Dame R.T., Roon H. van, Wuite G.J.L. & Frese R.N. (2011), Jumping Mode Atomic Force Microscopy on Grana Membranes from Spinach, Journal of Biological Chemistry 286(45): 39164-39171.
- Dame R.T., Kalmykowa O.J. & Grainger D.C. (2011), Chromosomal Macrodomains and Associated Proteins: Implications for DNA Organization and Replication in Gram Negative Bacteria, PLOS GENETICS 7(6): e1002123.
- Driessen R.P.C. & Dame R.T. (2011), Nucleoid-associated proteins in Crenarchaea, Biochemical Society Transactions 39: 116-121.
- Dame R.T., Laurens N., Noom M.C., Hol F.J.H., White M.F. & Wuite G.J.L. (2010), Unravelling the Role of Alba in the Organization of the Archaeal Nucleoid, BIOPHYSICAL JOURNAL 98(3): 206A-206A.
- Dame R.T. & Dorman C.J. (2010), Bacterial Chromatin: Springer.
- Dame R.T. (2010), Ultrastructure and organization of bacterial chromosomes. In: Dame R.T., Dorman C.J. (red.) Bacterial Chromatin. Dordrecht: Springer. 3-11.
- Wiggins P.A., Dame R.T., Noom M.C. & Wuite G.J.L. (2009), Protein-Mediated Molecular Bridging: A Key Mechanism in Biopolymer Organization, Biophysical Journal 97(7): 1997-2003.
- Luijsterburg M.S., White M.F., Driel R. van & Dame R.T. (2008), The Major Architects of Chromatin: Architectural Proteins in Bacteria, Archaea and Eukaryotes, CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY 43(6): 393-418.
- Dame R.T. (2008), Single-molecule micromanipulation studies of DNA and architectural proteins, Biochemical Society Transactions 36: 732-737.
- Noom M.C., Navarre W.W., Oshima T., Wuite G.J.L. & Dame R.T. (2007), H-NS promotes looped domain formation in the bacterial chromosome, CURRENT BIOLOGY 17(21): R913-R914.
- Luijsterburg M.S., Noom M.C., Wuite G.J.L. & Dame R.T. (2006), The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: A molecular perspective, Journal of Structural Biology 156(2): 262-272.
- Dame R.T., Noom M.C. & Wuite G.J.L. (2006), Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation, 444(7117): 387-390.
- Leliveld S.R., Dame R.T., Wuite G.J.L., Stitz L. & Korth C. (2006), The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions, Journal of Biological Chemistry 281(6): 3268-3275.
- Dame R.T., Mameren J. van, Luijsterburg M.S., Mysiak M.E., Janicijevic A., Pazdzior G., Vliet P.C. van der, Wyman C. & Wuite G.J.L. (2005), Analysis of scanning force microscopy images of protein-induced DNA bending using simulations, Nucleic Acids Research 33(7).
- Dame R.T. (2005), The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin, Molecular Microbiology 56(4): 858-870.
- Dame R.T., Luijsterburg M.S., Krin E., Bertin P.N., Wagner R. & Wuite G.J.L. (2005), DNA bridging: a property shared among H-NS-like proteins, Journal of Bacteriology 187(5): 1845-1848.
- 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 of the United States of America 101(18): 6969-6974.
- Leliveld S.R., Dame R.T., Rohn J.L., Noteborn M.H.M. & Abrahams J.P. (2004), Apoptin's functional N- and C-termini independently bind DNA, FEBS LETTERS 557(1-3): 155-158.
- Dame R.T., Wyman C. & Goosen N. (2003), Insights into the relation of transcription by scanning force microscopy, JOURNAL OF MICROSCOPY-OXFORD 212: 244-253.
- Dame R.T. & Wuite G.J.L. (2003), On the role of H-NS in the organization of bacterial chromatin: From bulk to single molecules and back .., Biophysical Journal 85(6): 4146-4148.
- Leliveld S.R., Dame R.T., Mommaas M.A., Koerten H.K., Wyman C., Danen-Van Oorschot A.A.A.M., Rohn J.L., Noteborn M.H.M. & Abrahams J.P. (2003), Apoptin protein multimers form distinct higher-order nucleoprotein complexes with DNA, Nucleic Acids Research 31(16): 4805-4813.
- Dame R.T. & Goosen N. (2002), HU: promoting or counteracting DNA compaction?, FEBS LETTERS 529(2-3): 151-156.
- Dame R.T., Wyman C., Wurm R., Wagner R. & Goosen N. (2002), Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1, Journal of Biological Chemistry 277(3): 2146-2150.
- Dame R.T., Wyman C. & Goosen N. (2001), Structural basis for preferential binding of H-NS to curved DNA, BIOCHIMIE 83(2): 231-234.
- Dame R.T., Wyman C. & Goosen N. (2000), H-NS mediated compaction of DNA visualised by atomic force microscopy, Nucleic Acids Research 28(18): 3504-3510.
- Zuccheri G., Dame R.T., Aquila M., Muzzalupo I. & Samori B. (1998), Conformational fluctuations of supercoiled DNA molecules observed in real time with a scanning force microscope, APPLIED PHYSICS A-MATERIALS SCIENCE & PROCESSING 66: S585-S589.
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