Remus Dame
Professor Molecular and Cellular Biochemistry
- Name
- Prof.dr. R.T. Dame
- Telephone
- +31 71 527 5605
- rtdame@chem.leidenuniv.nl
- ORCID iD
- 0000-0001-9863-1692
Remus Dame investigates the coupling of genome organization and genome activity and the factors that fine-tune these processes in bacteria and archaea. He studies the proteins involved in vitro as well as in vivo using state-of-the-art biochemical and biophysical approaches.
More information about Remus Dame
PhD candidates
News
-
The Nobel Prize in Chemistry went to an AI model (and rightly so) -
Leiden chemists discover new ways in which single-celled organisms organise their DNA -
Not wrapping but folding: Bacteria also organise their DNA (but they do it a bit differently) -
Caught in living cells: how bacteria regulate their genes to defend themselves -
Non-invasive DNA-labeling tool opens doors for new research -
‘Look beyond your own discipline’ -
Three new professors for the Leiden Institute of Chemistry -
Proteins and DNA loops: Science-Groot grant for Remus Dame -
Science Groot funding for Leiden scientists -
How our single-celled relatives package their DNA -
New fundamental insight into the battle against bacteria -
Vici grants for 7 Leiden researchers -
Mapping of bacterial genomes to combat infectious diseases
Teaching
Former PhD candidates
Curriculum Vitae
Personal information
Nationality: Dutch
Date of birth: 10 September 1974
Education
2003 PhD, Leiden Institute of Chemistry, Leiden University, the Netherlands, 23 January 2003
Thesis title: “Architectural roles of H-NS and HU in DNA compaction and transcription regulation”
Advisors: Dr. N. Goosen and Prof. Dr. ir. P. van der Putte
1997 MSc in Chemistry, Department of Chemistry, University of Amsterdam, the Netherlands
Current and previous research positions
2020 - now Full Professor in Molecular and Cellular Biochemistry, Leiden Institute of Chemistry, Leiden University, The Netherlands
2015 – 2020 Associate Professor, Leiden Institute of Chemistry, Leiden University, The Netherlands
2009 – 2015 Assistant Professor, Leiden Institute of Chemistry, Leiden University, The Netherlands
2007 Visiting scientist, Department of Physics, Cornell University, Ithaca, USA (Prof. M. Wang)
2006 Visiting scientist, Kavli Institute of Theoretical Physics, KITP, Santa Barbara, CA, USA
2004 Visiting scientist, European Laboratory for Non-linear Spectroscopy, LENS, Florence, Italy (Prof. F. Pavone)
2003 - 2009 Post-doctoral researcher (Veni), Department of Physics and Astronomy, VU University, Amsterdam, The Netherlands (Prof. G.J.L. Wuite)
Grants, awards, recognitions since 2010
2020 NWO ENW-Groot grant (programme leader) with 4 partners (k€ 3,000)
2016 NWO-ALW Vici grant (k€ 1,500)
2014 HFSP grant (programme leader) with 4 partners (k$ 1,300)
2013 FOM programme grant with Prof. Wuite (VU) (k€ 330)
2010 FES-HTSM NanoNextNL grant (k€ 257)
Contribution to teaching and supervision
Current: BSc Life Science and Technology (Leiden/Delft): Quantitative Molecular Biology. MSc Life Science and Technology at Leiden University: Cross-domain Chromatin Organisation. Guest lecturer: Dynamics of Biomolecules and Cells (VU University).
Previous: undergraduate courses Cell Signaling & Biophysics (2015-2018), Physics (2015-2017), Molecular Genetics 2 for Biopharmaceutical Sciences (2014-2015) and Molecular Biophysics (2010-2014). Guest lecturer in Global Regulatory Networks in Bacteria (2010-2012), Dynamics of Biomolecules and Cells (VU University, 2011-2018]), and Current Developments in Biophysics (VU University, 2009-2011).
Supervision of 17 PhD students and 8 postdoctoral fellows (one FEBS fellow) since 2009. Current employment of recent PhD students and postdocs: K. Gavvala (Indian Institute of Technology, Hyderabad, India); F. Crémazy ( Université Paris-Saclay); R.A. van der Valk (TU Delft); R.P.C. Driessen (TU Delft); R. Shahapure (Cambridge University).
Other responsibilities since 2010
- Editorial board member for Frontiers in Microbiology, Microorganisms, BMC Molecular and Cell Biology, Editor of ‘Bacterial chromatin’, Methods in Molecular Biology, Dame Ed., Springer (2024), Editor of ‘Bacterial chromatin’, Methods in Molecular Biology, Dame Ed., Springer (2018), Editor of the book ‘Bacterial chromatin, Dame & Dorman Eds., Springer (2010).
- Secretary of the Netherlands Society of Biochemistry and Molecular Biology (2013-2016), Secretary of the ‘Nora Baart Stichting’ (2013-2016), Secretary of the ‘Stichting Stimulering Biochemie Nederland’ (2013-2016)
- Member of the NWO working groups Chemistry of Life, Physics of Life, and Life Sciences research communities 'Biology of Molecules, Cells and Tissues'.
- Comité van Aanbeveling S.V. LIFE (Student union Life Science & Technology, Leiden University)
- Member of the organising committee of the Dutch Chromatin Meeting (2022), Member of the organising committee of ‘The biology and physics of prokaryotic chromosome organization’, Leiden, NL (2023), Member of the organising committee of ‘The biology and physics of bacterial chromosome organization’, online (2021), Member of the organising committee of ‘The biology and physics of bacterial chromosome organization’, Leiden, NL (2018), Member of the organising committee of the Dutch Chromatin Meeting (2016), Member of the organising committee of ‘The biology and physics of bacterial chromosome organization’ meeting in Paris (2016), Member of the organising committee of the 2nd International Workshop on “The Biology and Physics of Bacterial Genome Organisation” in Birmingham, UK (2014), Member of the organising committee of the Joint Dutch Chromatin Meeting and NVBMB Fall Symposium (2013), Chair of the organising committee of the Lorentz workshop ‘The biology and physics of bacterial genome organization’ (2012), Member of the organising committee of the bimonthly KNAW Biophysics meeting (2010-2014)
- Grant reviewer for the Agence Nationale pour la Recherche, BBSRC, Deutsche Forschungsgemeinschaft, FAPESP, Leverhulme Trust, National Science Centre, National Science Foundation , National University of Singapore, Netherlands Organisation of Scientific Research, Royal Society of Chemistry, Science Foundation Ireland , UK India Education and Research Initiative, Wellcome Trust
- Reviewer for Nature, Nature Chemical Biology, Nature Structural and Molecular Biology, Nature Microbiology, Nature Communications, Nature Reviews in Genetics, Nature Reviews in Microbiology, Science, Science Advances, PNAS, EMBO Journal, EMBO Reports, Nucleic Acids Research, PLOS Genetics and various other biochemistry, biophysics and microbiology journals
- Chair of Admission committee member of the MSc curriculum Molecular Science and Technology (Leiden/Delft)
- Chair of Examination Board Life Science & Technology
- External member for PhD committees across The Netherlands, Belgium, Finland, Ireland, Italy, United Kingdom
Publication record
Ca. 85 papers with ~4000 citations, H-index 30 (Web of Science)
Full publication record: ResearcherID, or Leiden University
Presentations including five presentations at international conferences since 2010
50 invited presentations at universities, companies and institutes, and invited, keynote and plenary lectures at international conferences since 2010
- 2020 Telluride Workshop on Physical Genomics and Transcriptional Engineering. February 2020, Telluride, CO, USA
- Gordon Research Conference: “Archaea - Unique Biology of the Archaea Bridging the Gap Between Bacteria and Eukaryotes”, July 2019, Les Diablerets, Switzerland
- 3rd International Workshop on “The Biology and Physics of Bacterial Genome Organisation”, September 2016, Paris, France
- Biophysical Society thematic meeting: “Significance of Knotted Structures for Function of Proteins and Nucleic Acids”, September 2014, Warszaw, Poland
- Gordon Conference Chromosome Dynamics, May 2013, Italy
Professor Molecular and Cellular Biochemistry
- Science
- Leiden Institute of Chemistry
- LIC/Chemical Biology
- LIC/CB/Macromolecular Biochemistry
- Rashid F.Z.M. & Dame R.T. (2024), 2024: a "nucleoid space" odyssey featuring H-NS, Bioessays 46(11): 2400098.
- Ben Bdira F. & Dame R.T. et al. (2024), AI is a viable alternative to high throughput screening: a 318-target study, Scientific Reports 14: 7526.
- Hu Y., Schwab S., Deiss S., Escudeiro P., Heesch T. van, Joiner J.D., Vreede J., Harmann M.D., Lupas A.N., Alvarez B.H., Alva V. & Dame R.T. (2024), Bacterial histone HBb from Bdellovibrio bacteriovorus compacts DNA by bending, Nucleic Acids Research 52(14): 8193-8204.
- Schwab S. & Dame R.T. (2024), Identification, characterization and classification of prokaryotic nucleoid‐associated proteins, Molecular Microbiology : .
- Seymonson X.M.R., Erkelens A.M., Bibricher A.S., Erp B. van, Dame R.T. & Wuite G.J.L. (2024), Rok and roll: unravelling Rok-mediated DNA bridges with force, Biophysical Journal 123(3): 320a.
- Erkelens A.M., Erp B. van, Meijer W.J.J. & Dame R.T. (2024), Rok from B. subtilis: bridging genome structure and transcription regulation, Molecular Microbiology : .
- Erkelens A.M., Henneman B., Valk R.A. van der, Kirolos N.C.S. & Dame R.T. (2023), Specific DNA binding of archaeal histones HMfA and HMfB, Frontiers in Microbiology 14: 1166608.
- Rashid F.Z.M. & Dame R.T. (2023), Three‐dimensional chromosome re‐modelling: the integral mechanism of transcription regulation in bacteria, Molecular Microbiology 120(1): 60-70.
- Ofer S., Blombach F., Erkelens A.M., Barker D., Soloviev Z., Schwab S., Smollett K., Matelska D., Fouqueau T., Vis N. van der, Kent N.A., Thalassinos K., Dame R.T. & Werner F. (2023), DNA-bridging by an archaeal histone variant via a unique tetramerisation interface, Communications Biology 6: 968.
- Rashid F.Z.M., Cremazy F.G.E., Hofmann A., Forrest D., Grainger D.C., Heermann D.W. & Dame R.T. (2023), The environmentally-regulated interplay between local three-dimensional chromatin organisation and transcription of proVWX in E. coli, Nature Communications 14(1): 7478.
- 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.
- 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.
- 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.
- Rashid F.M.Z., Detmar L. & Dame R.T. (2022), Chromosome conformation capture in bacteria and archaea. In: Peeters E. & Bervoets I. (Eds.), Prokaryotic gene regulation. Methods in Molecular Biology no. 2516. New York: Humana Press. 1-28.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Dame R.T. (2021), Special Issue: role of bacterial chromatin in environmental sensing, adaptation and evolution, Microorganisms 9(11): 2406.
- 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.
- 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.
- 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.
- Ultee E., Ramijan K., Dame R.T., Briegel A. & Claessen D. (2019), Stress-induced adaptive morphogenesis in bacteria. In: Poole R.K (Ed.), Advances in Microbial Physiology no. 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/JMB Online 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. (Eds.), Modelling the 3D conformation of genomes. Series in Computational Physics: CRC Press. 207-230.
- 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.
- Henneman B., Emmerik C.L. van, Ingen H. van & Dame R.T. (2018), Structure and function of archaeal histones, PLoS Genetics 14(9): e1007582.
- 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.
- 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.
- 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.
- 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.
- 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. (Ed.), Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology no. 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. (Ed.), Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology no. 1837 177-197.
- 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. (Ed.), Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology no. 1837. New York, NY, U.S.A.: Humana Press. 301-316.
- Chaurasiya K.R. & Dame R.T. (2018), Single molecule FRET analysis of DNA binding proteins. In: Peterman E. (Ed.), Single Molecule Analysis. Methods in Molecular Biology no. 1665. New York, NY, U.S.A.: Humana Press. 217-239.
- Henneman B., Heinsman J., Battjes J. & Dame R.T. (2018), Quantitation of DNA-binding affinity using Tethered Particle Motion. In: Dame R.T. (Ed.), Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology no. 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. (Ed.), Bacterial Chromatin: Methods and Protocols. Methods in Molecular Biology no. 1837. New York, NY, U.S.A.: Humana Press. 199-209.
- 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.
- 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.
- 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.
- 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. (Ed.), The Bacterial Nucleoid. Methods in Molecular Biology no. 1624. New York, NY, U.S.A.: Humana Press. 127-143.
- Dame R.T. (2016), Datamanagementplan. [other].
- 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.
- 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.
- Henneman B. & Dame R.T. (2015), Archaeal histones: dynamic and versatile genome architects, AIMS Microbiology 1(1): 72-81.
- 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.
- 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.
- 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.
- 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.
- Driessen R.P.C. & Dame R.T. (2013), Structure and dynamics of the crenarchaeal nucleoid, Biochemical Society Transactions 41: 321-325.
- 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., 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Liu Z., Galli F., Waterreus W.J., Meulenbroek E.M., Koning R.I., Lamers G.E.M., Olsthoorn 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.
- Driessen R.P.C. & Dame R.T. (2011), Nucleoid-associated proteins in Crenarchaea, Biochemical Society Transactions 39: 116-121.
- 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.
- 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.
- Dame R.T. (2010), Ultrastructure and organization of bacterial chromosomes. In: Dame R.T. & Dorman C.J. (Eds.), Bacterial Chromatin. Dordrecht: Springer. 3-11.
- Dame R.T. & Dorman C.J. (2010), Bacterial Chromatin: Springer.
- 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.
- 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.
- 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.
- 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.
- 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. (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.
- 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): .
- 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.
- 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.
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