Remus T. Dame - Publications

Affiliations: 
2009- Leiden University, Leiden, Netherlands 
Area:
Genome organization, biochemistry
Website:
https://www.universiteitleiden.nl/en/staffmembers/remus-dame

76 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Lin SN, Dame RT, Wuite GJL. Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions. Scientific Reports. 11: 18492. PMID 34531428 DOI: 10.1038/s41598-021-97763-w  1
2021 Bdira FB, Erkelens AM, Qin L, Volkov AN, Lippa AM, Bowring N, Boyle AL, Ubbink M, Dove SL, Dame RT. Novel anti-repression mechanism of H-NS proteins by a phage protein. Nucleic Acids Research. PMID 34520554 DOI: 10.1093/nar/gkab793  1
2021 Gilbert BR, Thornburg ZR, Lam V, Rashid FM, Glass JI, Villa E, Dame RT, Luthey-Schulten Z. Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps. Frontiers in Molecular Biosciences. 8: 644133. PMID 34368224 DOI: 10.3389/fmolb.2021.644133  1
2021 Jewett AI, Stelter D, Lambert J, Saladi SM, Roscioni OM, Ricci M, Autin L, Maritan M, Bashusqeh SM, Keyes T, Dame RT, Shea JE, Jensen GJ, Goodsell DS. Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics. Journal of Molecular Biology. 166841. PMID 33539886 DOI: 10.1016/j.jmb.2021.166841  0.01
2020 Henneman B, Brouwer TB, Erkelens AM, Kuijntjes GJ, van Emmerik C, van der Valk RA, Timmer M, Kirolos NCS, van Ingen H, van Noort J, Dame RT. Mechanical and structural properties of archaeal hypernucleosomes. Nucleic Acids Research. PMID 33341892 DOI: 10.1093/nar/gkaa1196  1
2020 Lin SN, Wuite GJL, Dame RT. Effect of Different Crowding Agents on the Architectural Properties of the Bacterial Nucleoid-Associated Protein HU. International Journal of Molecular Sciences. 21. PMID 33334011 DOI: 10.3390/ijms21249553  1
2020 Qin L, Bdira FB, Sterckx YGJ, Volkov AN, Vreede J, Giachin G, van Schaik P, Ubbink M, Dame RT. Structural basis for osmotic regulation of the DNA binding properties of H-NS proteins. Nucleic Acids Research. PMID 31925429 DOI: 10.1093/Nar/Gkz1226  1
2019 Qin L, Erkelens AM, Ben Bdira F, Dame RT. The architects of bacterial DNA bridges: a structurally and functionally conserved family of proteins. Open Biology. 9: 190223. PMID 31795918 DOI: 10.1098/Rsob.190223  1
2019 Dame RT, Rashid FM, Grainger DC. Chromosome organization in bacteria: mechanistic insights into genome structure and function. Nature Reviews. Genetics. PMID 31767998 DOI: 10.1038/S41576-019-0185-4  1
2019 Ultee E, Ramijan K, Dame RT, Briegel A, Claessen D. Stress-induced adaptive morphogenesis in bacteria. Advances in Microbial Physiology. 74: 97-141. PMID 31126537 DOI: 10.1016/Bs.Ampbs.2019.02.001  0.01
2019 Oliveira Paiva AM, Friggen AH, Qin L, Douwes R, Dame RT, Smits WK. The Bacterial Chromatin Protein HupA Can Remodel DNA and Associates with the Nucleoid in Clostridium difficile. Journal of Molecular Biology. PMID 30633871 DOI: 10.1016/J.Jmb.2019.01.001  1
2018 Dilweg IW, Dame RT. Post-translational modification of nucleoid-associated proteins: an extra layer of functional modulation in bacteria? Biochemical Society Transactions. 46: 1381-1392. PMID 30287510 DOI: 10.1042/Bst20180488  0.01
2018 Henneman B, van Emmerik C, van Ingen H, Dame RT. Structure and function of archaeal histones. Plos Genetics. 14: e1007582. PMID 30212449 DOI: 10.1371/Journal.Pgen.1007582  1
2018 Lin SN, Qin L, Wuite GJL, Dame RT. Unraveling the Biophysical Properties of Chromatin Proteins and DNA Using Acoustic Force Spectroscopy. Methods in Molecular Biology (Clifton, N.J.). 1837: 301-316. PMID 30109617 DOI: 10.1007/978-1-4939-8675-0_16  1
2018 Henneman B, Heinsman J, Battjes J, Dame RT. Quantitation of DNA-Binding Affinity Using Tethered Particle Motion. Methods in Molecular Biology (Clifton, N.J.). 1837: 257-275. PMID 30109615 DOI: 10.1007/978-1-4939-8675-0_14  1
2018 van der Valk RA, Qin L, Moolenaar GF, Dame RT. Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins. Methods in Molecular Biology (Clifton, N.J.). 1837: 199-209. PMID 30109613 DOI: 10.1007/978-1-4939-8675-0_12  1
2018 Corbeski I, Horn V, van der Valk RA, le Paige UB, Dame RT, van Ingen H. Microscale Thermophoresis Analysis of Chromatin Interactions. Methods in Molecular Biology (Clifton, N.J.). 1837: 177-197. PMID 30109612 DOI: 10.1007/978-1-4939-8675-0_11  1
2018 Crémazy FG, Rashid FM, Haycocks JR, Lamberte LE, Grainger DC, Dame RT. Determination of the 3D Genome Organization of Bacteria Using Hi-C. Methods in Molecular Biology (Clifton, N.J.). 1837: 3-18. PMID 30109602 DOI: 10.1007/978-1-4939-8675-0_1  1
2018 Boudreau BA, Hron DR, Qin L, van der Valk RA, Kotlajich MV, Dame RT, Landick R. StpA and Hha stimulate pausing by RNA polymerase by promoting DNA-DNA bridging of H-NS filaments. Nucleic Acids Research. PMID 29718386 DOI: 10.1093/Nar/Gky265  1
2018 Chaurasiya KR, Dame RT. Single Molecule FRET Analysis of DNA Binding Proteins. Methods in Molecular Biology (Clifton, N.J.). 1665: 217-239. PMID 28940072 DOI: 10.1007/978-1-4939-7271-5_12  0.01
2018 Brocken DJW, Tark-Dame M, Dame RT. dCas9: A Versatile Tool for Epigenome Editing. Current Issues in Molecular Biology. 26: 15-32. PMID 28879853 DOI: 10.21775/Cimb.026.015  1
2017 Liang Y, van der Valk RA, Dame RT, Roos WH, Wuite GJL. Probing the mechanical stability of bridged DNA-H-NS protein complexes by single-molecule AFM pulling. Scientific Reports. 7: 15275. PMID 29127381 DOI: 10.1038/S41598-017-15477-4  1
2017 van der Valk RA, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT. Mechanism of environmentally driven conformational changes that modulate H-NS DNA bridging activity. Elife. 6. PMID 28949292 DOI: 10.7554/Elife.27369  1
2017 van der Valk RA, Laurens N, Dame RT. Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins. Methods in Molecular Biology (Clifton, N.J.). 1624: 127-143. PMID 28842881 DOI: 10.1007/978-1-4939-7098-8_11  1
2017 Hoekstra TP, Depken M, Lin SN, Cabanas-Danés J, Gross P, Dame RT, Peterman EJ, Wuite GJ. Switching between Exonucleolysis and Replication by T7 DNA Polymerase Ensures High Fidelity. Biophysical Journal. 112: 575-583. PMID 28256218 DOI: 10.1016/J.Bpj.2016.12.044  1
2017 Valk RAvd, Vreede J, Qin L, Moolenaar GF, Hofmann A, Goosen N, Dame RT. Author response: Mechanism of environmentally driven conformational changes that modulate H-NS DNA-bridging activity Elife. DOI: 10.7554/Elife.27369.027  1
2017 Lin S, Dame RT, Wuite GJL. The Interplay between a Bacterial Chromatin Protein and DNA Polymerase Biophysical Journal. 112. DOI: 10.1016/J.Bpj.2016.11.2775  1
2016 Driessen RP, Lin SN, Waterreus WJ, van der Meulen AL, van der Valk RA, Laurens N, Moolenaar GF, Pannu NS, Wuite GJ, Goosen N, Dame RT. Diverse architectural properties of Sso10a proteins: Evidence for a role in chromatin compaction and organization. Scientific Reports. 6: 29422. PMID 27403582 DOI: 10.1038/Srep29422  1
2016 Dame RT, Tark-Dame M. Bacterial chromatin: converging views at different scales. Current Opinion in Cell Biology. 40: 60-65. PMID 26942688 DOI: 10.1016/J.Ceb.2016.02.015  1
2015 Peeters E, Driessen RP, Werner F, Dame RT. The interplay between nucleoid organization and transcription in archaeal genomes. Nature Reviews. Microbiology. 13: 333-41. PMID 25944489 DOI: 10.1038/Nrmicro3467  1
2015 Chintakayala K, Sellars LE, Singh SS, Shahapure R, Westerlaken I, Meyer AS, Dame RT, Grainger DC. DNA recognition by Escherichia coli CbpA protein requires a conserved arginine-minor-groove interaction. Nucleic Acids Research. 43: 2282-92. PMID 25670677 DOI: 10.1093/Nar/Gkv012  1
2015 Lin S, Danes JC, Hoekstra TP, Kamsma D, Sitters G, Depken M, Dame RT, Wuite G. Resolving the Kinetic States of a Proofreading DNA Polymerase Biophysical Journal. 108. DOI: 10.1016/J.Bpj.2014.11.417  1
2014 van der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic looping: a key principle of chromatin organization. Journal of Molecular Microbiology and Biotechnology. 24: 344-59. PMID 25732337 DOI: 10.1159/000368851  1
2014 Driessen RP, Sitters G, Laurens N, Moolenaar GF, Wuite GJ, Goosen N, Dame RT. Effect of temperature on the intrinsic flexibility of DNA and its interaction with architectural proteins. Biochemistry. 53: 6430-8. PMID 25291500 DOI: 10.1021/Bi500344J  1
2014 Shahapure R, Driessen RP, Haurat MF, Albers SV, Dame RT. The archaellum: a rotating type IV pilus. Molecular Microbiology. 91: 716-23. PMID 24330313 DOI: 10.1111/Mmi.12486  1
2014 Graumann PL, Borgmann LAKK, Waldminghaus T, Messerschmidt SJ, Rybenkov VV, Herrera V, Petrushenko ZM, Zhao H, Crozat E, Rousseau P, Cornet F, Fournes F, Dorman CJ, Valk RAvd, Vreede J, ... ... Dame RT, et al. Contents Vol. 24, 2014 Journal of Molecular Microbiology and Biotechnology. 24. DOI: 10.1159/000370228  1
2014 Van Der Valk RA, Vreede J, Crémazy F, Dame RT. Genomic looping: A key principle of chromatin organization Journal of Molecular Microbiology and Biotechnology. 24: 344-359. DOI: 10.1159/000368851  1
2014 Liang Y, Baclayon M, Valk Rvd, Dame RT, Roos WH, Wuite GJL. Probing the Unbinding Kinetics of DNA-H-NS-DNA Protein Complexes by a High-Speed and High-Throughput Single-Molecule Pulling Assay using Atomic Force Microscopy Biophysical Journal. 106: 386. DOI: 10.1016/J.Bpj.2013.11.2184  1
2013 Dame RT, Hall MA, Wang MD. Single-molecule unzipping force analysis of HU-DNA complexes. Chembiochem : a European Journal of Chemical Biology. 14: 1954-7. PMID 24000171 DOI: 10.1002/Cbic.201300413  0.01
2013 Driessen RPC, Dame RT. Structure and dynamics of the crenarchaeal nucleoid. Biochemical Society Transactions. 41: 321-325. PMID 23356305 DOI: 10.1042/Bst20120336  1
2013 Chintakayala K, Singh SS, Rossiter AE, Shahapure R, Dame RT, Grainger DC. E. coli Fis protein insulates the cbpA gene from uncontrolled transcription. Plos Genetics. 9: e1003152. PMID 23341772 DOI: 10.1371/Journal.Pgen.1003152  1
2013 Driessen RP, Meng H, Suresh G, Shahapure R, Lanzani G, Priyakumar UD, White MF, Schiessel H, van Noort J, Dame RT. Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends. Nucleic Acids Research. 41: 196-205. PMID 23155062 DOI: 10.1093/Nar/Gks1053  1
2013 Driessen R, Valk Rvd, Moolenaar G, Goosen N, Dame R. The Architects of the Archaeal Chromatin Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.3226  1
2012 Laurens N, Driessen RP, Heller I, Vorselen D, Noom MC, Hol FJ, White MF, Dame RT, Wuite GJ. Alba shapes the archaeal genome using a delicate balance of bridging and stiffening the DNA. Nature Communications. 3: 1328. PMID 23271660 DOI: 10.1038/Ncomms2330  1
2012 Dame RT, Espéli O, Grainger DC, Wiggins PA. Multidisciplinary perspectives on bacterial genome organization and dynamics. Molecular Microbiology. 86: 1023-30. PMID 23066904 DOI: 10.1111/Mmi.12055  1
2012 Westra ER, Nilges B, van Erp PB, van der Oost J, Dame RT, Brouns SJ. Cascade-mediated binding and bending of negatively supercoiled DNA. Rna Biology. 9: 1134-8. PMID 22954644 DOI: 10.4161/Rna.21410  1
2012 Tavita K, Mikkel K, Tark-Dame M, Jerabek H, Teras R, Sidorenko J, Tegova R, Tover A, Dame RT, Kivisaar M. Homologous recombination is facilitated in starving populations of Pseudomonas putida by phenol stress and affected by chromosomal location of the recombination target. Mutation Research. 737: 12-24. PMID 22917545 DOI: 10.1016/J.Mrfmmm.2012.07.004  1
2012 Vreede J, Dame RT. Predicting the effect of ions on the conformation of the H-NS dimerization domain Biophysical Journal. 103: 89-98. PMID 22828335 DOI: 10.1016/J.Bpj.2012.05.040  1
2012 Westra ER, van Erp PB, Künne T, Wong SP, Staals RH, Seegers CL, Bollen S, Jore MM, Semenova E, Severinov K, de Vos WM, Dame RT, de Vries R, Brouns SJ, van der Oost J. CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3. Molecular Cell. 46: 595-605. PMID 22521689 DOI: 10.1016/J.Molcel.2012.03.018  1
2012 Liu Z, Galli F, Waterreus WJ, Meulenbroek E, Koning RI, Lamers GE, Olsthoorn RC, Pannu N, Oosterkamp TH, Koster AJ, Dame RT, Abrahams JP. Single-walled carbon nanotubes as scaffolds to concentrate DNA for the study of DNA-protein interactions. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 13: 1569-75. PMID 22407519 DOI: 10.1002/Cphc.201100896  1
2011 Dame RT, Tark-Dame M, Schiessel H. A physical approach to segregation and folding of the Caulobacter crescentus genome. Molecular Microbiology. 82: 1311-5. PMID 22029843 DOI: 10.1111/J.1365-2958.2011.07898.X  1
2011 Sznee K, Dekker JP, Dame RT, van Roon H, Wuite GJ, Frese RN. Jumping mode atomic force microscopy on grana membranes from spinach. The Journal of Biological Chemistry. 286: 39164-71. PMID 21911498 DOI: 10.1074/Jbc.M111.284844  1
2011 Dame RT, Kalmykowa OJ, Grainger DC. Chromosomal macrodomains and associated proteins: implications for DNA organization and replication in gram negative bacteria. Plos Genetics. 7: e1002123. PMID 21698131 DOI: 10.1371/Journal.Pgen.1002123  1
2011 Driessen RPC, Dame RT. Nucleoid-associated proteins in Crenarchaea. Biochemical Society Transactions. 39: 116-121. PMID 21265758 DOI: 10.1042/Bst0390116  1
2011 Biebricher A, Wagner K, Moolenaar GF, Goosen N, Dame RT, Peterman EJG, Wuite GJL. Investigating the Interaction of Single UvrA Dimers with DNA Using a Combination of Fluorescent Microscopy and Optical Tweezers Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.592  1
2011 Laurens N, Vorselen D, Driessen RPC, Noom MC, Hol FJH, White MF, Dame RT, Wuite GJL. Archaeal DNA Organization: The Mechanism of Alba I & II Revealed Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.1469  1
2009 Wiggins PA, Dame RT, Noom MC, Wuite GJ. Protein-mediated molecular bridging: a key mechanism in biopolymer organization. Biophysical Journal. 97: 1997-2003. PMID 19804731 DOI: 10.1016/J.Bpj.2009.06.051  1
2009 Wiggins PA, Dame RT, Noom MC, Wuite GJL. Protein mediated bridging motifs: A key mechanism in biopolymer organization Biophysical Journal. 96: 1997-2003. DOI: 10.1016/J.Bpj.2008.12.2131  1
2008 Dame RT. Single-molecule micromanipulation studies of DNA and architectural proteins Biochemical Society Transactions. 36: 732-737. PMID 18631149 DOI: 10.1042/Bst0360732  0.01
2007 Noom MC, Navarre WW, Oshima T, Wuite GJ, Dame RT. H-NS promotes looped domain formation in the bacterial chromosome. Current Biology : Cb. 17: R913-4. PMID 17983565 DOI: 10.1016/J.Cub.2007.09.005  1
2006 Dame RT, Noom MC, Wuite GJ. Bacterial chromatin organization by H-NS protein unravelled using dual DNA manipulation. Nature. 444: 387-90. PMID 17108966 DOI: 10.1038/Nature05283  1
2006 Luijsterburg MS, Noom MC, Wuite GJ, Dame RT. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. Journal of Structural Biology. 156: 262-72. PMID 16879983 DOI: 10.1016/J.Jsb.2006.05.006  1
2005 Leliveld SR, Dame RT, Wuite GJ, Stitz L, Korth C. The expanded octarepeat domain selectively binds prions and disrupts homomeric prion protein interactions. The Journal of Biological Chemistry. 281: 3268-75. PMID 16352600 DOI: 10.1074/Jbc.M510606200  0.32
2005 Dame RT. The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Molecular Microbiology. 56: 858-70. PMID 15853876 DOI: 10.1111/J.1365-2958.2005.04598.X  0.01
2005 Dame RT, van Mameren J, Luijsterburg MS, Mysiak ME, Jani?ijevi? A, Pazdzior G, van der Vliet PC, Wyman C, Wuite GJ. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations. Nucleic Acids Research. 33: e68. PMID 15843682 DOI: 10.1093/Nar/Gni073  1
2005 Dame RT, Luijsterburg MS, Krin E, Bertin PN, Wagner R, Wuite GJ. DNA bridging: a property shared among H-NS-like proteins. Journal of Bacteriology. 187: 1845-8. PMID 15716456 DOI: 10.1128/Jb.187.5.1845-1848.2005  1
2005 Dame RT, Mameren Jv, Luijsterburg MS, Mysiak ME, Janicijevic A, Pazdzior G, Vliet PWv, Wyman C, Wuite GJL. Analysis of scanning force microscopy images of protein-induced DNA bending using simulations (vol 33, pg 68, 2005) Nucleic Acids Research. 33: 2767-2767. DOI: 10.1093/Nar/Gki577  1
2004 van Noort J, Verbrugge S, Goosen N, Dekker C, Dame RT. 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: 6969-74. PMID 15118104 DOI: 10.1073/Pnas.0308230101  0.32
2004 Leliveld SR, Dame RT, Rohn JL, Noteborn MH, Abrahams JP. Apoptin's functional N- and C-termini independently bind DNA. Febs Letters. 557: 155-8. PMID 14741359 DOI: 10.1016/S0014-5793(03)01465-0  1
2004 Dame RT, Wuite GJ. On the role of H-NS in the organization of bacterial chromatin: from bulk to single molecules and back. Biophysical Journal. 85: 4146-8. PMID 14645101 DOI: 10.1016/S0006-3495(03)74826-7  0.44
2003 Dame RT, Wyman C, Goosen N. Insights into the regulation of transcription by scanning force microscopy Journal of Microscopy. 212: 244-253. PMID 14629550 DOI: 10.1111/J.1365-2818.2003.01243.X  1
2003 Leliveld SR, Dame RT, Mommaas MA, Koerten HK, Wyman C, Danen-van Oorschot AA, Rohn JL, Noteborn MH, Abrahams JP. Apoptin protein multimers form distinct higher-order nucleoprotein complexes with DNA. Nucleic Acids Research. 31: 4805-13. PMID 12907722 DOI: 10.1093/Nar/Gkg661  1
2002 Dame RT, Goosen N. HU: promoting or counteracting DNA compaction? Febs Letters. 529: 151-6. PMID 12372591 DOI: 10.1016/S0014-5793(02)03363-X  0.72
2002 Dame RT, Wyman C, Wurm R, Wagner R, Goosen N. Structural basis for H-NS-mediated trapping of RNA polymerase in the open initiation complex at the rrnB P1 Journal of Biological Chemistry. 277: 2146-2150. PMID 11714691 DOI: 10.1074/Jbc.C100603200  1
2001 Dame RT, Wyman C, Goosen N. Structural basis for preferential binding of H-NS to curved DNA Biochimie. 83: 231-234. PMID 11278073 DOI: 10.1016/S0300-9084(00)01213-X  1
2000 Dame RT, Wyman C, Goosen N. H-NS mediated compaction of DNA visualised by atomic force microscopy Nucleic Acids Research. 28: 3504-3510. PMID 10982869 DOI: 10.1093/Nar/28.18.3504  1
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