Ralf Seidel - Single molecule investigations of DNA motors
- 2004: PhD in Physics, Dresden University of Technology, Germany
- 2003-2005: Postdoctoral work at the Kavli Institute of Nanoscience, Delft University of Technology, The Netherlands
- since 2006: Junior group leader, BIOTEC, TU-Dresden, Germany
Research
Translocation of enzymes along DNA, driven by molecular motors, plays a crucial role during many vital DNA-processing steps in the cellular cycle, including DNA repair, recombination, replication, transcription and restriction. These enzymes use the energy stored in ATP or other NTPs and convert it into directional motion along their template. Very often motion does not just occur just by itself but is accompanied by reshaping or processing the DNA template. Understanding the mechanisms how DNA motors couple the ATP hydrolysis to achieve their function (motion, DNA processing) will help to gain much deeper insight in the cellular processes, which are driven by these motors.
Artistic view on an enzyme motor pulling on DNA in a magnetic tweezers setup
In our biophysically oriented group we study DNA translocating motors on the level of a single-molecule. Recent advances in single-molecule techniques allow to follow the action of a single molecular motor in real time. We apply magnetic tweezers, which are an excellent tool to study the translocation of single enzyme complexes on DNA. They allow to stretch and twist a single DNA molecule and to measure its end-to-end distance in real-time, while it is getting processed by an enzyme. If a DNA translocating motor pulls in DNA, its end-to-end distance changes and can thus be monitored. Current research projects involve dsDNA motors, which belong to the Super family 2 of helicases (e.g. Type I and Type III restriction enzymes) as well as viral helicases, which function in DNA replication. More information can be found on the personal webpage.
Brownian motion of a magnetic bead in the tweezers bound to a stretched DNA molecule
Publications
2013
Klaue D, Kobbe D, Kemmerich F, Kozikowska A, Puchta P, Seidel R.
Fork sensing and strand switching control antagonistic activities of RecQ helicases.
Nat. Commun. accepted.
M Levikova, D Klaue, R Seidel, P Cejka.
The nuclease activity of Saccharomyces cerevisiae Dna2 inhibits its potent DNA helicase activity.
Proc Natl Acad Sci, accepted (2013) pdf
FW Schwarz*, J Tóth*, K van Aelst, G. Cui, S. Clausing, MD Szczelkun**, R Seidel**.
The Helicase-Like Domains of Type III Restriction Enzymes Trigger Long-Range Diffusion Along DNA.
Science 340(6130) 353-356 (2013). pdf SI
A Czogalla, EP Petrov, DJ Kauert, V Uzunova, Y Zhang, R Seidel, P Schwille.
Switchable domain partitioning and diffusion of DNA origami rods on membranes.
Faraday Discuss 161 31-43 (2013). pdf
2012
R Schöpflin, H Brutzer, O Müller, R Seidel**, G Wedemann**.
Probing the elasticity of DNA on short length scales by modeling supercoiling under tension.
Biophys J 103(2) 323-330 (2012). pdf SI
H Brutzer*, FW Schwarz*, R Seidel.
Scanning evanescent fields using a point-like light source and a nanomechanical DNA gear.
Nano Lett 12(1) 473-478 (2012). pdf SI
N Luzzietti, S Knappe, I Richter, R Seidel.
Nicking enzyme-based internal labelling of DNA at multiple loci.
Nat Protoc 7(4) 643-653 (2012). pdf
2011
DJ Kauert, T Kurth, T Liedl**, R Seidel**.
Direct mechanical measurements reveal the material properties of 3D DNA-origami.
Nano Lett 11(12) 5558-5563 (2011) pdf SI
FW Schwarz*, K van Aelst*, J Toth, R Seidel**, MD Szczelkun**.
DNA cleavage site selection by Type III restriction enzymes provides evidence for head-on protein collisions following 1D bidirectional motion.
Nucleic Acids Res 39(18) 8042-8051 (2011) pdf SI
N Luzzietti, H Brutzer, D Klaue, FW Schwarz, S Clausing, W Staroske, R Seidel.
Efficient preparation of internally modified single-molecule constructs using nicking enzymes.
Nucleic Acids Res 39(3) e15 (2011) pdf
O Otto, JL Gornall, G Stober, F Czerwinski, R Seidel, UF Keyser.
High-speed video-based tracking of optically trapped colloids.
J Opt 13, 044011 (2011) pdf
2010
O Otto, F Czerwinski, JL Gornall, G Stober, LB Oddershede, R Seidel, UF Keyser.
Real-time particle tracking at 10,000 fps using optical fiber illumination.
Opt Express 18(22) 22722?22733 (2010) pdf
C Maffeo*, R Schöpflin*, H Brutzer*, R Stehr, A Aksimentiev, G Wedemann, R Seidel.
A small effective charge describes DNA-DNA interactions in tight supercoils.
Phys Rev Lett 105(15) 158101 (2010) pdf SI
K Günter, M Mertig, R Seidel. Mechanical and structural properties of YOYO-1 complexed DNA.
Nucleic Acids Res 38(19) 6526-6532 (2010) pdf
K van Aelst, J Toth, SP Ramanathan, FW Schwarz, R Seidel**, MD Szczelkun**.
Type III restriction enzymes can cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.
Proc Natl Acad Sci 107(20) 9123-9128 (2010) pdf SI
MD Szczelkun, P Friedhoff, R Seidel.
Maintaining a sense of direction during long-range communication on DNA.
Biochem Soc Trans 38(2) 404-409 (2010) (Review)
H Brutzer, N Luzzietti, D Klaue, R Seidel. Energetics at the DNA supercoiling transition.
Biophys J 98 1267-1276 (2010)
2009
A Erler, S Wegmann, C Elie-Caille, CR Bradshaw, M Maresca, R Seidel, B Habermann, DJ Muller, AF Stewart. Conformational adaptability of Redbeta during DNA annealing and implications for its structural relationship with Rad52.
J Mol Biol 391(3) 586-598 (2009)
D Klaue, R Seidel. The torsional stiffness of single superparamagnetic microspheres.
Phys Rev Lett 102(2) 028302 (2009)
SP Ramanathan, K van Aelst, A Sears, LJ Peakman, FM Diffin, MD Szczelkun**, R Seidel**.
Type III restriction enzymes communicate in 1D without looping between their target sites.
Proc Natl Acad Sci 106(6) 1748-1753 (2009) pdf SI
2008
Sisáková E, Weiserová M, Dekker C, Seidel R, Szczelkun MD. The Interrelationship of Helicase and Nuclease Domains during DNA Translocation by the Molecular Motor EcoR124I.
J Mol Biol 384(5) 1273-1286 (2008)
R. Seidel, J.G.P. Bloom, C. Dekker, M. D. Szczelkun.
Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.
EMBO J 27(9) 1388-1398 (2008) pdf SI
2007
T. van der Heijden, R. Seidel, M. Modesti, R. Kanaar, C. Wyman, C. Dekker. Real-time assembly and disassembly of human Rad51 filaments on individual DNA molecules
Nucleic Acids Res 35(17) 5646-5657 (2007) pdf SI
A. Crut, D.A. Koster, R. Seidel, C. H. Wiggins, N.H. Dekker. Fast dynamics of supercoiled DNA revealed by single-molecule experiments.
Proc Natl Acad Sci 104(29) 11957-11962 (2007) pdf SI
R. Seidel, C. Dekker. Single-molecule studies of nucleic acid motors.
Curr Opin Struct Biol 17(1) 80-86 (2007) pdf (Review)
2006
F. Moreno-Herrero, R. Seidel, S.M. Johnson, A. Fire & N.H. Dekker. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans.
Nucleic Acids Res 34(10) 3057-3066 (2006) pdf
L.K. Stanley*, R. Seidel*, C. van der Scheer, N.H. Dekker, M.D. Szczelkun & C. Dekker. When a helicase is not a helicase: dsDNA tracking by the motor protein EcoR124I.
EMBO J 25(10) 2230-2239 (2006) pdf SI
2005
R. Seidel, J.G.P. Bloom, J. van Noort, C.F. Dutta, N.H. Dekker, K. Firman, M.D. Szczelkun & C. Dekker. Dynamics of initiation, termination and reinitiation of DNA translocation by the motor protein EcoR124I.
EMBO J 24(23), 4188-4197 (2005) pdf SI
2004
R. Seidel, J. van Noort, C. van der Scheer, J.G.P. Bloom, N.H. Dekker, C.F. Dutta, A. Blundell, T. Robinson, K. Firman & C. Dekker. Real-time observation of DNA translocation by the type I restriction modification enzyme EcoR124I.
Nat Struct Mol Biol 11(9), 838-843 (2004) pdf Niews & Views
R. Seidel, L. Colombi Ciacchi, M. Weigel, W. Pompe & M. Mertig. Synthesis of Platinum Cluster Chains on DNA Templates: Conditions for a Template-Controlled Cluster Growth.
J Phys Chem B 108(30), 10801-10811 (2004).
J. Opitz, F. Braun, R. Seidel, W. Pompe, B. Voit & M. Mertig, Site-specific binding and stretching of DNA molecules at UV-light patterned aminoterpolymer films.
Nanotechnology 15, 717-723 (2004)
2003
S. Diez , C. Reuther, C. Dinu, R. Seidel, M. Mertig, W. Pompe & J. Howard. Stretching and Transporting DNA Molecules using Motor Proteins.
Nano Lett 3, 1251-1254 (2003)
G Maubach, A Csáki, R Seidel, M Mertig, W Pompe, D Born, W Fritzsche. Controlled positioning of a DNA molecule in an electrode setup based on self-assembly and microstructuring.
Nanotechnology 14, 1055-1056 (2003).
L. Colombi Ciacchi, M. Mertig, R. Seidel, W. Pompe & A. De Vita. Nucleation of platinum clusters on biopolymers: A first principles study of the molecular mechanisms.
Nanotechnology 14, 840-848 (2003)
2002
M. Mertig, R. Seidel, L. Colombi Ciacchi & W. Pompe. Nucleation and growth of metal clusters on a DNA template.
AIP Conf Proc 633. 449-453 (2002)
M. Mertig, L. Colombi Ciacchi, R. Seidel, W. Pompe & A. De Vita, DNA as a selective metallization template.
Nano Lett 2, 841-844 (2002)
R. Seidel, M. Mertig & W. Pompe. Scanning force microscopy of DNA metallization.
Surf Interf Anal 33, 151-154 (2002)
2000
J. Richter, R. Seidel, R. Kirsch, M. Mertig, W. Pompe, J. Plaschke & H.-K. Schackert. Nanoscale Palladium Metallization of DNA.
Adv Mat 12, 507-510 (2000)
1999
W. Pompe, M. Mertig, R. Kirsch, R. Wahl, L. Ciacchi Colombi, J. Richter, R. Seidel & H. Vinzelberg, Formation of metallic nanostructures on biomiolecular templates. Zeitschrift für Metallkunde 90, 1085-1091 (1999)
*equal contribution, **corresponding authors
Links
Our group is funded by the Emmy-Noether program of the Deutsche Forschungsgemeinschaft (DFG)
Group Members
All current group members are listed on the Staff Page.
