2021

P Aldag, F Welzel, L Jakob, A Schmidbauer, M Rutkauskas, F Fettes, D Grohmann, Ralf Seidel
Probing the stability of the SpCas9–DNA complex after cleavage
Nucleic Acids Res. Accepted (2021) pdf

A Acharya, K Kasaciunaite, M Göse, V Kissling, R Guérois, R Seidel, P Cejka.
Distinct RPA domains promote recruitment and the helicase-nuclease activities of Dna2.
Nature Communications 12,  6521 (2021) pdf

G Bigelyte, J K Young, T Karvelis, K Budre, R Zedaveinyte, V Djukanovic, Elizabeth V Ginkel, S Paulraj, S Gasior, S Jones, L Feigenbutz, G St. Clair, P Barone, J Bohn, A Acharya, G Zastrow-Hayes, S Henkel-Heinecke, A Silanskas, R Seidel, V Siksnys.
Miniature type V-F CRISPR-Cas nucleases enable targeted DNA modification in cells.
Nature Communications 12, 6191 (2021) pdf

N Weizenmann, G Scheidgen-Kleyboldt, J Ye, C Krause, D Kauert, S Helmi, C Rouillond, R Seidel.
Chemical ligation of an entire DNA Origami nanostructure.
Nanoscale 13, 17556-17565 (2021) pdf

J Ye, J Teske, U Kemper, R Seidel.
Sequential Pull‐Down Purification of DNA Origami Superstructures.
Small 17, 2007218 (2021) pdf

J Ye, O Aftenieva, T Bayrak, A Jain, T König, A Erbe, R Seidel.
Complex Metal Nanostructures with Programmable Shapes from Simple DNA Building Blocks.
Adv. Mater. 33, 2100381 (2021) pdf

2020

I Ceppi, S M Howard, K Kasaciunaite, C Pinto, R Anand, R Seidel, P Cejka.
CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection.
Proc. Natl. Acad. Sci. U.S.A. 117 (16), 8859-8869 (2020) pdf

P Irmisch, T. E. Ouldridge, R Seidel.
Modelling DNA-strand displacement reactions in the presence of base-pair mismatches.
J. Am. Chem. Soc. 142, 11451-11463 (2020) pdf

R Grigaitis, L Ranjha, P Wild, K Kasaciunaite, I Ceppi, V Kissling, A Henggeler, A Susperregui, M Peter, R Seidel, P Cejka, J Matos.
Phosphorylation of the RecQ Helicase Sgs1/BLM Controls Its DNA Unwinding Activity during Meiosis and Mitosis.
Developmental Cell 53, 1-18 (2020) pdf

J Ye, R Weichelt, U Kemper, V Gupta, T König, A Eychmüller, R Seidel.
Casting of Gold Nanoparticles with High Aspect Ratios inside DNA Molds.
Small 16, 2003662 (2020) pdf

2019

F Scheffler, M Brueckner, J Ye, R Seidel, U Reibetanz.
A Hybrid Carrier System Based on Origami Nanostructures and Layer-by-Layer Microparticles.
Adv. Funct. Mat. 29, 1808116 (2019) pdf

J Dikic, R Seidel.
Anticooperative Binding Governs the Mechanics of Ethidium-Complexed DNA.
Biophys. J. 116, 1394-1405 (2019) pdf

R Weichelt, J Ye, U Banin, A Eychmüller, R Seidel.
DNA-mediated Self-assembly and Metallization of Semiconductor Nanorods for the Fabrication of Nanoelectronic Interfaces.
Chemistry 25, 9012-9016 (2019) pdf

J Ye, S Helmi, J Teske, R Seidel.
Fabrication of Metal Nanostructures with Programmable Length and Patterns Using a Modular DNA Platform.
Nano Lett. 19, 2707-2714 (2019) pdf

K Kasaciunaite, F Fettes, M Levikova, P Daldrop, R Anand, P Cejka, R Seidel.
Competing interaction partners modulate the activity of Sgs1 helicase during DNA end resection.
EMBO J. 38, e101516 (2019) pdf

I Songailiene, M Rutkauskas, T Sinkunas, E Manakova, S Wittig, C Schmidt, V Siksnys, R Seidel.
Decision-Making in Cascade Complexes Harboring crRNAs of Altered Length.
Cell Reports 28, 3157-3166 (2019) pdf

R Bosire, P Nánási Jr., L Imre, B Dienes, Á Szöőr, A Mázló, A Kovács, R Seidel, G Vámosi, G Szab.
Intercalation of small molecules into DNA in chromatin is primarily controlled by superhelical constraint.
PLoS ONE
14, e0224936 (2019) pdf

2018

A Krivoy, M Rutkauskas, K Kuznedelov, O Musharove, C Rouillon, K Severinov, R Seidel.
Primed CRISPR Adaptation in Escherichia Coli Cells Does Not Depend on Conformational Changes in the Cascade Effector Complex Detected in Vitro.
Nucleic Acids Res. 46 (8), 4087-4098(2018) pdf

T Bayrak, S Helmi, J Ye,  DJ Kauert, J Kelling, T Schönherr, R Weichelt, A Erbe, R Seidel.
DNA mold templated assembly of conductive gold nanowires.
Nano Lett. 18 (3), 2116-2123 (2018) pdf

2017

G Kostiuk, J Dikic, FW Schwarz, G Sasnauskas, R Seidel, V Siksnys.
The dynamics of the monomeric restriction endonuclease BcnI during its interaction with DNA.
Nucleic Acids Res. 45(10), 5968-5979 (2017) pdf

M Rutkauskas, A Krivoy, MD Szczelkun, C Rouillon, R Seidel.
Single-Molecule Insight Into Target Recognition by CRISPR-Cas Complexes.
Methods Enzymol. 582, 239-273 (2017) pdf

2016

C Pinto, K Kasaciunaite, R Seidel, P Cejka.
Human DNA2 possesses a cryptic DNA unwinding activity that functionally integrates with BLM or WRN helicases.
eLife 5, e18574 (2016) pdf

FE Kemmerich, K Kasaciunaite, R Seidel.
Modular magnetic tweezers for single-molecule characterizations of helicases.
Methods. S1046-2023(16) (2016) pdf

S Wierer, P Daldrop, M Ud Din Ahmad, W Boos, M Drescher, W Welte, R Seidel.
TrmBL2 from Pyrococcus furiosus Interacts Both with Double-Stranded and Single-Stranded DNA.
PLoS One 23, e0156098 (2016) pdf

FE Kemmerich, P Daldrop, C Pinto, M Levikova,P Cejka, R Seidel.
Force regulated dynamics of RPA on a DNA fork.
Nucleic Acids Res. 44, 5837-5848 pdf

FE Kemmerich, M Swoboda, DJ Kauert, MS Grieb, S Hahn, FW Schwarz, R Seidel, M Schlierf.
Simultaneous single-molecule force and fluorescence sampling of DNA nanostructure conformations using magnetic tweezers.
Nano Lett. 16, 381-386 (2016)  pdf

2015

P Daldrop, H Brutzer, A Huhle, DJ Kauert, R Seidel. 
Extending the range for force calibration in magnetic tweezers. 
Biophys J. 108, 2550-2561 (2015) pdf

M Rutkauskas, T Sinkunas, I Songailiene, MS Tikhomirova, V Siksnys, R Seidel.
Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection.
Cell Rep. 10, 1534-1543 (2015) pdf

A Czogalla, DJ Kauert, HG Franquelim, V Uzunova, Y Zhang, R Seidel, P Schwille.
Amphipathic DNA Origami Nanoparticles to Scaffold and Deform Lipid Membrane Vesicles.
Angew. Chem. Intl. Ed. 54, 6501-6505 (2015) pdf

A Huhle, D Klaue, H Brutzer, P Daldrop, S Joo, O Otto, UF Keyser, R Seidel.
Camera-based three-dimensional real-time particle tracking at kHz rates and Ångström accuracy.
Nat. Commun. 6, 5885 (2015) pdf

A Czogalla, DJ Kauert, R Seidel, P Schwille, EP Petrov.
DNA origami nanoneedles on freestanding lipid membranes as a tool to observe isotropic-nematic transition in two dimensions.
Nano Lett. 15, 649-655 (2015) pdf

H Brutzer, E Sperling, K. Günther, J Dikic, F Schwarz, D Klaue, F Cichos M Mertig, R Seidel.
DNA under confinement and the use of DNA as confinement
Diffusion fundamentals. 23 (2), 1-16 (2015) pdf

2014

S Helmi, C Ziegler, DJ Kauert, R Seidel.
Shape-controlled synthesis of gold nanostructures using DNA origami molds. 
Nano Lett. 14, 6693-6698 (2014) pdf

MD Szczelkun, MS Tikhomirova, T Sinkunas, G Gasiunas, T Karvelis, P Pschera, V Siksnys, R Seidel.
Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes.
Proc. Natl. Acad. Sci. U.S.A. 111, 9798-9803 (2014) pdf

2013

R Seidel, MD Szczelkun.
Switching roles for a helicase. 
Cell Cycle 12, 3125-3126 (2013) pdf

D Klaue, D Kobbe, F Kemmerich, A Kozikowska, H Puchta, R Seidel.
Fork sensing and strand switching control antagonistic activities of RecQ helicases.
Nat. Commun. 4, 2024 (2013) pdf

FW Schwarz, J Toth, 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, 353-356 (2013) pdf

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. 110, E1992–E200 (2013) pdf

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, 323-330 (2012) *corresponding author pdf

H Brutzer, FW Schwarz, R Seidel.
Scanning evanescent fields using a point-like light source and a nanomechanical DNA gear.
Nano Lett. 12, 473-478 (2012) pdf

N Luzzietti, S Knappe, I Richter, R Seidel.
Nicking enzyme-based internal labelling of DNA at multiple loci.
Nat. Protoc. 7, 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, 5558-5563 (2011) pdf

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, 8042-8051 (2011) pdf

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, 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

Brutzer H, Luzzietti N, Klaue D, Seidel R. 
Energetics at the DNA supercoiling transition.
Biophys J. 98(7), 1267-1276 (2010) pdf

Günther K, Mertig M, Seidel R.
Mechanical and structural properties of YOYO-1 complexed DNA.
Nucleic Acids Res. 38(19), 6526-6532 (2010) pdf

Szczelkun MD, Friedhoff P, Seidel R.
Maintaining a sense of direction during long-range communication on DNA.
Biochem. Soc. Trans. 38(2), 404-409 (2010) pdf

van Aelst K, Tóth J, Ramanathan SP, Schwarz FW, Seidel R, Szczelkun MD.
Type III restriction enzymes cleave DNA by long-range interaction between sites in both head-to-head and tail-to-tail inverted repeat.
Proc. Natl. Acad. Sci. U.S.A. 107(20), 9123-9128 (2010) pdf

Maffeo C, Schöpflin R, Brutzer H, Stehr R, Aksimentiev A, Wedemann G, Seidel R.
DNA-DNA interactions in tight supercoils are described by a small effective charge density..
Phys. Rev. Lett. 105(15), 158101 (2010) pdf

Otto O, Czerwinski F, Gornall JL, Stober G, Oddershede LB, Seidel R, Keyser UF.
Real-time particle tracking at 10,000 fps using optical fiber illumination.
Opt. Express 18(22), 22722-22733 (2010) pdf

2009

Erler A, Wegmann S, Elie-Caille C, Bradshaw CR, Maresca M, R Seidel, u. a.
Conformational Adaptability of Red$ß$ during DNA Annealing and Implications for Its Structural Relationship with Rad52.
J. Mol. Biol., 391(3), 586-598 (2009) pdf

Klaue D, Seidel R.
Torsional stiffness of single superparamagnetic microspheres in an external magnetic field.
Phys. Rev. Lett. 102(2), 028302 (2009) pdf

Ramanathan SP, van Aelst K, Sears A, Peakman LJ, Diffin FM, Szczelkun MD, Seidel R.
Type III restriction enzymes communicate in 1D without looping between their target sites.
Proc. Natl. Acad. Sci. U.S.A., 106(6), 1748-1753 (2009) pdf

2008

Seidel R, Bloom JGP, Dekker C, Szczelkun MD.
Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.
EMBO J., 27(9), 1388-1398 (2008) pdf

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) pdf

2007

van der Heijden T, Seidel R, Modesti M, Kanaar R, Wyman C, Dekker C.
Real-time assembly and disassembly of human RAD51 filaments on individual DNA molecules.
Nucleic Acids Res., 35(17), 5646-5657 (2007) pdf


Crut A, Koster DA, Seidel R, Wiggins CH, Dekker NH.
Fast dynamics of supercoiled DNA revealed by single-molecule experiments.
Proc. Natl. Acad. Sci. U.S.A., 104(29), 11957-11962 (2007) pdf

Seidel R, Dekker C.
Single-molecule studies of nucleic acid motors.
Curr. Opin. Struct. Biol., 17(1), 80-86 (2007) pdf