2024

• Stefanie D. Pritzl, Alptug Ulugöl, Caroline Körösy, Laura Filion, and Jan Lipfert
  Accurate drift-invariant single-molecule force calibration using the Hadamard variance
  Biophys J. 123(22):3964-3976 (2024)

• Marjolein de Jager, Pauline J. Kolbeck, Willem Vanderlinden, Jan Lipfert, and Laura Filion
  Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning
  Biophys J. 123(18):3231-3241 (2024)

• Yi-Yun Lin, Peter Müller, Evdoxia Karagianni, Nicola Hepp, Felix Mueller-Planitz, Willem Vanderlinden, and Jan Lipfert
  Epigenetic Histone Modifications H3K36me3 and H4K5/8/12/16ac Induce Open Polynucleosome Conformations via Different Mechanisms

  J. Mol. Biol. 436(16):168671 (2024)

• Hana Dohnalová, Mona Seifert, Eva Matoušková, Misha Klein, Flávia S. Papini, Jan Lipfert, David Dulin, and Filip Lankas
  Temperature-Dependent Twist of Double-Stranded RNA Probed by Magnetic Tweezer Experiments and Molecular Dynamics Simulations
  J. Phys. Chem. B  128(3):664-675 (2024)

• Aidin Lak, Yihao Wang, Pauline J. Kolbeck, Christoph Pauer, Mohammad Suman Chowdhury, Marco Cassani, Frank Ludwig, Thilo Viereck, Florian Selbach, Philip Tinnefeld, Meinhard Schilling, Tim Liedl, Joe Tavacoli, and Jan Lipfert
  Cooperative dynamics of DNA-grafted magnetic nanoparticles optimize magnetic biosensing and coupling to DNA origami
  Nanoscale 16(15):7678-7689 (2024)

• Magnus S. Bauer, Sophia Gruber, Adina Hausch, Marcelo C.R. Melo, Priscila S.F.C. Gomes, Thomas Nicolaus, Lukas F. Milles, Hermann E. Gaub, Rafael C. Bernardi, and Jan Lipfert

  Single-molecule force stability of the SARS-CoV-2–ACE2 interface in variants-of-concern

  Nature Nanotechnol. 3:399-405 (2024)

• Pauline J. Kolbeck, Miloš Tišma, Brian T. Analikwu, Willem Vanderlinden, Cees Dekker, and Jan Lipfert
  Supercoiling-dependent DNA binding: quantitative modeling and applications to bulk and single-molecule experiments
  Nucleic Acids Res. 52(1):59-72 (2024) 

   

2023

• Pauline J. Kolbeck, Dihia Benaoudia, Léa Chazot-Franguiadakis, Gwendoline Delecourt, Jérôme Mathé, Sha Li, Romeo Bonnet, Pascal Martin, Jan Lipfert, Anna Salvetti, Mordjane Boukhet, Véronique Bennevault, Jean-Christophe Lacroix, Philippe Guégan, and Fabien Montel
  Thermally Switchable Nanogate Based on Polymer Phase Transition

  Nano Letters 23:4862-4869 (2023)  [Link]
• Yi-Yun Lin, Tine Brouns, Pauline J. Kolbeck, Willem Vanderlinden, and Jan Lipfert
  High-yield, ligation-free assembly of DNA constructs with nucleosome positioning sequence repeats for single molecule manipulation assays
  J Biol Chem. 299(7):104874 (2023)  [Link]
• Pauline J. Kolbeck, Mihir Dass, Irina V. Martynenko, Relinde J.A. van Dijk-Moes, Kelly J.H. Brouwer, Alfons van Blaaderen, Willem Vanderlinden, Tim Liedl, and Jan Lipfert
  A DNA origami fiducial for accurate 3D AFM imaging
  Nano Letters 22:1236-1243 (2023) [Link]

2022

• Willem Vanderlinden†, Enrico Skoruppa†, Pauline J Kolbeck, Enrico Carlon*, and Jan Lipfert*
  DNA fluctuations reveal the size and dynamics of topological domains
  PNAS Nexus 1(5):pgac268 (2022) (†Authors contributed equally; *Joint corresponding authorship)
  [PDF][Supplementary Information PDF]
• Sophia Gruber†, Achim Löf†, Adina Hausch, Fabian Kutzki, Res Jöhr, Tobias Obser, Gesa König, Reinhard Schneppenheim, Camilo Aponte-Santamaría, Frauke Gräter, Maria A. Brehm, Martin Benoit*, and Jan Lipfert*
  A conformational transition of the D'D3 domain primes von Willebrand factor for multimerization
  Blood Adv. 6:5198-5209 (2022) (†Authors contributed equally; *Joint corresponding authorship)
  [PDF][Supplementary information PDF]
• Sergio Cruz-León†, Willem Vanderlinden†, Peter Müller, Tobias Forster, Georgina Staudt, Yi-Yun Lin, Jan Lipfert*, and Nadine Schwierz*
  Twisting DNA by Salt  
  Nucleic Acids Res. 50:5726-5738 (2022) (†Authors contributed equally; *Joint corresponding authorship)
  [PDF][Supplementary information PDF]
• Magnus Sebastian Bauer†, Sophia Gruber†, Adina Hausch, Priscila S.F.C. Gomes, Lukas F. Milles, Thomas Nicolaus, Leonard C. Schendel, Pilar López-Navajas, Erik Procko, Daniel Lietha, Marcelo C.R. Melo, Rafael C Bernardi, Hermann E. Gaub, and Jan Lipfert
  A Tethered Ligand Assay to Probe SARS-CoV-2:ACE2 Interactions
  Proc. Natl. Acad. Sci. U.S.A. 119:e2114397119 (†Authors contributed equally)
  [PDF][Supplementary information PDF]
• Sebastian F Konrad, Willem Vanderlinden, Jan Lipfert
  Quantifying epigenetic modulation of nucleosome breathing by high-throughput AFM imaging
  Biophys. J. 121:841-851 (2022)
  [PDF][Supplementary information PDF]

2021

• Sebastian F Konrad, Willem Vanderlinden, Jan Lipfert
  A High-throughput Pipeline to Determine DNA and Nucleosome Conformations by AFM Imaging
  Bio Protoc. 11(19):e4180 (2021)
• Willem Vanderlinden and Jan Lipfert
  A Gentle Twist on DNA
  Physics 14(98):1-3 (2021)
  [PDF]
• Pauline J. Kolbeck, Willem Vanderlinden*, Gerd Gemmecker, Christian Gebhardt, Martin Lehmann, Aidin Lak, Thomas Nicolaus, Thorben Cordes, and Jan Lipfert*
  Molecular structure, DNA binding mode, photophysical properties and recommendations for use of SYBR Gold
  Nucleic Acids Res. 49:5143–5158 (2021) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF][Correction]
• Ann-Kathrin Reichenwallner, Esma Vurmaz, Kristina Battis, Laura Handl, Helin Üstün, Tivadar Mach, Gabriele Hörnig, Jan Lipfert,  and Lukas Richter
  Optical Investigation of Individual Red Blood Cells for Determining Cell Count and Cellular Hemoglobin Concentration in a Microfluidic Channel
  Micromachines 12(4):358 (2021)
  [Link]
• Sebastian F. Konrad, Willem Vanderlinden, Wout Frederickx, Tine Brouns, Bjoern Menze, Steven De Feyter, and Jan Lipfert
  High-throughput AFM analysis reveals unwrapping pathways of H3 and CENP-A nucleosomes
  Nanoscale 13(10):5435-5447 (2021)
  [PDF][Supplementary information PDF]

2020

• Magnus S. Bauer, Sophia Gruber, Lukas F. Milles, Thomas Nicolaus, Leonard C. Schendel, Hermann E. Gaub, and Jan Lipfert
  A Tethered Ligand Assay to Probe the SARS-CoV-2 ACE2 Interaction under Constant Force
  [bioRxiv preprint]
• Helena Lipfert and Jan Lipfert
  Der Elektronikbaukasten Kosmos Easy Elektro – Start (Review, in German)
  Physik in unserer Zeit 51:307 (2020)
  [PDF]
• Sophia Gruber†, Achim Löf†, Steffen M. Sedlak†, Martin Benoit, Hermann E. Gaub, and Jan Lipfert
  Designed Anchoring Geometries Determine Lifetimes of Biotin-Streptavidin Bonds under Constant Load and Enable Ultra-Stable Coupling
  Nanoscale 12:21131-21137 (2020) (†Authors contributed equally)
  [PDF][Supplementary information PDF]
• Thomas Zettl, Xuesong Shi, Steve Bonilla, Steffen M. Sedlak, Jan Lipfert*, and Daniel Herschlag*
  The Structural Ensemble of a Holliday Junction Determined by X-Ray Scattering Interference
  Nucleic Acids Res. 48:8090-8098 (2020) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF]
• Willem Vanderlinden, Pauline J. Kolbeck, Franziska Kriegel, Philipp U. Walker, and Jan Lipfert
  A benchmark data set for the mechanical properties of double-stranded DNA and RNA under torsional constraint
  Data in Brief 30:105404 (2020)
  [PDF]
• Hana Dohnalová, Tomáš Dršata, Jiří Šponer, Martin Zacharias, Jan Lipfert*, Filip Lankaš*
  Compensatory Mechanisms in Temperature Dependence of DNA Double Helical Structure: Bending and Elongation
  Journal of Chemical Theory and Computation, doi.org/10.1021/acs.jctc.0c00037 (2020)  (*Joint corresponding authorship)
  [PDF][Supplementary information PDF]
• Katharina Ott, Linda Martini, Jan Lipfert, and Ulrich Gerland
  Dynamics of the Buckling Transition in Double-Stranded DNA and RNA
  Biophys. J. 118:1690–1701 (2020)
  [PDF]
• Shan Zhao, Mihail Ivilinov Todorov, Ruiyao Cai, Rami AI -Maskari, Hanno Steinke, Elisabeth Kemter, Hongcheng Mai, Zhouyi Rong, Martin Warmer, Karen Stanic, Oliver Schoppe, Johannes Christian Paetzold, Benno Gesierich, Milagros N. Wong, Tobias B. Huber, Marco Duering, Oliver Thomas Bruns, Bjoern Menze, Jan Lipfert, Victor G. Puelles, Eckhard Wolf, Ingo Bechmann, and Ali Ertürk
  Cellular and Molecular Probing of Intact Transparent Human Organs
  Cell 180:796–812 (2020)
  [PDF]
• Aidin Lak, Tamara Kahmann, Simon J. Schaper, Jaroslava Obel, Frank Ludwig, Peter Müller-Buschbaum, and Jan Lipfert
  The Dissociation Rate of Acetylacetonate Ligands Governs the Size of Ferrimagnetic Zinc Ferrite Nanocubes
  ACS Appl Mater Interfaces 12:217-226 (2020)
  [PDF][Supplementary information PDF]

2019

• Abhijeet Pataskar, Willem Vanderlinden, Johannes Emmerig, Aditi Singh, Jan Lipfert, and Vijay K. Tiwari
  Deciphering the Gene Regulatory Landscape Encoded in DNA Biophysical Features
  iScience 21:638–649 (2019)
  [PDF][Supplementary information PDF]
• Willem Vanderlinden, Tine Brouns, Philipp U. Walker, Pauline Kolbeck, Lukas Milles, Wolfgang Ott, Philipp Nickels, Zeger Debyser, and Jan Lipfert
  The Free Energy Landscape of Retroviral Integration
  Nature Communications 10:4738 (2019)
  [PDF][Supplementary information PDF]
• Achim Löf, Philipp U. Walker, Steffen M. Sedlak, Sophia Gruber, Tobias Obser, Maria A. Brehm, Martin Benoit, Jan Lipfert
  Multiplexed protein force spectroscopy reveals equilibrium protein folding dynamics and the low-force response of von Willebrand factor
  Proc. Natl. Acad. Sci. U.S.A. 116:18798-18807 (2019)
  [PDF][Supplementary information PDF]
• Willem Vanderlinden, Pauline J. Kolbeck, Wout Frederickx, Sebastian F. Konrad, Thomas Nicolaus, Carola Lampe, Alexander S. Urban, Cécile Moucheronc, and Jan Lipfert
  Ru(TAP)₃²⁺ uses multivalent binding to accelerate and constrain photo-adduct formation on DNA
  Chem. Commun. 55(60):8764-8767 (2019)
  [Cover][PDF][Supplementary information PDF]
• Jan Lipfert
  Halliday Physik (book review, in German)
  Physik in unserer Zeit 50:48 (2019)
  [PDF]

2018

• Tine Brouns, Herlinde De Keersmaecker, Sebastian Konrad, Noriyuki Kodera, Toshio Ando, Jan Lipfert*, Steven De Feyter*, Willem Vanderlinden*
  Free Energy Landscape and Dynamics of Supercoiled DNA by High-Speed Atomic Force Microscopy
  ACS Nano 12:11907−11916 (2018) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF]
• Miloš T. Ivanović, Linda K. Bruetzel, Roman Shevchuk, Jan Lipfert, and Jochen S. Hub
  Quantifying the influence of the ion cloud on SAXS profiles of charged proteins
  Phys. Chem. Chem. Phys., 20(41):26351-26361 (2018)
  [PDF][Supplementary information PDF] 
• Philipp U. Walker, Willem Vanderlinden, and Jan Lipfert
  Dynamics and Energy Landscape of DNA Plectoneme Nucleation
  Phys. Rev. E 0424121-13 (2018)
  [PDF][Supplementary information PDF]
• Franziska Kriegel, Christian Matek, Tomas Drsata, Klara Kulenkampff, Sophie Tschirpke, Martin Zacharias, Filip Lankas*, and Jan Lipfert*
  The Temperature Dependence of the Helical Twist of DNA
  Nucleic Acids Res. 46(15):7998-8009 (2018) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF] 
• Thomas Zettl, Rebecca S. Mathew, Xuesong Shi, Sebastian Doniach, Daniel Herschlag, Pehr A.B. Harbury, Jan Lipfert
  Gold Nanocrystal Labels Provide a Sequence-to-3D Structure Map in SAXS Reconstructions
  Science Advances 4:eaar4418 (2018)
  [PDF][Supplementary information PDF] 
• Thomas Zettl, Rhiju Das, Pehr A.B. Harbury*, Daniel Herschlag*, Jan Lipfert*, Rebecca S. Mathew, Xuesong Shi
  Recording and Analyzing Nucleic Acid Distance Distributions with X-ray Scattering Interferometry (XSI)
  Current Protocols e54 (2018) (*Joint corresponding authorship)
  [PDF] 
• Franziska Kriegel, Willem Vanderlinden, Thomas Nicolaus, Angelika Kardinal, and Jan Lipfert
  Measuring Single-Molecule Twist and Torque in Multiplexed Magnetic Tweezers
  Methods Mol. Biol. 1814:75-98 (2018)
  [PDF] 
• Linda K. Bruetzel, Philipp Walker, Thomas Gerling, Hendrik Dietz, and Jan Lipfert
  Time-Resolved Small-Angle X-Ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch
  Nano Letters 18:2672-2676 (2018)
  [PDF][Supplementary information PDF]
• Maarten M. van Oene†, Seungkyu Ha†, Tessa Jager, Mina Lee, Francesco Pedaci, Jan Lipfert*, and Nynke H. Dekker*
  Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance
  Biophys. J. 114:1970–1979 (2018) (†Authors contributed equally; *Joint corresponding authorship)
  [Article with supplementary information PDF] 
• Miloš T. Ivanović, Linda K. Bruetzel, Jan Lipfert*, and Jochen S. Hub*
  Temperature-dependent atomic models of detergent micelles refined against small-angle X-ray scattering data
  Angewandte Chemie 57 (2018) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF] 
• Nadine Harrer†, Christina E.M. Schindler†, Linda K. Bruetzel, Ignasi Forné, Johanna Ludwigsen, Axel Imhof, Martin Zacharias, Jan Lipfert*, Felix Mueller-Planitz*
  Structural architecture of the nucleosome remodeler ISWI determined from cross-linking, mass spectrometry, SAXS and modeling
  Structure 26:1-13 (2018) (†Authors contributed equally; *Joint corresponding authorship)
  [PDF][Supplementary information PDF] 

2017

• Sabrina Simoncelli*, Samuel Johnson, Franziska Kriegel, Jan Lipfert*, and Jochen Feldmann
  Stretching and heating single DNA molecules with optically trapped gold-silica Janus particles
  ACS Photonics 4:2843–2851 (*Joint corresponding authorship)
  [PDF][Supplementary information PDF] 
• Stefanos K. Nomidis, Franziska Kriegel, Willem Vanderlinden, Jan Lipfert, and Enrico Carlon
  Twist-Bend Coupling and the Torsional Response of Double-Stranded DNA
  Phys. Rev. Lett. 118:2178011-6 (2017)
  [PDF][Supplementary information PDF]  
• Franziska Kriegel, Niklas Ermann, Ruaridh Forbes, David Dulin, Nynke H. Dekker, and Jan Lipfert
  Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers
  Nucleic Acids Res. 45:5920-5929 (2017)
  [PDF][Supplementary information PDF] 
•  
• Steffen M. Sedlak, Linda K. Bruetzel, and Jan Lipfert
  Quantitative Evaluation of Statistical Errors in Small-Angle X-Ray Scattering Measurements
  J. Appl.Cryst. 50:621–630 (2017)
  [PDF][Supplementary information PDF] 
• Maarten M. van Oene, Laura E. Dickinson, Bronwen Cross, Francesco Pedaci, Jan Lipfert, and Nynke H. Dekker
  Applying torque to the Escherichia coli flagellar motor using magnetic tweezers
  Scientific Reports 7:43285 (2017)
  [PDF][Supplementary information PDF] 
• Franziska Kriegel, Niklas Ermann, and Jan Lipfert
  Probing the Mechanical Properties, Conformational Changes, and Interactions of Nucleic Acids with Magnetic Tweezers
  J. Struct. Biol. 197:26-36 (2017) 
  [PDF]

2016 

• Linda K. Bruetzel, Thomas Gerling, Steffen M. Sedlak, Philipp U. Walker, Wenjun Zheng, Hendrik Dietz, and Jan Lipfert
  Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-Ray Scattering
  Nano Letters 16:4871-9 (2016)
  [PDF][Supplementary information PDF] 
• Thomas Zettl, Rebecca S. Mathew, Sönke Seifert, Sebastian Doniach, Pehr A.B. Harbury, and Jan Lipfert
  Absolute Intra-Molecular Distance Measurements with Ångström-Resolution using Anomalous Small-Angle X-ray Scattering 
  Nano Letters 16:5353-7 (2016)
  [Cover][PDF][Supplementary information PDF] 
• Jochen P. Müller, Achim Löf, Salomé Mielke, Tobias Obser,  Linda Bruetzel, Willem Vanderlinden, Jan Lipfert, Reinhard Schneppenheim, and Martin Benoit
  pH-Dependent Interactions in Dimers Govern Mechanics and Structure of von Willebrand Factor
  Biophys. J. 111:321-322 (2016)
  [PDF with Supplement] 
• Linda K. Bruetzel, Stefan Fischer, Annalena Salditt, Steffen Sedlak, Bert Nickel, and Jan Lipfert
  A Mo-Anode-Based In-House Source for Small-Angle X-Ray Scattering Measurements of Biological Macromolecules
  Rev. Sci. Instrum. 87:025103 (2016)
  [PDF] 
• Jochen P. Müller, Salomé Mielke, Achim Löf, Tobias Obser, Christof Beer, Linda Bruetzel, Diana A. Pippig, Willem Vanderlinden, Jan Lipfert, Reinhard Schneppenheim, and Martin Benoit
  Force sensing by the vascular protein von Willebrand Factor is tuned by a strong intermonomer interaction
  Proc. Natl. Acad. Sci. U.S.A. 113:1208-13 (2016)
  [PDF with Supplement] 

2015  

• Magdalena Gebala, George M. Giambasu, Jan Lipfert, Namita Bisaria, Steve Bonilla, Guangchao Li, Darrin M. York, and Daniel Herschlag
  Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies
  J. Am. Chem. Soc. 137:14705-15 (2015)
  [PDF][Supplementary information PDF] 
• David Dulin, Thijs Cui, Jelmer Cnossen, Margreet W. Docter, Jan Lipfert, and Nynke H. Dekker
  High Spatiotemporal Resolution Magnetic Tweezers for Single-Molecule Force Spectroscopy: Calibration and Applications to DNA Dynamics
  Biophys. J. 109:2113–2125 (2015)
  [PDF] 
• Korbinian Liebl, Tomas Drsata, Filip Lankas, Jan Lipfert, and Martin Zacharias
  Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis
  Nucleic Acids Res. 43:10143-56 (2015)
  [PDF][Supplementary information PDF] 
• Jan Lipfert* and Nynke H. Dekker*
  De RNA-helix lijkt niet altijd op die van DNA (in Dutch)
  Nederlands Tijdschrift voor Natuurkunde 6:224-227 (2015) (*Joint corresponding authorship)
  [PDF] 
• Maarten M. van Oene, Laura E. Dickinson, Francesco Pedaci, Mariana Köber, David Dulin, Jacob W.J. Kerssemakers, Jan Lipfert*, and Nynke H. Dekker*
  Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields
  Phys. Rev. Lett. 114:218301-6 (2015) (*Joint corresponding authorship)
  [PDF][Supplementary information PDF] 
• Rifka Vlijm, Mina Lee, Jan Lipfert, Alexandra Lusser, Cees Dekker, and Nynke H. Dekker
  Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes
  Cell Reports 10:1-10 (2015)
  [PDF]
• Jan Lipfert, Maarten M. van Oene, Mina Lee, Francesco Pedaci, and Nynke H. Dekker
  Torque spectroscopy for the study of rotary motion in biological systems
  Chemical Reviews 115:1449-74 (2015)
  [Cover][PDF] 

2014

• Zhongbo Yu, David Dulin, Jelmer Cnossen, Mariana Köber, Maarten van Oene, Orkide Ordu, Bojk Berghuis, Jan Lipfert, and Nynke H. Dekker
  A force calibration standard for magnetic tweezers
  Rev. Sci. Instrum. 85:123114 (2014)
  [PDF] 
• Jan Lipfert, Gary M. Skinner, Johannes Keegstra, Toivo Hensgens, Tessa Jager, Mariana Köber, Zhongbo Yu, Serge Donkers, Fang-Chieh Chou, Rhiju Das, and Nynke H. Dekker
  Double-Stranded RNA under Force and Torque: Similarities to and Striking Differences from Double- Stranded DNA
  Proc. Natl. Acad. Sci. U.S.A. 111:15408-13 (2014)
  [PDF][Supplementary information PDF] 
• Ryan Oliver, Jan Lipfert, Daniel Fox, Ryan Lo, Justin Kim, Sebastian Doniach, and Linda Columbus
  Tuning micelle dimensions and properties with binary surfactant mixtures
  Langmuir 30:13353-61 (2014)
  [PDF][Supplementary information PDF] 
• Fang-Chieh Chou, Jan Lipfert, and Rhiju Das
  Blind predictions of DNA and RNA tweezers experiments with force and torque
  PLoS Comput. Biol. 10:e1003756 (2014)
  [PDF] 
• Jan Lipfert, Mina Lee, Orkide Ordu, Jacob W.J. Kerssemakers, and Nynke H. Dekker
  Magnetic tweezers for the measurement of twist and torque
  J. Vis. Exp. 19:87 (2014)
  [PDF] 
• Willem Vanderlinden, Jan Lipfert, Jonas Demeulemeester, Zeger Debyser, and Steven De Feyter
  Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes as revealed by scanning force microscopy
  Nanoscale 6:4611-9 (2014)
  [PDF][Supplementary information PDF] 
• Jan Lipfert, Sebastian Doniach, Rhiju Das, and Daniel Herschlag
  Understanding Nucleic Acid-Ion Interactions
  Annual Review of Biochemistry 83:813-41 (2014)
  [PDF] 

2013

• Mina Lee, Jan Lipfert, Humberto Sanchez, Claire Wyman, and Nynke H. Dekker
  Structural and torsional properties of the RAD51-dsDNA nucleoprotein filaments
  Nucleic Acids Res. 41:7023-30 (2013)
  [Cover][PDF][Supplementary information PDF] 
• Ryan C. Oliver, Jan Lipfert, Daniel A. Fox, Ryan H. Lo, Sebastian Doniach, and Linda Columbus
  Dependence of micelle size and shape on detergent alkyl chain length and head group
  PLOS ONE 8:62488 (2013)
  [PDF] 
• David Dulin, Jan Lipfert, M. Charl Moolman, and Nynke H. Dekker
  Studying genomic processes at the single-molecule level: introducing the tools and applications
  Nature Reviews Genetics 14:9-22 (2013)
  [Cover][PDF]

2012

• Adelene Y.L. Sim, Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
  Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering
  Phys. Rev. E 86:021901 (2012)
  [PDF][Supplementary information PDF]
• Xander Janssen†, Jan Lipfert†, Tessa Jager, Renier Daudey, and Nynke H. Dekker
  Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque
  Nano Lett. 12:3634-9 (2012) (†Authors contributed equally)
  [PDF][Supplementary information PDF] 
• Sebastian Doniach and Jan Lipfert
  Small and wide angle X-ray scattering of biological macromolecules and their complexes in solution
  Comprehensive Biophysics 1:376-397 (2012)
  [PDF] 

2011

• Jan Lipfert†, Jacob W.J. Kerssemakers†, Maylon Rojer, and Nynke H. Dekker
  A method to track rotational motion for use in single-molecule biophysics
  Rev. Sci. Instrum. 82:103707 (2011) (†Authors contributed equally)
  [PDF]
• Jan Lipfert†, Matthew Wiggin†, Jacob W.J. Kerssemakers, Francesco Pedaci, and Nynke H. Dekker
  Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids 
  Nature Communications 2:439 (2011) (†Authors contributed equally)
  [PDF][Supplementary information PDF]
  See also:
  Corrigendum: Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids
  Nature Communications 6:7192 (2015)
  [PDF] 

2010

• Jan Lipfert, Jacob W.J. Kerssemakers, Tessa Jager, and Nynke H. Dekker
  Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
  Nature Methods 7:977-80 (2010)
  [PDF][Supplementary information PDF]
• Jan Lipfert, Sven Klijnhout, and Nynke H. Dekker
  Torsional sensing of small-molecule binding using magnetic tweezers 
  Nucleic Acids Res. 38:7122-32 (2010)
  [PDF] 
• Aartjan J. teVelthuis, Jacob W.J. Kerssemakers, Jan Lipfert, and Nynke H. Dekker
  Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data
  Biophys. J. 99:1292-302 (2010)
  [PDF] 
• Jan Lipfert†, Adelene Y.L. Sim†, Daniel Herschlag, and Sebastian Doniach
  Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding
  RNA 16:708-19 (2010) (†Authors contributed equally)
  [PDF] 
• Mona Ali, Jan Lipfert, Sönke Seifert, Daniel Herschlag, and Sebastian Doniach
  The ligand-free state of the TPP riboswitch: a partially folded RNA structure
  J. Mol. Biol. 396:153-65 (2010)
  [PDF] 
• S. Menze, C. Menze, J. Lipfert, B. Menze, and G. Harsch
  Der Vorfahr aus der Bronzezeit (in German)
  Praxis der Naturwissenschaften - Chemie in der Schule 5:6 (2010) 

2009

• Vincent B. Chu, Jan Lipfert, Yu Bai, Vijay S. Pande, Sebastian Doniach, and Daniel Herschlag
  Do conformational biases of simple helical junctions influence RNA folding stability and specificity?
  RNA 15:2195-205 (2009)
  [PDF]
• Jan Lipfert, Xiaomin Hao, and Nynke H. Dekker
  Quantitative modeling and optimization of magnetic tweezers
  Biophys. J. 96:5040-9 (2009)
  [PDF] [Supplementary information PDF] [Example calculations]
• Jan Lipfert, Daniel A. Koster, Igor D. Vilfan, Susanne Hage, and Nynke H. Dekker
  Single-molecule magnetic tweezers studies of type IB topoisomerases
  Methods Mol. Biol. 582:71-89 (2009)
  [PDF] 
• Igor D. Vilfan, Jan Lipfert, Daniel A. Koster, Serge G. Lemay, and Nynke H. Dekker
  Magnetic tweezers for single-molecule experiments
  Handbook of Single-Molecule Biophysics, Springer (2009)
  [PDF] 
• Linda Columbus, Jan Lipfert, K. Jambunathan, Daniel A. Fox, Adelene Y.L. Sim, Sebastian Doniach, and Scott A. Lesley
  Mixing and matching detergents for membrane protein NMR structure determination
  J. Am. Chem. Soc. 131:7320-6 (2009)
  [PDF] [Supplementary information PDF] 
• Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
  Riboswitch conformations revealed by small-angle X-ray scattering
  Methods Mol. Biol. 540:141-59 (2009)
  [PDF] 
• Sebastian Doniach and Jan Lipfert
  Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs
  Methods Enzymol. 469:237-51 (2009)
  [PDF] 

2008

• Vincent B. Chu, Yu Bai, Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
  A repulsive field: advances in the electrostatics of the ion atmosphere
  Curr. Opin. Chem. Biol. 12:619-25 (2008)
  [PDF] 
• JanLipfert†,JonathanOuellet†,DavidG.Norman,SebastianDoniach,andDavidM.J.Lilley
  The complete VS ribozyme in solution studied by small-angle X-ray scattering
  Structure 16:1357-67 (2008) (†Authors contributed equally)
  [PDF] [Supplementary information PDF] 
• Yu Bai, Vincent B. Chu, Jan Lipfert, Vijay S. Pande, Daniel Herschlag, and Sebastian Doniach
  Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble
  J. Am. Chem. Soc. 130:12334-41 (2008)
  [PDF] [Supplementary information PDF] 
• Benjamin J. Spink, Sivaraj Sivaramakrishnan, Jan Lipfert, Sebastian Doniach, and James A. Spudich
  Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI
  Nature Struct. Mol. Biol. 15:591-7 (2008)
  [PDF] [Supplementary information PDF] 

2007