Molecular Biophysics (Jan Lipfert)
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Publications

Many of our journal publications are available through PubMed and Google Scholar. 

2021

  • 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. doi.org/10.1093/nar/gkab265 (2021) (*Joint corresponding authorship)
    [PDF][Supplementary information PDF]
  • 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
    Submitted [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

  • Yu Bai, Kevin Travers, Vincent B. Chu, Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
    Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids
    J. Am. Chem. Soc. 129:14981-8 (2007)
    [PDF] [Supplementary information PDF] 
  • Jan Lipfert, Linda Columbus, Vincent B. Chu, Scott A. Lesley, and Sebastian Doniach
    Size and shape of detergent micelles determined by small-angle X-ray scattering
    J. Phys. Chem. B. 111:12427-38 (2007)
    [PDF] 
  • Vincent B. Chu, Yu Bai, Jan Lipfert, Daniel Herschlag, and Sebastian Doniach
    Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory
    Biophys. J. 93:3202-9 (2007)
    [PDF] 
  • Jan Lipfert and Sebastian Doniach
    Small-angle X-ray scattering from RNA, proteins, and protein complexes
    Annual Reviews Biophys. Biomol. Struct. 36:307-27 (2007)
    [PDF] 
  • Jan Lipfert, Rhiju Das, Vincent B. Chu, Madhuri Kudaravalli, Nathan Boyd, Daniel Herschlag, and Sebastian Doniach
    Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
    J. Mol. Biol. 365:1393-406 (2007)
    [PDF] [Supplementary information PDF] 
  • Jan Lipfert, Vincent B. Chu, Yu Bai, Daniel Herschlag, and Sebastian Doniach
    Low resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling
    J. Appl. Cryst. 40:235-239 (2007)
    [PDF] 
  • Jan Lipfert, Linda Columbus, Vincent B. Chu, and Sebastian Doniach
    Analysis of small-angle X-ray scattering data of protein-detergent complexes by singular value decomposition
    J. Appl. Cryst. 40:229-234 (2007)
    [PDF]
     

2006

  • Gautam Dantas, Alexander L. Watters, Bradley Lunde, Ziad Eletr, Nancy Isern, Jan Lipfert, Sebastian Doniach, Brian Kuhlman, Barry L. Stoddard, Gabriele Varani, and David Baker
    Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution
    J. Mol. Biol. 362:1004-1024 (2006)
    [PDF] [Supplementary information 1] [Supplementary information 2]
  • Jan Lipfert, Ian S. Millett, Sönke Seifert, and Sebastian Doniach
    A sample holder for small-angle X-ray scattering static and flow cell measurements
    Rev. Sci. Instrum. 77:046108 (2006)
    [PDF] [Supplementary information PDF] 
  • Linda Columbus, Jan Lipfert, Heath Klock, Ian S. Millett, Sebastian Doniach, and Scott Lesley
    Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination 
    Protein Sci. 15:1-15 (2006)
    [PDF] [Supplementary information PDF] 

2005

  • Bojan Zagrovic, Jan Lipfert, Erik J. Sorin, Ian S. Millett, Wilfred F. van Gunsteren, Sebastian Doniach, and Vijay S. Pande
    Unusual compactness of a polyproline type II structure
    Proc. Natl. Acad. Sci. U.S.A. 102:11698-11703 (2005)
    [PDF]
  • Jan Lipfert, Joel Franklin, Fang Wu, and Sebastian Doniach
    Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing
    J. Mol. Biol. 349:648-658 (2005)
    [PDF] [Supplementary information PDF] 

2004

  • Jan Lipfert, Jorge Llano, and Leif A. Eriksson
    Radiation-Induced Damage in Serine Phosphate - Insights into a Mechanism for Direct DNA Strand Breakage
    J. Phys. Chem. B 108:8036-8042 (2004)
    [PDF]

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