Jan Lipfert, Ph.D. - Publications

Affiliations: 
Physics University of Munich, München, Bayern, Germany 
Area:
biophysics, nucleic acids, magnetic tweezers, SAXS
Website:
http://www.biophysik.physik.uni-muenchen.de/personen/group_leader/lipfert_jan/

80 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
2020 Zettl T, Shi X, Bonilla S, Sedlak SM, Lipfert J, Herschlag D. The structural ensemble of a Holliday junction determined by X-ray scattering interference. Nucleic Acids Research. PMID 32597986 DOI: 10.1093/Nar/Gkaa509  0.72
2018 Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X. Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Current Protocols in Nucleic Acid Chemistry. 73: e54. PMID 29927110 DOI: 10.1002/Cpnc.54  0.72
2018 Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J. Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions. Science Advances. 4: eaar4418. PMID 29806025 DOI: 10.1126/Sciadv.Aar4418  1
2016 Zettl T, Mathew RS, Seifert S, Harbury PA, Doniach S, Lipfert J. Absolute Intra-Molecular Distance Measurements with Ångström-Resolution using Anomalous Small-Angle X-ray Scattering. Nano Letters. PMID 27244097 DOI: 10.1021/Acs.Nanolett.6B01160  1
2016 Bruetzel LK, Fischer S, Salditt A, Sedlak SM, Nickel B, Lipfert J. A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules. The Review of Scientific Instruments. 87: 025103. PMID 26931887 DOI: 10.1063/1.4940936  1
2016 Müller JP, Mielke S, Löf A, Obser T, Beer C, Bruetzel LK, Pippig DA, Vanderlinden W, Lipfert J, Schneppenheim R, Benoit M. Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction. Proceedings of the National Academy of Sciences of the United States of America. PMID 26787887 DOI: 10.1073/Pnas.1516214113  1
2015 Dulin D, Cui TJ, Cnossen J, Docter MW, Lipfert J, Dekker NH. High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics. Biophysical Journal. 109: 2113-25. PMID 26588570 DOI: 10.1016/J.Bpj.2015.10.018  1
2015 Gebala M, Giambasu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D. Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting Studies. Journal of the American Chemical Society. PMID 26517731 DOI: 10.1021/Jacs.5B08395  1
2015 Vlijm R, Lee M, Lipfert J, Lusser A, Dekker C, Dekker NH. Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes. Cell Reports. 10: 216-25. PMID 25578730 DOI: 10.1016/J.Celrep.2014.12.022  1
2015 Van Oene MM, Dickinson LE, Pedaci F, Köber M, Dulin D, Lipfert J, Dekker NH. Biological magnetometry: Torque on superparamagnetic beads in magnetic fields Physical Review Letters. 114. DOI: 10.1103/PhysRevLett.114.218301  1
2015 Lipfert J, Van Oene MM, Lee M, Pedaci F, Dekker NH. Torque spectroscopy for the study of rotary motion in biological systems Chemical Reviews. 115: 1449-1474. DOI: 10.1021/cr500119k  1
2014 Yu Z, Dulin D, Cnossen J, Köber M, van Oene MM, Ordu O, Berghuis BA, Hensgens T, Lipfert J, Dekker NH. A force calibration standard for magnetic tweezers. The Review of Scientific Instruments. 85: 123114. PMID 25554279 DOI: 10.1063/1.4904148  1
2014 Yu Z, Dulin D, Cnossen J, Köber M, van Oene MM, Ordu O, Berghuis BA, Hensgens T, Lipfert J, Dekker NH. A force calibration standard for magnetic tweezers. The Review of Scientific Instruments. 85: 123114. PMID 25554279 DOI: 10.1063/1.4904148  1
2014 Lipfert J, Skinner GM, Keegstra JM, Hensgens T, Jager T, Dulin D, Köber M, Yu Z, Donkers SP, Chou FC, Das R, Dekker NH. Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA. Proceedings of the National Academy of Sciences of the United States of America. 111: 15408-13. PMID 25313077 DOI: 10.1073/Pnas.1407197111  0.72
2014 Oliver RC, Lipfert J, Fox DA, Lo RH, Kim JJ, Doniach S, Columbus L. Tuning micelle dimensions and properties with binary surfactant mixtures. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 13353-61. PMID 25312254 DOI: 10.1021/La503458N  1
2014 Oliver RC, Lipfert J, Fox DA, Lo RH, Kim JJ, Doniach S, Columbus L. Tuning micelle dimensions and properties with binary surfactant mixtures. Langmuir : the Acs Journal of Surfaces and Colloids. 30: 13353-61. PMID 25312254 DOI: 10.1021/La503458N  1
2014 Chou FC, Lipfert J, Das R. Blind predictions of DNA and RNA tweezers experiments with force and torque Plos Computational Biology. 10: e1003756. PMID 25102226 DOI: 10.1371/Journal.Pcbi.1003756  1
2014 Lipfert J, Lee M, Ordu O, Kerssemakers JWJ, Dekker NH. Magnetic tweezers for the measurement of twist and torque Journal of Visualized Experiments : Jove. PMID 24894412 DOI: 10.3791/51503  1
2014 Vanderlinden W, Lipfert J, Demeulemeester J, Debyser Z, De Feyter S. Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes revealed by scanning force microscopy. Nanoscale. 6: 4611-9. PMID 24632996 DOI: 10.1039/C4Nr00022F  1
2014 Vanderlinden W, Lipfert J, Demeulemeester J, Debyser Z, De Feyter S. Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes revealed by scanning force microscopy. Nanoscale. 6: 4611-9. PMID 24632996 DOI: 10.1039/C4Nr00022F  1
2014 Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/Annurev-Biochem-060409-092720  1
2014 Lipfert J, Doniach S, Das R, Herschlag D. Understanding nucleic acid-ion interactions. Annual Review of Biochemistry. 83: 813-41. PMID 24606136 DOI: 10.1146/Annurev-Biochem-060409-092720  1
2013 Lee M, Lipfert J, Sanchez H, Wyman C, Dekker NH. Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament Nucleic Acids Research. 41: 7023-7030. PMID 23703213 DOI: 10.1093/Nar/Gkt425  1
2013 Oliver RC, Lipfert J, Fox DA, Lo RH, Doniach S, Columbus L. Dependence of micelle size and shape on detergent alkyl chain length and head group. Plos One. 8: e62488. PMID 23667481 DOI: 10.1371/Journal.Pone.0062488  1
2013 Oliver RC, Lipfert J, Fox DA, Lo RH, Doniach S, Columbus L. Dependence of micelle size and shape on detergent alkyl chain length and head group. Plos One. 8: e62488. PMID 23667481 DOI: 10.1371/Journal.Pone.0062488  1
2013 Dulin D, Lipfert J, Moolman MC, Dekker NH. Studying genomic processes at the single-molecule level: Introducing the tools and applications Nature Reviews Genetics. 14: 9-22. PMID 23150038 DOI: 10.1038/Nrg3316  1
2012 Sim AY, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 021901. PMID 23005779 DOI: 10.1103/Physreve.86.021901  1
2012 Sim AY, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 021901. PMID 23005779 DOI: 10.1103/Physreve.86.021901  1
2012 Janssen XJA, Lipfert J, Jager T, Daudey R, Beekman J, Dekker NH. Electromagnetic torque tweezers: A versatile approach for measurement of single-molecule twist and torque Nano Letters. 12: 3634-3639. DOI: 10.1021/nl301330h  1
2012 Doniach S, Lipfert J. Small and wide angle x-ray scattering from biological macromolecules and their complexes in solution Comprehensive Biophysics. 1: 376-397. DOI: 10.1016/B978-0-12-374920-8.00122-3  1
2011 Lipfert J, Kerssemakers JJW, Rojer M, Dekker NH. A method to track rotational motion for use in single-molecule biophysics Review of Scientific Instruments. 82. PMID 22047303 DOI: 10.1063/1.3650461  1
2011 Lipfert J, Wiggin M, Kerssemakers JWJ, Pedaci F, Dekker NH. Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids Nature Communications. 2. PMID 21863006 DOI: 10.1038/Ncomms1450  1
2010 Lipfert J, Kerssemakers JWJ, Jager T, Dekker NH. Magnetic torque tweezers: Measuring torsional stiffness in DNA and RecA-DNA filaments Nature Methods. 7: 977-980. PMID 20953173 DOI: 10.1038/Nmeth.1520  1
2010 Te Velthuis AJW, Kerssemakers JWJ, Lipfert J, Dekker NH. Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data Biophysical Journal. 99: 1292-1302. PMID 20713015 DOI: 10.1016/J.Bpj.2010.06.008  1
2010 Lipfert J, Klijnhout S, Dekker NH. Torsional sensing of small-molecule binding using magnetic tweezers Nucleic Acids Research. 38: 7122-7132. PMID 20624816 DOI: 10.1093/Nar/Gkq598  1
2010 Lipfert J, Sim AY, Herschlag D, Doniach S. Dissecting electrostatic screening, specific ion binding, and ligand binding in an energetic model for glycine riboswitch folding. Rna (New York, N.Y.). 16: 708-19. PMID 20194520 DOI: 10.1261/Rna.1985110  1
2010 Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure. Journal of Molecular Biology. 396: 153-65. PMID 19925806 DOI: 10.1016/J.Jmb.2009.11.030  1
2010 Ali M, Lipfert J, Seifert S, Herschlag D, Doniach S. The ligand-free state of the TPP riboswitch: a partially folded RNA structure. Journal of Molecular Biology. 396: 153-65. PMID 19925806 DOI: 10.1016/J.Jmb.2009.11.030  1
2009 Doniach S, Lipfert J. Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods in Enzymology. 469: 237-51. PMID 20946792 DOI: 10.1016/S0076-6879(09)69011-X  1
2009 Doniach S, Lipfert J. Use of small angle X-ray scattering (SAXS) to characterize conformational states of functional RNAs. Methods in Enzymology. 469: 237-51. PMID 20946792 DOI: 10.1016/S0076-6879(09)69011-X  1
2009 Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? Rna (New York, N.Y.). 15: 2195-205. PMID 19850914 DOI: 10.1261/Rna.1747509  1
2009 Chu VB, Lipfert J, Bai Y, Pande VS, Doniach S, Herschlag D. Do conformational biases of simple helical junctions influence RNA folding stability and specificity? Rna (New York, N.Y.). 15: 2195-205. PMID 19850914 DOI: 10.1261/Rna.1747509  1
2009 Lipfert J, Koster DA, Vilfan ID, Hage S, Dekker NH. Single-molecule magnetic tweezers studies of type IB topoisomerases. Methods in Molecular Biology (Clifton, N.J.). 582: 71-89. PMID 19763943 DOI: 10.1007/978-1-60761-340-4_7  1
2009 Lipfert J, Hao X, Dekker NH. Quantitative modeling and optimization of magnetic tweezers Biophysical Journal. 96: 5040-5049. PMID 19527664 DOI: 10.1016/J.Bpj.2009.03.055  1
2009 Columbus L, Lipfert J, Jambunathan K, Fox DA, Sim AY, Doniach S, Lesley SA. Mixing and matching detergents for membrane protein NMR structure determination. Journal of the American Chemical Society. 131: 7320-6. PMID 19425578 DOI: 10.1021/Ja808776J  1
2009 Columbus L, Lipfert J, Jambunathan K, Fox DA, Sim AY, Doniach S, Lesley SA. Mixing and matching detergents for membrane protein NMR structure determination. Journal of the American Chemical Society. 131: 7320-6. PMID 19425578 DOI: 10.1021/Ja808776J  1
2009 Lipfert J, Herschlag D, Doniach S. Riboswitch conformations revealed by small-angle X-ray scattering. Methods in Molecular Biology (Clifton, N.J.). 540: 141-59. PMID 19381558 DOI: 10.1007/978-1-59745-558-9_11  1
2009 Lipfert J, Herschlag D, Doniach S. Riboswitch conformations revealed by small-angle X-ray scattering. Methods in Molecular Biology (Clifton, N.J.). 540: 141-59. PMID 19381558 DOI: 10.1007/978-1-59745-558-9_11  1
2008 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. A repulsive field: advances in the electrostatics of the ion atmosphere. Current Opinion in Chemical Biology. 12: 619-25. PMID 19081286 DOI: 10.1016/J.Cbpa.2008.10.010  1
2008 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. A repulsive field: advances in the electrostatics of the ion atmosphere. Current Opinion in Chemical Biology. 12: 619-25. PMID 19081286 DOI: 10.1016/J.Cbpa.2008.10.010  1
2008 Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure (London, England : 1993). 16: 1357-67. PMID 18786398 DOI: 10.1016/J.Str.2008.07.007  1
2008 Lipfert J, Ouellet J, Norman DG, Doniach S, Lilley DM. The complete VS ribozyme in solution studied by small-angle X-ray scattering. Structure (London, England : 1993). 16: 1357-67. PMID 18786398 DOI: 10.1016/J.Str.2008.07.007  1
2008 Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society. 130: 12334-41. PMID 18722445 DOI: 10.1021/Ja800854U  1
2008 Bai Y, Chu VB, Lipfert J, Pande VS, Herschlag D, Doniach S. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society. 130: 12334-41. PMID 18722445 DOI: 10.1021/Ja800854U  1
2008 Spink BJ, Sivaramakrishnan S, Lipfert J, Doniach S, Spudich JA. Long single alpha-helical tail domains bridge the gap between structure and function of myosin VI. Nature Structural & Molecular Biology. 15: 591-7. PMID 18511944 DOI: 10.1038/Nsmb.1429  1
2008 Lipfert J. Physics in daily life: Drink or drive - Commentary Europhysics News. 39: 37. DOI: 10.1051/epn:2008306  1
2007 Bai Y, Greenfeld M, Travers KJ, Chu VB, Lipfert J, Doniach S, Herschlag D. Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids. Journal of the American Chemical Society. 129: 14981-8. PMID 17990882 DOI: 10.1021/Ja075020G  1
2007 Lipfert J, Columbus L, Chu VB, Lesley SA, Doniach S. Size and shape of detergent micelles determined by small-angle X-ray scattering. The Journal of Physical Chemistry. B. 111: 12427-38. PMID 17924686 DOI: 10.1021/Jp073016L  1
2007 Lipfert J, Columbus L, Chu VB, Lesley SA, Doniach S. Size and shape of detergent micelles determined by small-angle X-ray scattering. The Journal of Physical Chemistry. B. 111: 12427-38. PMID 17924686 DOI: 10.1021/Jp073016L  1
2007 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophysical Journal. 93: 3202-9. PMID 17604318 DOI: 10.1529/Biophysj.106.099168  1
2007 Chu VB, Bai Y, Lipfert J, Herschlag D, Doniach S. Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory. Biophysical Journal. 93: 3202-9. PMID 17604318 DOI: 10.1529/Biophysj.106.099168  1
2007 Lipfert J, Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Review of Biophysics and Biomolecular Structure. 36: 307-27. PMID 17284163 DOI: 10.1146/Annurev.Biophys.36.040306.132655  1
2007 Lipfert J, Doniach S. Small-angle X-ray scattering from RNA, proteins, and protein complexes. Annual Review of Biophysics and Biomolecular Structure. 36: 307-27. PMID 17284163 DOI: 10.1146/Annurev.Biophys.36.040306.132655  1
2007 Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/J.Jmb.2006.10.022  1
2007 Lipfert J, Das R, Chu VB, Kudaravalli M, Boyd N, Herschlag D, Doniach S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. Journal of Molecular Biology. 365: 1393-406. PMID 17118400 DOI: 10.1016/J.Jmb.2006.10.022  1
2007 Lipfert J, Columbus L, Chu VB, Doniach S. Analysis of small-angle X-ray scattering data of protein-detergent complexes by singular value decomposition Journal of Applied Crystallography. 40: s235-s239. DOI: 10.1107/S0021889807005791  1
2007 Lipfert J, Columbus L, Chu VB, Doniach S. Analysis of small-angle X-ray scattering data of protein-detergent complexes by singular value decomposition Journal of Applied Crystallography. 40: s235-s239. DOI: 10.1107/S0021889807005791  1
2007 Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S. Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling Journal of Applied Crystallography. 40: s229-s234. DOI: 10.1107/S0021889807001707  1
2007 Lipfert J, Chu VB, Bai Y, Herschlag D, Doniach S. Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling Journal of Applied Crystallography. 40: s229-s234. DOI: 10.1107/S0021889807001707  1
2006 Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/J.Jmb.2006.07.092  1
2006 Dantas G, Watters AL, Lunde BM, Eletr ZM, Isern NG, Roseman T, Lipfert J, Doniach S, Tompa M, Kuhlman B, Stoddard BL, Varani G, Baker D. Mis-translation of a computationally designed protein yields an exceptionally stable homodimer: implications for protein engineering and evolution. Journal of Molecular Biology. 362: 1004-24. PMID 16949611 DOI: 10.1016/J.Jmb.2006.07.092  1
2006 Columbus L, Lipfert J, Klock H, Millett I, Doniach S, Lesley SA. Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination. Protein Science : a Publication of the Protein Society. 15: 961-75. PMID 16597824 DOI: 10.1110/Ps.051874706  1
2006 Columbus L, Lipfert J, Klock H, Millett I, Doniach S, Lesley SA. Expression, purification, and characterization of Thermotoga maritima membrane proteins for structure determination. Protein Science : a Publication of the Protein Society. 15: 961-75. PMID 16597824 DOI: 10.1110/Ps.051874706  1
2006 Lipfert J, Millett IS, Seifert S, Doniach S. Sample holder for small-angle x-ray scattering static and flow cell measurements Review of Scientific Instruments. 77. DOI: 10.1063/1.2194484  1
2006 Lipfert J, Millett IS, Seifert S, Doniach S. Sample holder for small-angle x-ray scattering static and flow cell measurements Review of Scientific Instruments. 77. DOI: 10.1063/1.2194484  1
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  1
2005 Zagrovic B, Lipfert J, Sorin EJ, Millett IS, van Gunsteren WF, Doniach S, Pande VS. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Sciences of the United States of America. 102: 11698-703. PMID 16085707 DOI: 10.1073/Pnas.0409693102  1
2005 Lipfert J, Franklin J, Wu F, Doniach S. Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. Journal of Molecular Biology. 349: 648-58. PMID 15896350 DOI: 10.1016/J.Jmb.2005.03.083  1
2005 Lipfert J, Franklin J, Wu F, Doniach S. Protein misfolding and amyloid formation for the peptide GNNQQNY from yeast prion protein Sup35: simulation by reaction path annealing. Journal of Molecular Biology. 349: 648-58. PMID 15896350 DOI: 10.1016/J.Jmb.2005.03.083  1
2004 Lipfert J, Llano J, Eriksson LA. Radiation-induced damage in serine phosphate - Insights into a mechanism for direct DNA strand breakage Journal of Physical Chemistry B. 108: 8036-8042. DOI: 10.1021/Jp037499E  1
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