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Items: 1 to 50 of 75

1.

Ru(TAP)32+ uses multivalent binding to accelerate and constrain photo-adduct formation on DNA.

Vanderlinden W, Kolbeck PJ, Frederickx W, Konrad SF, Nicolaus T, Lampe C, Urban AS, Moucheron C, Lipfert J.

Chem Commun (Camb). 2019 Jul 23;55(60):8764-8767. doi: 10.1039/c9cc02838b.

PMID:
31139806
2.

Free Energy Landscape and Dynamics of Supercoiled DNA by High-Speed Atomic Force Microscopy.

Brouns T, De Keersmaecker H, Konrad SF, Kodera N, Ando T, Lipfert J, De Feyter S, Vanderlinden W.

ACS Nano. 2018 Dec 26;12(12):11907-11916. doi: 10.1021/acsnano.8b06994. Epub 2018 Oct 29.

PMID:
30346700
3.

Quantifying the influence of the ion cloud on SAXS profiles of charged proteins.

Ivanović MT, Bruetzel LK, Shevchuk R, Lipfert J, Hub JS.

Phys Chem Chem Phys. 2018 Nov 7;20(41):26351-26361. doi: 10.1039/c8cp03080d. Epub 2018 Oct 10.

PMID:
30303199
4.

The temperature dependence of the helical twist of DNA.

Kriegel F, Matek C, Dršata T, Kulenkampff K, Tschirpke S, Zacharias M, Lankaš F, Lipfert J.

Nucleic Acids Res. 2018 Sep 6;46(15):7998-8009. doi: 10.1093/nar/gky599.

5.

Publisher's Note: Biological Magnetometry: Torque on Superparamagnetic Beads in Magnetic Fields [Phys. Rev. Lett. 114, 218301 (2015)].

van Oene MM, Dickinson LE, Pedaci F, Köber M, Dulin D, Lipfert J, Dekker NH.

Phys Rev Lett. 2018 Jun 22;120(25):259901. doi: 10.1103/PhysRevLett.120.259901.

PMID:
29979053
6.

Measuring Single-Molecule Twist and Torque in Multiplexed Magnetic Tweezers.

Kriegel F, Vanderlinden W, Nicolaus T, Kardinal A, Lipfert J.

Methods Mol Biol. 2018;1814:75-98. doi: 10.1007/978-1-4939-8591-3_6.

PMID:
29956228
7.

Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).

Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X.

Curr Protoc Nucleic Acid Chem. 2018 Jun;73(1):e54. doi: 10.1002/cpnc.54. Epub 2018 Jun 7.

8.

Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.

Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J.

Sci Adv. 2018 May 25;4(5):eaar4418. doi: 10.1126/sciadv.aar4418. eCollection 2018 May.

9.

Corrigendum: Applying torque to the Escherichia coli flagellar motor using magnetic tweezers.

van Oene MM, Dickinson LE, Cross B, Pedaci F, Lipfert J, Dekker NH.

Sci Rep. 2018 May 18;8:46980. doi: 10.1038/srep46980.

10.

Quantifying the Precision of Single-Molecule Torque and Twist Measurements Using Allan Variance.

van Oene MM, Ha S, Jager T, Lee M, Pedaci F, Lipfert J, Dekker NH.

Biophys J. 2018 Apr 24;114(8):1970-1979. doi: 10.1016/j.bpj.2018.02.039.

11.

Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch.

Bruetzel LK, Walker PU, Gerling T, Dietz H, Lipfert J.

Nano Lett. 2018 Apr 11;18(4):2672-2676. doi: 10.1021/acs.nanolett.8b00592. Epub 2018 Mar 27.

PMID:
29554806
12.

Temperature-Dependent Atomic Models of Detergent Micelles Refined against Small-Angle X-Ray Scattering Data.

Ivanović MT, Bruetzel LK, Lipfert J, Hub JS.

Angew Chem Int Ed Engl. 2018 May 14;57(20):5635-5639. doi: 10.1002/anie.201713303. Epub 2018 Apr 18.

PMID:
29532982
13.

Structural Architecture of the Nucleosome Remodeler ISWI Determined from Cross-Linking, Mass Spectrometry, SAXS, and Modeling.

Harrer N, Schindler CEM, Bruetzel LK, Forné I, Ludwigsen J, Imhof A, Zacharias M, Lipfert J, Mueller-Planitz F.

Structure. 2018 Feb 6;26(2):282-294.e6. doi: 10.1016/j.str.2017.12.015. Epub 2018 Jan 27.

14.

Twist-Bend Coupling and the Torsional Response of Double-Stranded DNA.

Nomidis SK, Kriegel F, Vanderlinden W, Lipfert J, Carlon E.

Phys Rev Lett. 2017 May 26;118(21):217801. doi: 10.1103/PhysRevLett.118.217801. Epub 2017 May 26.

PMID:
28598642
15.

Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers.

Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J.

Nucleic Acids Res. 2017 Jun 2;45(10):5920-5929. doi: 10.1093/nar/gkx280.

16.

Quantitative evaluation of statistical errors in small-angle X-ray scattering measurements.

Sedlak SM, Bruetzel LK, Lipfert J.

J Appl Crystallogr. 2017 Mar 29;50(Pt 2):621-630. doi: 10.1107/S1600576717003077. eCollection 2017 Apr 1.

17.

Applying torque to the Escherichia coli flagellar motor using magnetic tweezers.

van Oene MM, Dickinson LE, Cross B, Pedaci F, Lipfert J, Dekker NH.

Sci Rep. 2017 Mar 7;7:43285. doi: 10.1038/srep43285. Erratum in: Sci Rep. 2018 May 18;8:46980.

18.

Risk factors for cartilage damage and osteoarthritis of the elbow joint: case-control study and systematic literature review.

Spahn G, Lipfert JU, Maurer C, Hartmann B, Schiele R, Klemm HT, Grifka J, Hofmann GO.

Arch Orthop Trauma Surg. 2017 Apr;137(4):557-566. doi: 10.1007/s00402-017-2654-6. Epub 2017 Feb 24. Review.

PMID:
28236186
19.

pH-Dependent Interactions in Dimers Govern the Mechanics and Structure of von Willebrand Factor.

Müller JP, Löf A, Mielke S, Obser T, Bruetzel LK, Vanderlinden W, Lipfert J, Schneppenheim R, Benoit M.

Biophys J. 2016 Jul 26;111(2):312-322. doi: 10.1016/j.bpj.2016.06.022.

20.

Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers.

Kriegel F, Ermann N, Lipfert J.

J Struct Biol. 2017 Jan;197(1):26-36. doi: 10.1016/j.jsb.2016.06.022. Epub 2016 Jun 29. Review.

PMID:
27368129
21.

Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering.

Bruetzel LK, Gerling T, Sedlak SM, Walker PU, Zheng W, Dietz H, Lipfert J.

Nano Lett. 2016 Aug 10;16(8):4871-9. doi: 10.1021/acs.nanolett.6b01338. Epub 2016 Jul 27.

PMID:
27356232
22.

Absolute Intramolecular Distance Measurements with Angstrom-Resolution Using Anomalous Small-Angle X-ray Scattering.

Zettl T, Mathew RS, Seifert S, Doniach S, Harbury PA, Lipfert J.

Nano Lett. 2016 Sep 14;16(9):5353-7. doi: 10.1021/acs.nanolett.6b01160. Epub 2016 Jun 22.

PMID:
27244097
23.

A Mo-anode-based in-house source for small-angle X-ray scattering measurements of biological macromolecules.

Bruetzel LK, Fischer S, Salditt A, Sedlak SM, Nickel B, Lipfert J.

Rev Sci Instrum. 2016 Feb;87(2):025103. doi: 10.1063/1.4940936.

PMID:
26931887
24.

Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction.

Müller JP, Mielke S, Löf A, Obser T, Beer C, Bruetzel LK, Pippig DA, Vanderlinden W, Lipfert J, Schneppenheim R, Benoit M.

Proc Natl Acad Sci U S A. 2016 Feb 2;113(5):1208-13. doi: 10.1073/pnas.1516214113. Epub 2016 Jan 19.

25.

High Spatiotemporal-Resolution Magnetic Tweezers: Calibration and Applications for DNA Dynamics.

Dulin D, Cui TJ, Cnossen J, Docter MW, Lipfert J, Dekker NH.

Biophys J. 2015 Nov 17;109(10):2113-25. doi: 10.1016/j.bpj.2015.10.018.

26.

Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.

Gebala M, Giambaşu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D.

J Am Chem Soc. 2015 Nov 25;137(46):14705-15. doi: 10.1021/jacs.5b08395. Epub 2015 Nov 12.

27.

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis.

Liebl K, Drsata T, Lankas F, Lipfert J, Zacharias M.

Nucleic Acids Res. 2015 Dec 2;43(21):10143-56. doi: 10.1093/nar/gkv1028. Epub 2015 Oct 12.

28.

Biological magnetometry: torque on superparamagnetic beads in magnetic fields.

van Oene MM, Dickinson LE, Pedaci F, Köber M, Dulin D, Lipfert J, Dekker NH.

Phys Rev Lett. 2015 May 29;114(21):218301. Epub 2015 May 27. Erratum in: Phys Rev Lett. 2018 Jun 22;120(25):259901.

PMID:
26066460
29.

Corrigendum: Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids.

Lipfert J, Wiggin M, Kerssemakers JW, Pedaci F, Dekker NH.

Nat Commun. 2015 May 27;6:7192. doi: 10.1038/ncomms8192. No abstract available.

30.

Nucleosome assembly dynamics involve spontaneous fluctuations in the handedness of tetrasomes.

Vlijm R, Lee M, Lipfert J, Lusser A, Dekker C, Dekker NH.

Cell Rep. 2015 Jan 13;10(2):216-25. doi: 10.1016/j.celrep.2014.12.022. Epub 2015 Jan 8.

31.

A force calibration standard for magnetic tweezers.

Yu Z, Dulin D, Cnossen J, Köber M, van Oene MM, Ordu O, Berghuis BA, Hensgens T, Lipfert J, Dekker NH.

Rev Sci Instrum. 2014 Dec;85(12):123114. doi: 10.1063/1.4904148.

PMID:
25554279
32.

Torque spectroscopy for the study of rotary motion in biological systems.

Lipfert J, van Oene MM, Lee M, Pedaci F, Dekker NH.

Chem Rev. 2015 Feb 11;115(3):1449-74. doi: 10.1021/cr500119k. Epub 2014 Dec 26. Review. No abstract available.

PMID:
25541648
33.

Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.

Lipfert J, Skinner GM, Keegstra JM, Hensgens T, Jager T, Dulin D, Köber M, Yu Z, Donkers SP, Chou FC, Das R, Dekker NH.

Proc Natl Acad Sci U S A. 2014 Oct 28;111(43):15408-13. doi: 10.1073/pnas.1407197111. Epub 2014 Oct 13.

34.

Tuning micelle dimensions and properties with binary surfactant mixtures.

Oliver RC, Lipfert J, Fox DA, Lo RH, Kim JJ, Doniach S, Columbus L.

Langmuir. 2014 Nov 11;30(44):13353-61. doi: 10.1021/la503458n. Epub 2014 Oct 28.

PMID:
25312254
35.

Blind predictions of DNA and RNA tweezers experiments with force and torque.

Chou FC, Lipfert J, Das R.

PLoS Comput Biol. 2014 Aug 7;10(8):e1003756. doi: 10.1371/journal.pcbi.1003756. eCollection 2014 Aug.

36.

Magnetic tweezers for the measurement of twist and torque.

Lipfert J, Lee M, Ordu O, Kerssemakers JW, Dekker NH.

J Vis Exp. 2014 May 19;(87). doi: 10.3791/51503.

37.

Structure, mechanics, and binding mode heterogeneity of LEDGF/p75-DNA nucleoprotein complexes revealed by scanning force microscopy.

Vanderlinden W, Lipfert J, Demeulemeester J, Debyser Z, De Feyter S.

Nanoscale. 2014 May 7;6(9):4611-9. doi: 10.1039/c4nr00022f.

PMID:
24632996
38.

Understanding nucleic acid-ion interactions.

Lipfert J, Doniach S, Das R, Herschlag D.

Annu Rev Biochem. 2014;83:813-41. doi: 10.1146/annurev-biochem-060409-092720. Epub 2014 Mar 5. Review.

39.

Structural and torsional properties of the RAD51-dsDNA nucleoprotein filament.

Lee M, Lipfert J, Sanchez H, Wyman C, Dekker NH.

Nucleic Acids Res. 2013 Aug;41(14):7023-30. doi: 10.1093/nar/gkt425. Epub 2013 May 22.

40.

Dependence of micelle size and shape on detergent alkyl chain length and head group.

Oliver RC, Lipfert J, Fox DA, Lo RH, Doniach S, Columbus L.

PLoS One. 2013 May 8;8(5):e62488. doi: 10.1371/journal.pone.0062488. Print 2013.

41.

CXCR4 and CXCR7 form a functional receptor unit for SDF-1/CXCL12 in primary rodent microglia.

Lipfert J, Ödemis V, Wagner DC, Boltze J, Engele J.

Neuropathol Appl Neurobiol. 2013 Oct;39(6):667-80. doi: 10.1111/nan.12015.

PMID:
23289420
42.

Studying genomic processes at the single-molecule level: introducing the tools and applications.

Dulin D, Lipfert J, Moolman MC, Dekker NH.

Nat Rev Genet. 2013 Jan;14(1):9-22. doi: 10.1038/nrg3316. Epub 2012 Oct 30. Review.

PMID:
23150038
43.

Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering.

Sim AY, Lipfert J, Herschlag D, Doniach S.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Aug;86(2 Pt 1):021901. Epub 2012 Aug 1.

PMID:
23005779
44.

Grk2 is an essential regulator of CXCR7 signalling in astrocytes.

Lipfert J, Ödemis V, Engele J.

Cell Mol Neurobiol. 2013 Jan;33(1):111-8. doi: 10.1007/s10571-012-9876-5. Epub 2012 Sep 2.

PMID:
22940879
45.

Electromagnetic torque tweezers: a versatile approach for measurement of single-molecule twist and torque.

Janssen XJ, Lipfert J, Jager T, Daudey R, Beekman J, Dekker NH.

Nano Lett. 2012 Jul 11;12(7):3634-9. doi: 10.1021/nl301330h. Epub 2012 Jun 8.

PMID:
22642488
46.

The presumed atypical chemokine receptor CXCR7 signals through G(i/o) proteins in primary rodent astrocytes and human glioma cells.

Odemis V, Lipfert J, Kraft R, Hajek P, Abraham G, Hattermann K, Mentlein R, Engele J.

Glia. 2012 Mar;60(3):372-81. doi: 10.1002/glia.22271. Epub 2011 Nov 14.

PMID:
22083878
47.

A method to track rotational motion for use in single-molecule biophysics.

Lipfert J, Kerssemakers JJ, Rojer M, Dekker NH.

Rev Sci Instrum. 2011 Oct;82(10):103707. doi: 10.1063/1.3650461.

PMID:
22047303
48.

Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids.

Lipfert J, Wiggin M, Kerssemakers JW, Pedaci F, Dekker NH.

Nat Commun. 2011 Aug 23;2:439. doi: 10.1038/ncomms1450. Erratum in: Nat Commun. 2015;6:7192.

49.

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments.

Lipfert J, Kerssemakers JW, Jager T, Dekker NH.

Nat Methods. 2010 Dec;7(12):977-80. doi: 10.1038/nmeth.1520. Epub 2010 Oct 17.

PMID:
20953173
50.

Quantitative guidelines for force calibration through spectral analysis of magnetic tweezers data.

te Velthuis AJ, Kerssemakers JW, Lipfert J, Dekker NH.

Biophys J. 2010 Aug 9;99(4):1292-302. doi: 10.1016/j.bpj.2010.06.008.

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